Updated on 2025/07/01

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写真a

 
Mitsunori Ikeguchi
 
Organization
Graduate School of Medical Life Science Department of Medical Life Science Professor
School of Science Department of Science
Graduate School of Medical Life Science Dean
Title
Professor
Homepage
http://www.tsurumi.yokohama-cu.ac.jp/bioinfo/
Profile

タンパク質など生体系の分子シミュレーションを専門にして研究をしている。標的タンパク質の立体構造ベースにしたインシリコ創薬の研究も行い、生命系のハイ・パフォーマンス・コンピューティング（HPC）の分野で活動を行っている。

External link

Degree

  • 博士(農学) ( 東京大学 )

Research Interests

  • バイオインフォマティクス

  • 分子シミュレーション

  • 生物物理学

Research Areas

  • Informatics / Life, health and medical informatics

  • Natural Science / Biophysics, chemical physics and soft matter physics

  • Life Science / Biophysics

Education

  • The University of Tokyo

    - 1994

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    Country： Japan

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  • The University of Tokyo   The Faculty of Engineering   Department of Mathematical Engineering and Information Physics

    - 1989

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    Country： Japan

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Research History

  • 東京大学農学部助手

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  • Yokohama City University International College of Arts and Sciences Medical Life Science Graduate School of Medical Life Science Department of Medical Life Science   Professor

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Professional Memberships

Papers

  • Machine learning to estimate the local quality of protein crystal structures Reviewed

    Ikuko Miyaguchi, Miwa Sato, Akiko Kashima, Hiroyuki Nakagawa, Yuichi Kokabu, Biao Ma, Shigeyuki Matsumoto, Atsushi Tokuhisa, Masateru Ohta, Mitsunori Ikeguchi

    Scientific Reports   11 ( 1 )   2021.12

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    Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    Low-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, called quality assessment based on an electron density map (QAEmap), which evaluates local protein structures determined by X-ray crystallography and could be applied to correct structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and putative high-resolution experimental electron density map. This correlation could be used as a metric to modify the structure. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.

    DOI： 10.1038/s41598-021-02948-y

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    Other Link： https://www.nature.com/articles/s41598-021-02948-y

  • Synergistic Activation of TLR7 and 8 Mediated by Reduction of Electrostatic Repulsion Reviewed

    Toru Ekimoto, Masami Nomura, Yuri Saito, Minami Suzuki, Tsutomu Yamane, Zhikuan Zhang, Umeharu Ohto, Mitsunori Ikeguchi, Toshiyuki Shimizu

    Chemical and Pharmaceutical Bulletin   72 ( 11 )   1005 - 1013   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：Pharmaceutical Society of Japan  

    DOI： 10.1248/cpb.c24-00409

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  • Na+-V-ATPase inhibitor curbs VRE growth and unveils Na+ pathway structure Reviewed

    Kano Suzuki, Yoshiyuki Goto, Akihiro Otomo, Kouki Shimizu, Shohei Abe, Katsuhiko Moriyama, Satoshi Yasuda, Yusuke Hashimoto, Jun Kurushima, Sho Mikuriya, Fabiana L. Imai, Naruhiko Adachi, Masato Kawasaki, Yumi Sato, Satoshi Ogasawara, So Iwata, Toshiya Senda, Mitsunori Ikeguchi, Haruyoshi Tomita, Ryota Iino, Toshio Moriya, Takeshi Murata

    Nature Structural & Molecular Biology   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    DOI： 10.1038/s41594-024-01419-y

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    Other Link： https://www.nature.com/articles/s41594-024-01419-y

  • Structural basis for hepatitis B virus restriction by a viral receptor homologue. Reviewed International journal

    Kaho Shionoya, Jae-Hyun Park, Toru Ekimoto, Junko S Takeuchi, Junki Mifune, Takeshi Morita, Naito Ishimoto, Haruka Umezawa, Kenichiro Yamamoto, Chisa Kobayashi, Atsuto Kusunoki, Norimichi Nomura, So Iwata, Masamichi Muramatsu, Jeremy R H Tame, Mitsunori Ikeguchi, Sam-Yong Park, Koichi Watashi

    Nature communications   15 ( 1 )   9241 - 9241   2024.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    Macaque restricts hepatitis B virus (HBV) infection because its receptor homologue, NTCP (mNTCP), cannot bind preS1 on viral surface. To reveal how mNTCP loses the viral receptor function, we here solve the cryo-electron microscopy structure of mNTCP. Superposing on the human NTCP (hNTCP)-preS1 complex structure shows that Arg158 of mNTCP causes steric clash to prevent preS1 from embedding onto the bile acid tunnel of NTCP. Cell-based mutation analysis confirms that only Gly158 permitted preS1 binding, in contrast to robust bile acid transport among mutations. As the second determinant, Asn86 on the extracellular surface of mNTCP shows less capacity to restrain preS1 from dynamic fluctuation than Lys86 of hNTCP, resulting in unstable preS1 binding. Additionally, presence of long-chain conjugated-bile acids in the tunnel induces steric hindrance with preS1 through their tailed-chain. This study presents structural basis in which multiple sites in mNTCP constitute a molecular barrier to strictly restrict HBV.

    DOI： 10.1038/s41467-024-53533-6

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  • Statistical-Mechanics Analyses on Thermodynamics of Protein Folding Constructed by Privalov and Co-Workers. Reviewed International journal

    Masao Inoue, Tomohiko Hayashi, Satoshi Yasuda, Minoru Kato, Mitsunori Ikeguchi, Takeshi Murata, Masahiro Kinoshita

    The journal of physical chemistry. B   128 ( 41 )   10110 - 10125   2024.10

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    Privalov and co-workers estimated the changes in hydration enthalpy and entropy upon ubiquitin unfolding and their temperature dependences denoted by ΔHhyd(T) and ΔShyd(T), respectively, from experimentally measured enthalpies and entropies of transfer of various model compounds from gaseous phase to water. We calculate ΔHhyd(T) and ΔShyd(T) for ubiquitin by our statistical-mechanics theory where molecular and atomistic models are employed for water and protein structure, respectively. ΔHhyd(T) and ΔShyd(T) calculated are in remarkably good agreement with those estimated by Privalov and co-workers. By examining relative magnitudes and signs of the changes in a variety of constituents of ΔHhyd(T) and ΔShyd(T), we confirm that the hydrophobic effect is an essential force driving a protein to fold. Detailed and comprehensive explanations are given for our claim that the prevailing views of the hydrophobic effect are not capable of elucidating its weakening at low temperatures, whereas our updated view is. We find out problematic points of the changes in enthalpy and entropy upon protein unfolding denoted by ΔH°(T) and ΔS°(T), respectively, which are measured using the differential scanning calorimetry at low pH, suggesting a theoretical method of calculating ΔH°(T) and ΔS°(T) at pH ∼ 7.

    DOI： 10.1021/acs.jpcb.4c05811

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  • Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase Reviewed

    Mitsugu Araki, Toru Ekimoto, Kazuhiro Takemura, Shigeyuki Matsumoto, Yunoshin Tamura, Hironori Kokubo, Gert-Jan Bekker, Tsutomu Yamane, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Mitsunori Ikeguchi, Yasushi Okuno

    Journal of the American Chemical Society   2024.10

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    Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/jacs.4c04648

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  • A machine learning model for predicting quantum chemistry based protein-drug molecule interactions Reviewed

    Ryosuke KITA, Chiduru WATANABE, Masateru OHTA, Naoki TANIMURA, Koji OKUWAKI, Mitsunori IKEGUCHI, Kaori FUKUZAWA, Teruki HONMA, Tsuyohiko FUJIGAYA, Koichiro KATO

    The 38th Annual Conference of the Japanese Society for Artificial Intelligence   38   2024.5

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    Language：English   Publishing type：Research paper (international conference proceedings)  

    DOI： 10.11517/pjsai.JSAI2024.0_4Q3IS2d05

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  • Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model Reviewed

    Masao Inoue, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi

    Journal of Chemical Information and Modeling   64 ( 9 )   3884 - 3895   2024.4

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    Authorship：Last author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society (ACS)  

    DOI： 10.1021/acs.jcim.4c00172

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  • Nanohoops in Membranes: Confined Supramolecular Spaces within Phospholipid Bilayer Membranes Reviewed

    Kylie Chinner, Niklas Grabicki, Rei Hamaguchi, Mitsunori Ikeguchi, Kazushi Kinbara, Sayaka Toyoda, Kohei Sato, Oliver Dumele

    Chemical Science   2024

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    Publishing type：Research paper (scientific journal)   Publisher：Royal Society of Chemistry (RSC)  

    Nanohoops, an exciting class of fluorophores with supramolecular binding abilities, have the potential to become innovative tools within biological imaging and sensing. Given the biological importance of cell membranes, incorporation...

    DOI： 10.1039/d4sc03408b

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  • Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2. Reviewed International journal

    Jae-Hyun Park, Kouki Kawakami, Naito Ishimoto, Tatsuya Ikuta, Mio Ohki, Toru Ekimoto, Mitsunori Ikeguchi, Dong-Sun Lee, Young-Ho Lee, Jeremy R H Tame, Asuka Inoue, Sam-Yong Park

    Nature communications   14 ( 1 )   7150 - 7150   2023.11

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    Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce Gi/o signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with lipolytic and atherogenic activity, and neuroinflammation. Although many reports have elucidated the function of HCAR2 and its potential as a therapeutic target for treating not only dyslipidemia but also neuroimmune disorders such as multiple sclerosis and Parkinson's disease, the structural basis of ligand recognition and ligand-induced Gi-coupling remains unclear. Here we report three cryo-EM structures of the human HCAR2-Gi signaling complex, each bound with different ligands: niacin, acipimox or GSK256073. All three agonists are held in a deep pocket lined by residues that are not conserved in HCAR1 and HCAR3. A distinct hairpin loop at the HCAR2 N-terminus and extra-cellular loop 2 (ECL2) completely enclose the ligand. These structures also reveal the agonist-induced conformational changes propagated to the G-protein-coupling interface during activation. Collectively, the structures presented here are expected to help in the design of ligands specific for HCAR2, leading to new drugs for the treatment of various diseases such as dyslipidemia and inflammation.

    DOI： 10.1038/s41467-023-42764-8

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  • Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study Reviewed

    Tsutomu Yamane, Takahiro Nakayama, Toru Ekimoto, Masao Inoue, Keigo Ikezaki, Hiroshi Sekiguchi, Masahiro Kuramochi, Yasuo Terao, Ken Judai, Minoru Saito, Mitsunori Ikeguchi, Yuji C. Sasaki

    International Journal of Molecular Sciences   24 ( 20 )   15423 - 15423   2023.10

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    Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

    Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.

    DOI： 10.3390/ijms242015423

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  • Dynamic solution structures of whole human NAP1 dimer bound to one and two histone H2A-H2B heterodimers obtained by integrative methods Reviewed

    Hideaki Ohtomo, Tsutomu Yamane, Takashi Oda, Noriyuki Kodera, Jun-ichi Kurita, Yasuo Tsunaka, Romain Amyot, Mitsunori Ikeguchi, Yoshifumi Nishimura

    Journal of Molecular Biology   168189 - 168189   2023.6

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.jmb.2023.168189

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  • Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding. Reviewed International journal

    Yukiko Kurihara, Toru Ekimoto, Christopher T Gordon, Yasunobu Uchijima, Ryo Sugiyama, Taro Kitazawa, Akiyasu Iwase, Risa Kotani, Rieko Asai, Véronique Pingault, Mitsunori Ikeguchi, Jeanne Amiel, Hiroki Kurihara

    The Journal of clinical investigation   133 ( 4 )   2023.2

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    Mutations of G protein-coupled receptors (GPCRs) cause various human diseases, but the mechanistic details are limited. Here, we establish p.E303K in the gene encoding the endothelin receptor type A (ETAR/EDNRA) as a recurrent mutation causing mandibulofacial dysostosis with alopecia (MFDA), with craniofacial changes similar to those caused by p.Y129F. Mouse models carrying either of these missense mutations exhibited a partial maxillary-to-mandibular transformation, which was rescued by deleting the ligand endothelin 3 (ET3/EDN3). Pharmacological experiments confirmed the causative ETAR mutations as gain of function, dependent on ET3. To elucidate how an amino acid substitution far from the ligand binding site can increase ligand affinity, we used molecular dynamics (MD) simulations. E303 is located at the intracellular end of transmembrane domain 6, and its replacement by a lysine increased flexibility of this portion of the helix, thus favoring G protein binding and leading to G protein-mediated enhancement of agonist affinity. The Y129F mutation located under the ligand binding pocket reduced the sodium-water network, thereby affecting the extracellular portion of helices in favor of ET3 binding. These findings provide insight into the pathogenesis of MFDA and into allosteric mechanisms regulating GPCR function, which may provide the basis for drug design targeting GPCRs.

    DOI： 10.1172/JCI151536

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  • TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction Reviewed

    Kentaro Sakaniwa, Akiko Fujimura, Takuma Shibata, Hideki Shigematsu, Toru Ekimoto, Masaki Yamamoto, Mitsunori Ikeguchi, Kensuke Miyake, Umeharu Ohto, Toshiyuki Shimizu

    Nature Communications   14 ( 1 )   2023.1

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    Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    Toll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous biochemical and structural studies have revealed that a minimum length of approximately 40–50 base pairs of dsRNA is necessary for TLR3 binding and dimerization. However, efficient TLR3 activation requires longer dsRNA and the molecular mechanism underlying its dsRNA length-dependent activation remains unknown. Here, we report cryo-electron microscopy analyses of TLR3 complexed with longer dsRNA. TLR3 dimers laterally form a higher multimeric complex along dsRNA, providing the basis for cooperative binding and efficient signal transduction.

    DOI： 10.1038/s41467-023-35844-2

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    Other Link： https://www.nature.com/articles/s41467-023-35844-2

  • Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease. Reviewed International journal

    Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi, Akinori Kidera

    Journal of chemical information and modeling   63 ( 1 )   240 - 250   2023.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    Based on many crystal structures of ligand complexes, much study has been devoted to understanding the molecular recognition of SARS-CoV-2 3C-like protease (3CLpro), a potent drug target for COVID-19. In this research, to extend this present static view, we examined the kinetic process of binding/unbinding of an eight-residue substrate peptide to/from 3CLpro by evaluating the path ensemble with the weighted ensemble simulation. The path ensemble showed the mechanism of how a highly flexible peptide folded into the bound form. At the early stage, the dominant motion was the diffusion on the protein surface showing a broad distribution, whose center was led into the cleft of the chymotrypsin fold. We observed a definite sequential formation of the hydrogen bonds at the later stage occurring in the cleft, initiated between Glu166 (3CLpro) and P3_Val (peptide), followed by binding to the oxyanion hole and completed by the sequence-specific recognition at P1_Gln.

    DOI： 10.1021/acs.jcim.2c00946

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  • Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA. Reviewed International journal

    Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

    Biophysical reviews   14 ( 6 )   1473 - 1485   2022.12

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    UNLABELLED: SARS-CoV-2 3C-like protease (3CLpro), a potential therapeutic target for COVID-19, consists of a chymotrypsin fold and a C-terminal α-helical domain (domain III), the latter of which mediates dimerization required for catalytic activation. To gain further understanding of the functional dynamics of SARS-CoV-2 3CLpro, this review extends the scope to the comparative study of many crystal structures of proteases having the chymotrypsin fold (clan PA of the MEROPS database). First, the close correspondence between the zymogen-enzyme transformation in chymotrypsin and the allosteric dimerization activation in SARS-CoV-2 3CLpro is illustrated. Then, it is shown that the 3C-like proteases of family Coronaviridae (the protease family C30), which are closely related to SARS-CoV-2 3CLpro, have the same homodimeric structure and common activation mechanism via domain III mediated dimerization. The survey extended to order Nidovirales reveals that all 3C-like proteases belonging to Nidovirales have domain III, but with various chain lengths, and 3CLpro of family Mesoniviridae (family C107) has the same homodimeric structure as that of C30, even though they have no sequence similarity. As a reference, monomeric 3C proteases belonging to the more distant family Picornaviridae (family C3) lacking domain III are compared with C30, and it is shown that the 3C proteases are rigid enough to maintain their structures in the active state. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12551-022-01020-x.

    DOI： 10.1007/s12551-022-01020-x

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  • Hybrid in vitro/in silico analysis of low-affinity protein-protein interactions that regulate signal transduction by Sema6D. Reviewed International journal

    Tsubasa Tanaka, Toru Ekimoto, Meri Nagatomo, Makiko Neyazaki, Erena Shimoji, Tsutomu Yamane, Sakura Kanagawa, Rika Oi, Emiko Mihara, Junichi Takagi, Satoko Akashi, Mitsunori Ikeguchi, Terukazu Nogi

    Protein science : a publication of the Protein Society   31 ( 11 )   e4452   2022.11

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    Semaphorins constitute a large family of secreted and membrane-bound proteins that signal through cell-surface receptors, plexins. Semaphorins generally use low-affinity protein-protein interactions to bind with their specific plexin(s) and regulate distinct cellular processes such as neurogenesis, immune response, and organogenesis. Sema6D is a membrane-bound semaphorin that interacts with class A plexins. Sema6D exhibited differential binding affinities to class A plexins in prior cell-based assays, but the molecular mechanism underlying this selectivity is not well understood. Therefore, we performed hybrid in vitro/in silico analysis to examine the binding mode of Sema6D to class A plexins and to identify residues that give rise to the differential affinities and thus contribute to the selectivity within the same class of semaphorins. Our biophysical binding analysis indeed confirmed that Sema6D has a higher affinity for Plexin-A1 than for other class A plexins, consistent with the binding selectivity observed in the previous cell-based assays. Unexpectedly, our present crystallographic analysis of the Sema6D-Plexin-A1 complex showed that the pattern of polar interactions is not interaction-specific because it matches the pattern in the prior structure of the Sema6A-Plexin-A2 complex. Thus, we performed in silico alanine scanning analysis and discovered hotspot residues that selectively stabilized the Sema6D-Plexin-A1 pair via Van der Waals interactions. We then validated the contribution of these hotspot residues to the variation in binding affinity with biophysical binding analysis and molecular dynamics simulations on the mutants. Ultimately, our present results suggest that shape complementarity in the binding interfaces is a determinant for binding selectivity.

    DOI： 10.1002/pro.4452

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  • gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins Reviewed

    Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta, Takashi Yoshidome

    Journal of Chemical Information and Modeling   2022.9

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    DOI： 10.1021/acs.jcim.2c00987

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  • 3D-RISM-AI: A Machine Learning Approach to Predict Protein-Ligand Binding Affinity Using 3D-RISM. Reviewed International journal

    Kazu Osaki, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi

    The journal of physical chemistry. B   126 ( 33 )   6148 - 6158   2022.8

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    Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions solely evaluated using 3D-RISM are not correlated to the experimental BFE for abundant protein-ligand pairs. In this study, to predict the BFE for multiple sets of protein-ligand pairs, we propose a machine learning approach incorporating the HFEs obtained using 3D-RISM, termed 3D-RISM-AI. In the learning process, structural metrics, intra-/intermolecular energies, and HFEs obtained via 3D-RISM of ∼4000 complexes in the PDBbind database (ver. 2018) were used. The BFEs predicted using 3D-RISM-AI were well correlated to the experimental data (Pearson's correlation coefficient of 0.80 and root-mean-square error of 1.91 kcal/mol). As important factors for the prediction, the difference in the solvent accessible surface area between the bound and unbound structures and the hydration properties of the ligands were detected during the learning process.

    DOI： 10.1021/acs.jpcb.2c03384

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  • Structure of SARS-CoV-2 membrane protein essential for virus assembly. Reviewed International journal

    Zhikuan Zhang, Norimichi Nomura, Yukiko Muramoto, Toru Ekimoto, Tomoko Uemura, Kehong Liu, Moeko Yui, Nozomu Kono, Junken Aoki, Mitsunori Ikeguchi, Takeshi Noda, So Iwata, Umeharu Ohto, Toshiyuki Shimizu

    Nature communications   13 ( 1 )   4399 - 4399   2022.8

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    The coronavirus membrane protein (M) is the most abundant viral structural protein and plays a central role in virus assembly and morphogenesis. However, the process of M protein-driven virus assembly are largely unknown. Here, we report the cryo-electron microscopy structure of the SARS-CoV-2 M protein in two different conformations. M protein forms a mushroom-shaped dimer, composed of two transmembrane domain-swapped three-helix bundles and two intravirion domains. M protein further assembles into higher-order oligomers. A highly conserved hinge region is key for conformational changes. The M protein dimer is unexpectedly similar to SARS-CoV-2 ORF3a, a viral ion channel. Moreover, the interaction analyses of M protein with nucleocapsid protein (N) and RNA suggest that the M protein mediates the concerted recruitment of these components through the positively charged intravirion domain. Our data shed light on the M protein-driven virus assembly mechanism and provide a structural basis for therapeutic intervention targeting M protein.

    DOI： 10.1038/s41467-022-32019-3

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  • Correction to "Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane". International journal

    Kohei Sato, Ryo Sasaki, Ryoto Matsuda, Mayuko Nakagawa, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

    Journal of the American Chemical Society   144 ( 30 )   13983 - 13984   2022.8

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  • Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane. Reviewed International journal

    Kohei Sato, Ryo Sasaki, Ryoto Matsuda, Mayuko Nakagawa, Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi, Kazuhito V Tabata, Hiroyuki Noji, Kazushi Kinbara

    Journal of the American Chemical Society   144 ( 26 )   11802 - 11809   2022.6

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    Inspired by mechanosensitive potassium channels found in nature, we developed a fluorinated amphiphilic cyclophane composed of fluorinated rigid aromatic units connected via flexible hydrophilic octa(ethylene glycol) chains. Microscopic and emission spectroscopic studies revealed that the cyclophane could be incorporated into the hydrophobic layer of the lipid bilayer membranes and self-assembled to form a supramolecular transmembrane ion channel. Current recording measurements using cyclophane-containing planer lipid bilayer membranes successfully demonstrated an efficient transmembrane ion transport. We also demonstrated that the ion transport property was sensitive to the mechanical forces applied to the membranes. In addition, ion transport assays using pH-sensitive fluorescence dye revealed that the supramolecular channel possesses potassium ion selectivity. We also performed all-atom hybrid quantum-mechanical/molecular mechanical simulations to assess the channel structures at atomic resolution and the mechanism of selective potassium ion transport. This research demonstrated the first example of a synthetic mechanosensitive potassium channel, which would open a new door to sensing and manipulating biologically important processes and purification of key materials in industries.

    DOI： 10.1021/jacs.2c04118

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  • Development of the force field for cyclosporine A. Reviewed

    Tsutomu Yamane, Toru Ekimoto, Mitsunori Ikeguchi

    Biophysics and physicobiology   19   e190045   2022

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    Membrane permeability of cyclic peptides is an important factor in drug design. To investigate the membrane permeability of cyclic peptides using molecular dynamics (MD) simulations, the accurate force fields for unnatural amino acids present in the cyclic peptides are required. Therefore, we developed the CHARMM force fields of the unnatural amino acids present in cyclosporin A (CsA), a cyclic peptide used as an immune suppressor. Especially for N-methyl amino acids, which contribute to the membrane permeability of cyclic peptides, we developed a grid correction map (CMAP) of the energy surface using the φ and ψ dihedral angles in the main chain of CsA. To validate the developed force field, we performed MD simulations, including the generalized replica exchange with solute tempering method, of CsA in water and chloroform solvents. The conformations of CsA in water and chloroform sampled using the developed force field were consistent with those of the experimental results of the solution nuclear magnetic resonance spectroscopy.

    DOI： 10.2142/biophysico.bppb-v19.0045

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  • Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble. Reviewed International journal

    Akinori Kidera, Kei Moritsugu, Toru Ekimoto, Mitsunori Ikeguchi

    Journal of molecular biology   433 ( 24 )   167324 - 167324   2021.12

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    The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)-disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.

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  • Structure-based screening combined with computational and biochemical analyses identified the inhibitor targeting the binding of DNA Ligase 1 to UHRF1 Reviewed

    Satomi Kori, Yuki Shibahashi, Toru Ekimoto, Atsuya Nishiyama, Sae Yoshimi, Kosuke Yamaguchi, Satoru Nagatoishi, Masateru Ohta, Kouhei Tsumoto, Makoto Nakanishi, Pierre-Antoine Defossez, Mitsunori Ikeguchi, Kyohei Arita

    Bioorganic & Medicinal Chemistry   52   116500 - 116500   2021.12

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    DOI： 10.1016/j.bmc.2021.116500

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  • Molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain. Reviewed International journal

    Keijun Kakihara, Kengo Asamizu, Kei Moritsugu, Masahide Kubo, Tetsuya Kitaguchi, Akinori Endo, Akinori Kidera, Mitsunori Ikeguchi, Akira Kato, Masayuki Komada, Toshiaki Fukushima

    Communications biology   4 ( 1 )   1272 - 1272   2021.11

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    Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme involved in multiple membrane trafficking pathways. The enzyme activity is inhibited by binding to 14-3-3 proteins. Mutations in the 14-3-3-binding motif in USP8 are related to Cushing's disease. However, the molecular basis of USP8 activity regulation remains unclear. This study identified amino acids 645-684 of USP8 as an autoinhibitory region, which might interact with the catalytic USP domain, as per the results of pull-down and single-molecule FRET assays performed in this study. In silico modelling indicated that the region forms a WW-like domain structure, plugs the catalytic cleft, and narrows the entrance to the ubiquitin-binding pocket. Furthermore, 14-3-3 inhibited USP8 activity partly by enhancing the interaction between the WW-like and USP domains. These findings provide the molecular basis of USP8 autoinhibition via the WW-like domain. Moreover, they suggest that the release of autoinhibition may underlie Cushing's disease due to USP8 mutations.

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  • Mechanism of Vitamin D Receptor Ligand-Binding Domain Regulation Studied by gREST Simulations. Reviewed International journal

    Toru Ekimoto, Takafumi Kudo, Tsutomu Yamane, Mitsunori Ikeguchi

    Journal of chemical information and modeling   61 ( 7 )   3625 - 3637   2021.7

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    The vitamin D receptor ligand-binding domain (VDR-LBD) undergoes conformational changes upon ligand binding. In this nuclear receptor family, agonistic or antagonistic activities are controlled by the conformation of the helix (H)12. However, all crystal structures of VDR-LBD reported to date correspond to the active H12 conformation, regardless of agonist/antagonist binding. To understand the mechanism of VDR-LBD regulation structurally, conformational samplings of agonist- and antagonist-bound rat VDR-LBD were performed using the generalized replica exchange with solute tempering (gREST) method. The gREST simulations demonstrated different structural responses of rat VDR-LBD to agonist or antagonist binding, whereas in conventional molecular dynamics simulations, the conformation was the same as that of the crystal structures, regardless of agonist/antagonist binding. In the gREST simulations, a spontaneous conformational change of H12 was observed only for the antagonist complex. The different responses to agonist/antagonist binding were attributed to hydrophobic core formation at the ligand-binding pocket and cooperative rearrangements of H11. The gREST method can be applied to the examination of structure-activity relationships for multiple VDR-LBD ligands.

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  • Effect of Water Molecules on the Activating S810L Mutation of the Mineralocorticoid Receptor. Reviewed International journal

    Kei Takedomi, Masateru Ohta, Toru Ekimoto, Mitsunori Ikeguchi

    Journal of chemical information and modeling   61 ( 7 )   3583 - 3592   2021.7

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    The mineralocorticoid receptor (MR) is a nuclear receptor whose endogenous ligands are mineralocorticoids, a type of steroid hormone. The activating S810L mutation is known to cause severe early-onset and pregnancy-related hypertension. Progesterone binds to the wild-type (WT) MR as a passive antagonist with fast dissociation; however, it binds to the S810L mutant as a full agonist with slow dissociation. The switch in the biological activity of progesterone is considered to be one of the causes of the disease. First, we used steered molecular dynamics simulations to analyze the dissociation process of progesterone for the WT and the S810L mutant. Progesterone in the WT dissociated from the ligand-binding pocket with a weak force in comparison with progesterone in the S810L mutant due to the large inflow of water molecules into the pocket. Therefore, we used conventional molecular dynamics simulations for the ligand-free structures of the WT and the S810L mutant to investigate the effect of the mutation on the inflow of water. In the WT, water molecules enter the ligand-binding pocket in two ways: in the vicinity of (i) Arg817 and (ii) Ser810. In contrast, few water molecules enter the pocket in the S810L mutant because of the large size and hydrophobic nature of the Leu810 side chain. Fast dissociation is a common feature among passive antagonists of MR; therefore, we inferred that the water inflow could be responsible for the dissociation kinetics of progesterone in the WT and the S810L mutant.

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  • QAEmap: A Novel Local Quality Assessment Method for Protein Crystal Structures Using Machine Learning Reviewed

    Ikuko Miyaguchi, Miwa Sato, Akiko Kashima, Hiroyuki Nakagawa, Yuichi Kokabu, Biao Ma, Shigeyuki Matsumoto, Atsushi Tokuhisa, Masateru Ohta, Mitsunori Ikeguchi

    2021.7

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    Abstract

    Low-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, quality assessment based on an electron density map (QAEmap), that evaluates local protein structures determined by X-ray crystallography and corrects structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and the putative high-resolution experimental electron density map. This estimates how well the structure fits the high-resolution map. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.

    DOI： 10.21203/rs.3.rs-687363/v1

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  • Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion. Reviewed International journal

    Risako Tamura-Sakaguchi, Rie Aruga, Mika Hirose, Toru Ekimoto, Takuya Miyake, Yohei Hizukuri, Rika Oi, Mika K Kaneko, Yukinari Kato, Yoshinori Akiyama, Mitsunori Ikeguchi, Kenji Iwasaki, Terukazu Nogi

    Acta crystallographica. Section D, Structural biology   77 ( Pt 5 )   645 - 662   2021.5

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    Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

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  • Structural and dynamical insights into the PH domain of p62 in human TFIIH. International journal

    Masahiko Okuda, Toru Ekimoto, Jun-Ichi Kurita, Mitsunori Ikeguchi, Yoshifumi Nishimura

    Nucleic acids research   49 ( 5 )   2916 - 2930   2021.3

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    TFIIH is a crucial transcription and DNA repair factor consisting of the seven-subunit core. The core subunit p62 contains a pleckstrin homology domain (PH-D), which is essential for locating TFIIH at transcription initiation and DNA damage sites, and two BSD (BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins) domains. A recent cryo-electron microscopy (cryo-EM) structure of human TFIIH visualized most parts of core, except for the PH-D. Here, by nuclear magnetic resonance spectroscopy we have established the solution structure of human p62 PH-D connected to the BSD1 domain by a highly flexible linker, suggesting the flexibility of PH-D in TFIIH. Based on this dynamic character, the PH-D was modeled in the cryo-EM structure to obtain the whole human TFIIH core structure, which indicates that the PH-D moves around the surface of core with a specific but limited spatial distribution; these dynamic structures were refined by molecular dynamics (MD) simulations. Furthermore, we built models, also refined by MD simulations, of TFIIH in complex with five p62-binding partners, including transcription factors TFIIEα, p53 and DP1, and nucleotide excision repair factors XPC and UVSSA. The models explain why the PH-D is crucially targeted by these factors, which use their intrinsically disordered acidic regions for TFIIH recruitment.

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  • Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter

    Miki Mori, Kohei Sato, Toru Ekimoto, Shinichi Okumura, Mitsunori Ikeguchi, Kazuhito V. Tabata, Hiroyuki Noji, Kazushi Kinbara

    Chemistry – An Asian Journal   16 ( 2 )   147 - 157   2021.1

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    DOI： 10.1002/asia.202001106

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  • Front Cover: Imidazolinium‐based Multiblock Amphiphile as Transmembrane Anion Transporter (2/2021)

    Miki Mori, Kohei Sato, Toru Ekimoto, Shinichi Okumura, Mitsunori Ikeguchi, Kazuhito V. Tabata, Hiroyuki Noji, Kazushi Kinbara

    Chemistry – An Asian Journal   16 ( 2 )   110 - 110   2021.1

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    DOI： 10.1002/asia.202001415

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  • Structural analysis reveals TLR7 dynamics underlying antagonism

    Shingo Tojo, Zhikuan Zhang, Hiroyuki Matsui, Masahiro Tahara, Mitsunori Ikeguchi, Mami Kochi, Mami Kamada, Hideki Shigematsu, Akihisa Tsutsumi, Naruhiko Adachi, Takuma Shibata, Masaki Yamamoto, Masahide Kikkawa, Toshiya Senda, Yoshiaki Isobe, Umeharu Ohto, Toshiyuki Shimizu

    Nature Communications   11 ( 1 )   2020.12

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    <title>Abstract</title>
    Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus erythematosus (SLE). Here, by modifying potent TLR7 agonists, we develop a series of TLR7-specific antagonists as promising therapeutic agents for SLE. These compounds protect mice against lethal autoimmunity. Combining crystallography and cryo-electron microscopy, we identify the open conformation of the receptor and reveal the structural equilibrium between open and closed conformations that underlies TLR7 antagonism, as well as the detailed mechanism by which TLR7-specific antagonists bind to their binding pocket in TLR7. Our work provides small-molecule TLR7-specific antagonists and suggests the TLR7-targeting strategy for treating autoimmune diseases.

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  • Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures

    Takashi Yoshidome, Mitsunori Ikeguchi, Masateru Ohta

    Journal of Computational Chemistry   41 ( 28 )   2406 - 2419   2020.10

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    DOI： 10.1002/jcc.26406

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  • Comparison based on statistical thermodynamics between globule-to-coil transition of poly(N-isopropylacrylamide) and cold denaturation of a protein Reviewed

    Masao Inoue, Tomohiko Hayashi, Simon Hikiri, Mitsunori Ikeguchi, Masahiro Kinoshita

    Journal of Molecular Liquids   114129 - 114129   2020.8

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    DOI： 10.1016/j.molliq.2020.114129

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  • High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

    Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, Teruki Honma

    JOURNAL OF CHEMICAL INFORMATION AND MODELING   60 ( 7 )   3361 - 3368   2020.7

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    DOI： 10.1021/acs.jcim.0c00273

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  • Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51. Reviewed International journal

    Kentaro Ito, Yasuto Murayama, Yumiko Kurokawa, Shuji Kanamaru, Yuichi Kokabu, Takahisa Maki, Tsutomu Mikawa, Bilge Argunhan, Hideo Tsubouchi, Mitsunori Ikeguchi, Masayuki Takahashi, Hiroshi Iwasaki

    Nature communications   11 ( 1 )   2950 - 2950   2020.6

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    During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases.

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  • A synthetic ion channel with anisotropic ligand response. Reviewed International journal

    Takahiro Muraoka, Daiki Noguchi, Rinshi S Kasai, Kohei Sato, Ryo Sasaki, Kazuhito V Tabata, Toru Ekimoto, Mitsunori Ikeguchi, Kiyoto Kamagata, Norihisa Hoshino, Hiroyuki Noji, Tomoyuki Akutagawa, Kazuaki Ichimura, Kazushi Kinbara

    Nature communications   11 ( 1 )   2924 - 2924   2020.6

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    Biological membranes play pivotal roles in the cellular activities. Transmembrane proteins are the central molecules that conduct membrane-mediated biochemical functions such as signal transduction and substance transportation. Not only the molecular functions but also the supramolecular properties of the transmembrane proteins such as self-assembly, delocalization, orientation and signal response are essential for controlling cellular activities. Here we report anisotropic ligand responses of a synthetic multipass transmembrane ion channel. An unsymmetrical molecular structure allows for oriented insertion of the synthetic amphiphile to a bilayer by addition to a pre-formed membrane. Complexation with a ligand prompts ion transportation by forming a supramolecular channel, and removal of the ligand deactivates the transportation function. Biomimetic regulation of the synthetic channel by agonistic and antagonistic ligands is also demonstrated not only in an artificial membrane but also in a biological membrane of a living cell.

    DOI： 10.1038/s41467-020-16770-z

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  • Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain Reviewed

    Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Miwa Sato, Fumie Kusano, Takashi Oda, Motoko Unoki, Mitsunori Ikeguchi, Kyohei Arita

    Journal of Molecular Biology   14 ( 432 )   59 - 77   2020.5

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    DOI： 10.1016/j.jmb.2020.05.006

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  • Hydration properties of a protein at low and high pressures: Physics of pressure denaturation Reviewed

    Masao Inoue, Tomohiko Hayashi, Simon Hikiri, Mitsunori Ikeguchi, Masahiro Kinoshita

    The Journal of Chemical Physics   152 ( 6 )   065103 - 065103   2020.2

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    DOI： 10.1063/1.5140499

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  • Real-time tracking reveals the catalytic process of Rad51-driven DNA strand exchange

    Kentaro Ito, Yasuto Murayama, Yumiko Kurokawa, Shuji Kanamaru, Yuichi Kokabu, Takahisa Maki, Bilge Argunhan, Hideo Tsubouchi, Mitsunori Ikeguchi, Masayuki Takahashi, Hiroshi Iwasaki

    2019.11

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    Publisher：Cold Spring Harbor Laboratory  

    Abstract

    During homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1-C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for second donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA family recombinases.

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  • Force-field parametrization based on radial and energy distribution functions Reviewed

    Shuntaro Chiba, Yasushi Okuno, Teruki Honma, Mitsunori Ikeguchi

    Journal of Computational Chemistry   40   2577 - 2585   2019.11

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  • Mechanism of globule-to-coil transition of poly(N-isopropylacrylamide) in water: Relevance to cold denaturation of a protein Reviewed

    Masao Inoue, Tomohiko Hayashi, Simon Hikiri, Mitsunori Ikeguchi, Masahiro Kinoshita

    Journal of Molecular Liquids   292   111374 - 111374   2019.10

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    DOI： 10.1016/j.molliq.2019.111374

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  • How does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2? Reviewed

    Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata T, Kinoshita M

    Journal of Chemical Information and Modeling, doi: 10.1021/acs.jcim.9b00226   59   3533 - 3544   2019.8

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  • An Accurate and Rapid Method for Calculating Solvation Free Energies of a Variety of Solutes Including Proteins Reviewed

    Simon HIKIRI, Tomohiko HAYASHI, Masao INOUE, Toru EKIMOTO, Mitsunori IKEGUCHI, Masahiro KINOSHITA

    Journal of Chemical Physics   150 ( 17 )   175101-1 - 175101-12   2019

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  • Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments. Reviewed

    Toru Ekimoto, Yuichi Kokabu, Tomotaka Oroguchi, Mitsunori Ikeguchi

    Biophysics and physicobiology   16   377 - 390   2019

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    The combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), called the MD-SAXS method, is efficient for investigating protein dynamics. To overcome the time-scale limitation of all-atom MD simulations, coarse-grained (CG) representations are often utilized for biomolecular simulations. In this study, we propose a method to combine CG MD simulations with SAXS, termed the CG-MD-SAXS method. In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high-resolution structural data in the Protein Data Bank, and the excluded volume and the hydration shell are modeled using two adjustable parameters to incorporate solvent effects. To avoid overfitting, only the two parameters are adjusted for an entire structure ensemble. To verify the developed method, theoretical SAXS profiles for various proteins, DNA/RNA, and a protein-RNA complex are compared with both experimental profiles and theoretical profiles obtained by the all-atom representation. In the present study, we applied the CG-MD-SAXS method to the Swi5-Sfr1 complex and three types of nucleosomes to obtain reliable ensemble models consistent with the experimental SAXS data.

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  • Rotational Mechanism Model of the Bacterial V<sub>1</sub> Motor Based on Structural and Computational Analyses. Reviewed

    Singharoy A, Chipot C, Ekimoto T, Suzuki K, Ikeguchi M, Yamato I, Murata T

    Frontiers in physiology   10   46   2019

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  • Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid Reviewed

    Yosuke Isobe, Mai Itagaki, Yuko Ito, Satoko Naoe, Kotoe Kojima, Mitsunori Ikeguchi, Makoto Arita

    Scientific Reports   8 ( 1 )   7954   2018.12

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    DOI： 10.1038/s41598-018-26325-4

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  • Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method. Reviewed

    Ekimoto T, Yamane T, Ikeguchi M

    Journal of chemical theory and computation   14 ( 12 )   6544 - 6559   2018.11

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  • Physical Origin of Thermostabilization by a Quadruple Mutation for the Adenosine A2a Receptor in the Active State Reviewed

    Yuta Kajiwara, Satoshi Yasuda, Simon Hikiri, Tomohiko Hayashi, Mitsunori Ikeguchi, Takeshi Murata, Masahiro Kinoshita

    The Journal of Physical Chemistry B   122 ( 16 )   4418 - 4427   2018.4

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    DOI： 10.1021/acs.jpcb.8b00443

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  • Multiscale molecular dynamics simulations of rotary motor proteins Reviewed

    Toru Ekimoto, Mitsunori Ikeguchi

    Biophysical Reviews   10 ( 2 )   605 - 615   2018.4

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    DOI： 10.1007/s12551-017-0373-4

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  • Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB Reviewed

    Yasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada, Kei Moritsugu, Hiroshi Fujisaki, Satoshi Murakami, Mitsunori Ikeguchi, Akinori Kidera

    eLife   7   e31715   2018.3

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    DOI： 10.7554/eLife.31715

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  • Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. Reviewed

    Ekimoto T, Ikeguchi M

    Advances in experimental medicine and biology   1105   237 - 258   2018

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  • Ionic scattering factors of atoms that compose biological molecules Reviewed

    Koji Yonekura, Rei Matsuoka, Yoshiki Yamashita, Tsutomu Yamane, Mitsunori Ikeguchi, Akinori Kidera, Saori Maki-Yonekura

    IUCrJ   5 ( Pt 3 )   348 - 353   2018

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    DOI： 10.1107/S2052252518005237

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  • Statistical thermodynamics for the unexpectedly large difference between disaccharide stereoisomers in terms of solubility in water Reviewed

    Simon Hikiri, Tomohiko Hayashi, Mitsunori Ikeguchi, Masahiro Kinoshita

    Physical Chemistry Chemical Physics   20 ( 36 )   23684 - 23693   2018

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    <p>We unravel the physical origins of the large difference between cellobiose and maltose, which consist of two β-1,4 and α-1,4 linked <sc>d</sc>-glucose units, respectively, in terms of the solubility in water.</p>

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  • Apo- and Antagonist-Binding Structures of Vitamin D Receptor LigandBinding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics

    Anami Yasuaki, Shimizu Nobutaka, Ekimoto Toru, Egawa Daichi, Itoh Toshimasa, Ikeguchi Mitsunori, Yamamoto Keiko

    VITAMINS   92 ( 1 )   18 - 20   2018

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    DOI： 10.20632/vso.92.1_18

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  • MD-SAXS法によるビタミンD受容体リガンド結合ドメインの不活性型および活性阻害型の溶液構造解析 Reviewed

    清水伸隆, 浴本 亨, 穴見康昭, 伊藤俊将, 池口満徳, 山本恵子

    放射光   30 ( 6 )   264 - 276   2017.11

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  • Structureof the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance Reviewed

    Satoshi Ishiyama, Atsuya Nishiyama, Yasushi Saeki, Kei Moritsugu, Daichi Morimoto, Luna Yamaguchi, Naoko Arai, Rumie Matsumura, Toru Kawakami, Yuichi Mishima, Hironobu Hojo, Shintaro Shimamura, Fuyuki Ishikawa, Shoji Tajima, Keiji Tanaka, Mariko Ariyoshi, Masahiro Shirakawa, Mitsunori Ikeguchi, Akinori Kidera, Isao Suetake, Kyohei Arita, Makoto Nakanishi

    MOLECULAR CELL   68 ( 2 )   350 - +   2017.10

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    DOI： 10.1016/j.molcel.2017.09.037

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  • Dissection of the angle of single fluorophore attached to the nucleotide in corkscrewing microtubules Reviewed

    Shoko Fujimura, Yuko Ito, Mitsunori Ikeguchi, Kengo Adachi, Junichiro Yajima, Takayuki Nishizaka

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   485 ( 3 )   614 - 620   2017.4

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    DOI： 10.1016/j.bbrc.2017.01.165

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  • Rotation Mechanism of Molecular Motor V-1-ATPase Studied by Multiscale Molecular Dynamics Simulation Reviewed

    Yuta Isaka, Toru Ekimoto, Yuichi Kokabu, Ichiro Yamato, Takeshi Murata, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   112 ( 5 )   911 - 920   2017.3

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    DOI： 10.1016/j.bpj.2017.01.029

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  • SAXS-MD解析を用いたビタミンD受容体のアポ型及びアンタゴニスト結合型構造の解析

    山本 恵子, 穴見 康昭, 清水 伸隆, 浴本 亨, 江川 大地, 伊藤 俊将, 池口 満徳

    日本薬学会年会要旨集   137年会 ( 2 )   94 - 94   2017.3

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  • Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates Reviewed

    Simon Hikiri, Takashi Yoshidome, Mitsunori Ikeguchi

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   12 ( 12 )   5990 - 6000   2016.12

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    DOI： 10.1021/acs.jctc.6b00563

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  • Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics Reviewed

    Yasuaki Anami, Nobutaka Shimizu, Toni Eldmoto, Daichi Egawa, Toshimasa Itoh, Mitsunori Ikeguchi, Keiko Yamamoto

    JOURNAL OF MEDICINAL CHEMISTRY   59 ( 17 )   7888 - 7900   2016.9

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    DOI： 10.1021/acs.jmedchem.6b00682

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  • Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan Reviewed

    Naoyuki Kuwabara, Hiroshi Manya, Takeyuki Yamada, Hiroaki Tateno, Motoi Kanagawa, Kazuhiro Kobayashi, Keiko Akasaka-Manya, Yuriko Hirose, Mamoru Mizuno, Mitsunori Ikeguchi, Tatsushi Toda, Jun Hirabayashi, Toshiya Senda, Tamao Endo, Ryuichi Kato

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   113 ( 33 )   9280 - 9285   2016.8

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    DOI： 10.1073/pnas.1525545113

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  • Solution structure of the isolated histone H2A-H2B heterodimer Reviewed

    Yoshihito Moriwaki, Tsutomu Yamane, Hideaki Ohtomo, Mitsunori Ikeguchi, Jun-ichi Kurita, Masahiko Sato, Aritaka Nagadoi, Hideaki Shimojo, Yoshifumi Nishimura

    SCIENTIFIC REPORTS   6   24999   2016.5

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    DOI： 10.1038/srep24999

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  • An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules Reviewed

    Yoshidome Takashi, Ekimoto Toru, Matubayasi Nobuyuki, Harano Yuichi, Kinoshita Masahiro, Ikeguchi Mitsunori

    BIOPHYSICAL JOURNAL   110 ( 3 )   328A - 329A   2016.2

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  • Conformational Change in gamma(120) and gamma(240) of F-1-ATPase from the Aspect of Difference of Nucleotides by Advanced TIRF Microscope Reviewed

    Mikami Nagisa, Ito Yuko, Adachi Kengo, Ikeguchi Mitsunori, Nishizaka Takayuki

    Biophysical Journal   110 ( 3 )   164A   2016

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  • 19pBW-10 Classification of two-dimensional diffraction patterns of a protein with structural polymorphism using the diffusion-map method

    Yoshidome T., Sekiguchi Y., Oroguchi T., Nakasako M., Ikeguchi M.

    Meeting Abstracts of the Physical Society of Japan   71   3180 - 3180   2016

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    DOI： 10.11316/jpsgaiyo.71.1.0_3180

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  • Itinerary profiling to analyze a large number of protein-folding trajectories. Reviewed

    Ota M, Ikeguchi M, Kidera A

    Biophysics and physicobiology   13   295 - 304   2016

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    <p>Understanding how proteins fold through a vast number of unfolded states is a major subject in the study of protein folding. Herein, we present itinerary profiling as a simple method to analyze molecular dynamics trajectories, and apply this method to Trp-cage. In itinerary profiling, structural clusters included in a trajectory are represented by a bit sequence, and a number of trajectories, as well as the structural clusters, can be compared and classified. As a consequence, the structural clusters that characterize the foldability of trajectories were able to be identified. The connections between the clusters were then illustrated as a network and the structural features of the clusters were examined. We found that in the true folding funnel, Trp-cage formed a left-handed main-chain topology and the Trp6 side-chain was located at the front of the main-chain ring, even in the initial unfolded states. In contrast, in the false folding funnel of the pseudo-native states, in which the Trp6 side-chain is upside down in the protein core, Trp-cage had a right-handed main-chain topology and the Trp side-chain was at the back. The initial topological partition, as determined by the main-chain handedness and the location of the Trp residue, predetermines Trp-cage foldability and the destination of the trajectory to the native state or the pseudo-native states.</p>

    DOI： 10.2142/biophysico.13.0_295

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  • Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for x-ray free-electron laser diffraction imaging Reviewed

    Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics   92 ( 3 )   032710   2015.9

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    DOI： 10.1103/PhysRevE.92.032710

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  • An accurate and efficient computation method of the hydration free energy of a large, complex molecule Reviewed

    Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

    JOURNAL OF CHEMICAL PHYSICS   142 ( 17 )   175101   2015.5

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    DOI： 10.1063/1.4919636

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  • 全原子分子動力学計算が解き明かす分子モーターの回転機構 Invited Reviewed

    伊藤 祐子, 池口 満徳

    生物物理   55   23 - 26   2015.2

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    DOI： 10.2142/biophys.55.023

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  • Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free-Energy Simulations Reviewed

    Yuko Ito, Mitsunori Ikeguchi

    Biophysical Journal   108 ( 1 )   85 - 97   2015.1

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    DOI： 10.1016/j.bpj.2014.11.1853

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  • Finite-Size Effect on the Charging Free Energy of Protein in Explicit Solvent Reviewed

    Toru Ekimoto, Nobuyuki Matubayasi, Mitsunori Ikeguchi

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   11 ( 1 )   215 - 223   2015.1

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    DOI： 10.1021/ct5008394

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  • 19aCT-9 Classification of phase-retrieved projection electron density maps using the diffusion-map method

    Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M.

    Meeting Abstracts of the Physical Society of Japan   70   3019 - 3019   2015

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    DOI： 10.11316/jpsgaiyo.70.2.0_3019

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  • 3SBA-02 The conformational change mechanism of the β subunit in F1-ATPase revealed by all-atom MD simulations(Rise of molecular machines,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Yuko Ito, Mitsunori Ikeguchi

    Seibutsu Butsuri   54 ( 1 )   S136   2014

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    DOI： 10.2142/biophys.54.S136_6

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  • 3P149 Molecular dynamics simulations of the β subunit in F_1-ATPase : Relation between the large-scale structural change and common motifs(11. Molecular motor,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Ito Yuko, Ikeguchi Mitsunori

    Seibutsu Butsuri   54 ( 1 )   S273   2014

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    DOI： 10.2142/biophys.54.S273_5

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  • Molecular Dynamics Simulations of F-1-ATPase Reviewed

    Yuko Ito, Mitsunori Ikeguchi

    PROTEIN CONFORMATIONAL DYNAMICS   805   411 - 440   2014

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    DOI： 10.1007/978-3-319-02970-2_17

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  • Free Energy Simulations for the Conformational Change of the alpha beta Subunits in F-1-ATPase After the ATP Hydrolysis Reviewed

    Ito Yuko, Ikeguchi Mitsunori

    Biophysical Journal   106 ( 2 )   611A   2014

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  • 2P120 Structural dynamics of tri-nucleosome studied by combination of coarse grained molecular simulation and SAXS(05A. Nucleic acid: Structure & Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Takagi Yusuke, Kokabu Yuichi, Oda Takashi, Tachiwana Hiroaki, Kenzaki Hiroo, Kurumizaka Hitoshi, Sato Mamoru, Ikeguchi Mitsunori, Takada Shoji

    Seibutsu Butsuri   54 ( 1 )   S214   2014

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    DOI： 10.2142/biophys.54.S214_6

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  • 1P294 Analysis of the projection images using the novel classification protocol based on the concept of manifold(27. Bioimaging,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Yoshidome Takashi, Oroguchi Tomotaka, Nakasako Masayoshi, Ikeguchi Mitsunori

    Seibutsu Butsuri   54 ( 1 )   S189   2014

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    DOI： 10.2142/biophys.54.S189_6

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  • 2P052 Calculation methods for configurational entropy from molecular dynamics simulations(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Hikiri Simon, Yoshidome Takashi, Ikeguchi Mitsunori

    Seibutsu Butsuri   54 ( 1 )   S203   2014

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    DOI： 10.2142/biophys.54.S203_4

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  • Functional Rotation Induced by Alternating Protonation States in the Multidrug Transporter AcrB: All-Atom Molecular Dynamics Simulations Reviewed

    Tsutomu Yamane, Satoshi Murakami, Mitsunori Ikeguchi

    BIOCHEMISTRY   52 ( 43 )   7648 - 7658   2013.10

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    DOI： 10.1021/bi400119v

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  • Molecular modeling and molecular dynamics simulations of recombinase Rad51 Reviewed

    Yuichi Kokabu, Mitsunori Ikeguchi

    Biophysical Journal   104 ( 7 )   1556 - 1565   2013.4

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    DOI： 10.1016/j.bpj.2013.02.014

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  • Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation Reviewed

    Kazumi Saikusa, Sotaro Fuchigami, Kyohei Takahashi, Yuuki Asano, Aritaka Nagadoi, Hiroaki Tachiwana, Hitoshi Kurumizaka, Mitsunori Ikeguchi, Yoshifumi Nishimura, Satoko Akashi

    ANALYTICAL CHEMISTRY   85 ( 8 )   4165 - 4171   2013.4

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    DOI： 10.1021/ac400395j

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  • Molecular Dynamics Simulations of Yeast F-1-ATPase before and after 16 degrees Rotation of the gamma Subunit Reviewed

    Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori Ikeguchi

    JOURNAL OF PHYSICAL CHEMISTRY B   117 ( 12 )   3298 - 3307   2013.3

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    DOI： 10.1021/jp312499u

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  • Molecular Dynamics Simulations of Yeast F-1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit Reviewed

    Ito Yuko, Yoshidome Takashi, Matubayasi Nobuyuki, Kinoshita Masahiro, Ikeguchi Mitsunori

    BIOPHYSICAL JOURNAL   104 ( 2 )   332A   2013.1

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  • Protein dynamics investigated by small-angle x-ray scattering and molecular dynamics simulations Reviewed

    Tomotaka Oroguchi, Mitsunori Ikeguchi, Mamoru Sato

    日本結晶学会誌   55   24-31   2013

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  • 1P059 Comparison of calculation methods of configurational entropy from molecular dynamics simulation trajectories(01C. Protein:Property,Poster)

    Hikiri Simon, Yoshidome Takashi, Ikeguchi Mitsunori

    Seibutsu Butsuri   53 ( 1 )   S115   2013

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    DOI： 10.2142/biophys.53.S115_5

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  • Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering Reviewed

    Kazumi Saikusa, Naoyuki Kuwabara, Yuichi Kokabu, Yu Inoue, Mamoru Sato, Hiroshi Iwasaki, Toshiyuki Shimizu, Mitsunori Ikeguchi, Satoko Akashi

    ANALYST   138 ( 5 )   1441 - 1449   2013

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    DOI： 10.1039/c2an35878f

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  • 3P166 Free energy simulations for the conformational change of the αβ subunits in F_1-ATPase after the ATP hydrolysis(11. Molecular motor,Poster)

    Ito Yuko, Ikeguchi Mitsunori

    Seibutsu Butsuri   53 ( 1 )   S239   2013

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    DOI： 10.2142/biophys.53.S239_3

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  • 3P164 All-atom hydration analysis of the β subunit in F1-ATPase(11. Molecular motor,Poster)

    Ekimoto Toru, Ikeguchi Mitsunori, Matubayasi Nobuyuki

    Seibutsu Butsuri   53 ( 1 )   S239   2013

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    DOI： 10.2142/biophys.53.S239_1

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  • 3P165 Rotation mechanism of V_1-ATPase studied by steered MD simulations(11. Molecular motor,Poster)

    Isaka Yuta, Yamato Ichiro, Murata Takeshi, Ikeguchi Mitsunori

    Seibutsu Butsuri   53 ( 1 )   S239   2013

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    DOI： 10.2142/biophys.53.S239_2

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  • Role of the DELSEED Loop in Torque Transmission of F-1-ATPase Reviewed

    Mizue Tanigawara, Kazuhito V. Tabata, Yuko Ito, Jotaro Ito, Rikiya Watanabe, Hiroshi Ueno, Mitsunori Ikeguchi, Hiroyuki Noji

    BIOPHYSICAL JOURNAL   103 ( 5 )   970 - 978   2012.9

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    DOI： 10.1016/j.bpj.2012.06.054

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  • MD-SAXS method with nonspherical boundaries Reviewed

    Tomotaka Oroguchi, Mitsunori Ikeguchi

    Chemical Physics Letter   541   117-121   2012.7

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  • Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function Reviewed

    Hirokazu Mishima, Satoshi Yasuda, Takashi Yoshidome, Hiraku Oshima, Yuichi Harano, Mitsunori Ikeguchi, Masahiro Kinoshita

    JOURNAL OF PHYSICAL CHEMISTRY B   116 ( 27 )   7776 - 7786   2012.7

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    DOI： 10.1021/jp301541z

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  • Comparative Simulations of the Ground State and the M-Intermediate State of the Sensory Rhodopsin II-Transducer Complex with a HAMP Domain Model Reviewed

    Koro Nishikata, Mitsunori Ikeguchi, Akinori Kidera

    BIOCHEMISTRY   51 ( 30 )   5958 - 5966   2012.7

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    DOI： 10.1021/bi300696b

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  • Molecular Mechanism of ATP Hydrolysis in F-1-ATPase Revealed by Molecular Simulations and Single-Molecule Observations Reviewed

    Shigehiko Hayashi, Hiroshi Ueno, Abdul Rajjak Shaikh, Myco Umemura, Motoshi Kamiya, Yuko Ito, Mitsunori Ikeguchi, Yoshihito Komoriya, Ryota Iino, Hiroyuki Noji

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   134 ( 20 )   8447 - 8454   2012.5

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    DOI： 10.1021/ja211027m

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  • Mechanistic Insights into the Activation of Rad51-Mediated Strand Exchange from the Structure of a Recombination Activator, the Swi5-Sfr1 Complex Reviewed

    Naoyuki Kuwabara, Yasuto Murayama, Hiroshi Hashimoto, Yuuichi Kokabu, Mitsunori Ikeguchi, Mamoru Sato, Kouta Mayanagi, Yasuhiro Tsutsui, Hiroshi Iwasaki, Toshiyuki Shimizu

    STRUCTURE   20 ( 3 )   440 - 449   2012.3

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    DOI： 10.1016/j.str.2012.01.005

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  • 1PT190 Characterization of histone multimers in the gas phase by ion mobility mass spectrometry and molecular dynamics simulation(The 50th Annual Meeting of the Biophysical Society of Japan)

    Saikusa Kazumi, Fuchigami Sotaro, Takahashi Kyohei, Asano Yuuki, Nagadoi Aritaka, Tachiwana Hiroaki, Kurumizaka Hitoshi, Ikeguchi Mitsunori, Nishimura Yoshifumi, Akashi Satoko

    Seibutsu Butsuri   52   S101   2012

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    DOI： 10.2142/biophys.52.S101_4

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  • 1PS034 Molecular Dynamics Simulation on Structural Characteristics of Yeast F1-ATPase before and after 16-degree Rotation of Gamma Subunit(The 50th Annual Meeting of the Biophysical Society of Japan)

    Ito Yuko, Yoshidome Takashi, Matsubayashi Nobuyuki, Kinoshita Masahiro, Ikeguchi Mitsunori

    Seibutsu Butsuri   52   S80   2012

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    DOI： 10.2142/biophys.52.S80_1

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  • 2PT134 Molecular dynamics simulation study of Lys48-linked diubiquitin in compact conformation(The 50th Annual Meeting of the Biophysical Society of Japan)

    Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   52   S127   2012

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    DOI： 10.2142/biophys.52.S127_5

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  • Mechanism of the Conformational Change of the F-1-ATPase beta Subunit Revealed by Free-Energy Simulations Reviewed

    Ito Yuko, Oroguchi Tomotaka, Ikeguchi Mitsunori

    Biophysical Journal   102 ( 3 )   712A   2012

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  • Structural characteristics of yeast F <sub>1</sub>-ATPase before and after 16-degree rotation of the γ subunit: Theoretical analysis focused on the water-entropy effect Reviewed

    T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, M. Kinoshita

    Journal of Chemical Physics   137 ( 3 )   035102   2012

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    DOI： 10.1063/1.4734298

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  • A Native Disulfide Stabilizes Non-Native Helical Structures in Partially Folded States of Equine beta-Lactoglobulin Reviewed

    Mio Yamamoto, Kanako Nakagawa, Kazuo Fujiwara, Akio Shimizu, Mitsunori Ikeguchi, Masamichi Ikeguchi

    BIOCHEMISTRY   50 ( 49 )   10590 - 10597   2011.12

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    DOI： 10.1021/bi2013239

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  • Fission Yeast Swi5-Sfr1 Protein Complex, an Activator of Rad51 Recombinase, Forms an Extremely Elongated Dogleg-shaped Structure Reviewed

    Yuichi Kokabu, Yasuto Murayama, Naoyuki Kuwabara, Tomotaka Oroguchi, Hiroshi Hashimoto, Yasuhiro Tsutsui, Naohito Nozaki, Satoko Akashi, Satoru Unzai, Toshiyuki Shimizu, Hiroshi Iwasaki, Mamoru Sato, Mitsunori Ikeguchi

    JOURNAL OF BIOLOGICAL CHEMISTRY   286 ( 50 )   43569 - 43576   2011.12

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    DOI： 10.1074/jbc.M111.303339

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  • Homology-modelled structure of the beta B2B3-crystallin heterodimer studied by ion mobility and radical probe MS Reviewed

    Kevin M. Downard, Yuichi Kokabu, Mitsunori Ikeguchi, Satoko Akashi

    FEBS JOURNAL   278 ( 21 )   4044 - 4054   2011.11

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    DOI： 10.1111/j.1742-4658.2011.08309.x

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  • Free-energy function for discriminating the native fold of a protein from misfolded decoys Reviewed

    Satoshi Yasuda, Takashi Yoshidome, Yuichi Harano, Roland Roth, Hiraku Oshima, Koji Oda, Yuji Sugita, Mitsunori Ikeguchi, Masahiro Kinoshita

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   79 ( 7 )   2161 - 2171   2011.7

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    DOI： 10.1002/prot.23036

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  • Classification and Annotation of the Relationship between Protein Structural Change and Ligand Binding Reviewed

    Takayuki Amemiya, Ryotaro Koike, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

    JOURNAL OF MOLECULAR BIOLOGY   408 ( 3 )   568 - 584   2011.5

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    DOI： 10.1016/j.jmb.2011.02.058

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  • Mechanism of the Conformational Change of the F-1-ATPase beta Subunit Revealed by Free Energy Simulations Reviewed

    Yuko Ito, Tomotaka Oroguchi, Mitsunori Ikeguchi

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   133 ( 10 )   3372 - 3380   2011.3

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    DOI： 10.1021/ja1070152

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  • Rotation Mechanism of F-1-ATPase: Crucial Importance of the Water Entropy Effect Reviewed

    Takashi Yoshidome, Yuko Ito, Mitsunori Ikeguchi, Masahiro Kinoshita

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   133 ( 11 )   4030 - 4039   2011.3

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  • Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations Reviewed

    Tomotaka Oroguchi, Mitsunori Ikeguchi

    JOURNAL OF CHEMICAL PHYSICS   134 ( 2 )   025102   2011.1

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    DOI： 10.1063/1.3526488

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  • Towards the structural characterization of intrinsically disordered proteins by SAXS and MD simulation Reviewed

    Tomotaka Oroguchi, Mitsunori Ikeguchi, Mamoru Sato

    Journal of Physics: Conference Series   272 ( 1 )   012005   2011.1

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  • 3D1136 Molecular dynamics simulation study of diubiquitins : Analysis of ubiquitin-ubiquitin interactions(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

    Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   51   S118 - S119   2011

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    DOI： 10.2142/biophys.51.S118_6

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  • Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes Reviewed

    Hiraku Oshima, Satoshi Yasuda, Takashi Yoshidome, Mitsunori Ikeguchi, Masahiro Kinoshita

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS   13 ( 36 )   16236 - 16246   2011

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    DOI： 10.1039/c1cp21597c

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  • 3H1024 P24 Analysis on dynamical structure of intrinsically disordered protein Hef, using MD-SAXS method(3H Protein: Property 4,The 49th Annual Meeting of the Biophysical Society of Japan)

    Oroguchi Tomotaka, Oda Takashi, Hashimoto Hiroshi, Ishino Yoshizumi, Ikeguchi Mitsunori, Sato Mamoru

    Seibutsu Butsuri   51   S133   2011

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    DOI： 10.2142/biophys.51.S133_4

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  • 1H1436 Crucial Importance of Water-Entropy Effect for Hot Spots in Protein-Protein Complexes(Protein: Property 2,The 49th Annual Meeting of the Biophysical Society of Japan)

    Oshima Hiraku, Yasuda Satoshi, Yoshidome Takashi, Ikeguchi Mitsunori, Kinoshita Masahiro

    Seibutsu Butsuri   51   S49   2011

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    DOI： 10.2142/biophys.51.S49_4

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  • Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations Reviewed

    Yuji Sugita, Mitsunori Ikeguchi, Chikashi Toyoshima

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   107 ( 50 )   21465 - 21469   2010.12

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    DOI： 10.1073/pnas.1015819107

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  • Side-Chain Conformational Changes of Transcription Factor PhoB upon DNA Binding: A Population-Shift Mechanism Reviewed

    Tsutomu Yamane, Hideyasu Okamura, Yoshifumi Nishimura, Akinori Kidera, Mitsunori Ikeguchi

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   132 ( 36 )   12653 - 12659   2010.9

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    DOI： 10.1021/ja103218x

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  • Expression, purification and crystallization of Swi5 and the Swi5-Sfr1 complex from fission yeast Reviewed

    Naoyuki Kuwabara, Hiroshi Hashimoto, Noriyo Yamada, Satoru Unzai, Mitsunori Ikeguchi, Mamoru Sato, Yasuto Murayama, Hiroshi Iwasaki, Toshiyuki Shimizu

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   66 ( Pt 9 )   1124 - 1126   2010.9

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    DOI： 10.1107/S1744309110032239

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  • Structural fluctuation and concerted motions in f1-atpase: A molecular dynamics study Reviewed

    Ito Yuko, Ikeguchi Mitsunori

    Journal of Computational Chemistry   31 ( 11 )   2175 - 2185   2010.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/jcc.21508

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  • Structure and Functional Characterization of Vibrio parahaemolyticus Thermostable Direct Hemolysin Reviewed

    Itaru Yanagihara, Kumiko Nakahira, Tsutomu Yamane, Shuji Kaieda, Kouta Mayanagi, Daizo Hamada, Takashi Fukui, Kiyouhisa Ohnishi, Shin'ichiro Kajiyama, Toshiyuki Shimizu, Mamoru Sato, Takahisa Ikegami, Mitsunori Ikeguchi, Takeshi Honda, Hiroshi Hashimoto

    JOURNAL OF BIOLOGICAL CHEMISTRY   285 ( 21 )   16267 - 16274   2010.5

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    DOI： 10.1074/jbc.M109.074526

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  • Latent dynamics of a protein molecule observed in dihedral angle space Reviewed

    Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

    JOURNAL OF CHEMICAL PHYSICS   132 ( 11 )   115103   2010.3

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    DOI： 10.1063/1.3360144

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  • Normal mode analysis of protein dynamics in a non-Eckart frame Reviewed

    Sotaro Fuchigami, Satoshi Omori, Mitsunori Ikeguchi, Akinori Kidera

    JOURNAL OF CHEMICAL PHYSICS   132 ( 10 )   104109   2010.3

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    DOI： 10.1063/1.3352566

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  • Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F-1-ATPase from photosynthetic organisms Reviewed

    Hiromasa Yagi, Hiroki Konno, Tomoe Murakami-Fuse, Atsuko Isu, Tomotaka Oroguchi, Hideo Akutsu, Mitsunori Ikeguchi, Toru Hisabori

    BIOCHEMICAL JOURNAL   425 ( 1 )   85 - 94   2010.1

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    DOI： 10.1042/BJ20091247

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  • 1P013 Solution structure of S.pombe Swi5-Sfr1 studied by smallangle X-ray scattering(Protein:Structure,The 48th Annual Meeting of the Biophysical Society of Japan)

    Kokabu Yuichi, Murayama Yasuto, Kuwabara Naoyuki, Oroguchi Tomotaka, Hashimoto Hiroshi, Shimizu Toshiyuki, Iwasaki Hiroshi, Sato Mamoru, Ikeguchi Mitsunori

    Seibutsu Butsuri   50 ( 2 )   S21   2010

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    DOI： 10.2142/biophys.50.S21_2

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  • MEASUREMENT OF THE CONFORMATIONAL STATE OF F-1-ATPASE BY SINGLE-MOLECULE ROTATION Reviewed

    Daichi Okuno, Mitsunori Ikeguchi, Hiroyuki Noji

    METHODS IN ENZYMOLOGY, VOL 475: SINGLE MOLECULE TOOLS, PT B   475   279 - 296   2010

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    DOI： 10.1016/S0076-6879(10)75012-6

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  • Molecular dynamics simulations of the isolated beta subunit of F-1-ATPase Reviewed

    Ito Yuko, Ikeguchi Mitsunori

    Chemical Physics Letters   490 ( 1-3 )   80 - 83   2010

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  • 1P073 Development of a free-energy function toward predicting the native structure of a protein(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan)

    Yasuda Satoshi, Yoshidome Takashi, Harano Yuichi, Roth Roland, Sugita Yuji, Ikeguchi Mitsunori, Kinoshita Masahiro

    Seibutsu Butsuri   50 ( 2 )   S32   2010

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    DOI： 10.2142/biophys.50.S32_1

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  • Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis Reviewed

    Koro Nishikata, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

    Biophysics   6   27 - 36   2010

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    DOI： 10.2142/biophysics.6.27

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  • 1P186 1YA1115 Crucial importance of translational entropy of water in rotation mechanism of F1-ATPase(Molecular motor,Early Research in Biophysics Award Candidate Presentations,Early Research in Biophysics Award,The 48th Annual Meeting of the Biophysical Society of Japan)

    Yoshidome Takashi, Ito Yuko, Ikeguchi Mitsunori, Kinoshita Masahiro

    Seibutsu Butsuri   50 ( 2 )   S52   2010

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    DOI： 10.2142/biophys.50.S52_2

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  • 3P044 The development of multi-dimensional replica-exchange molecular dynamics program (REIN)(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

    Miyashita Naoyuki, Ikeguchi Mitsunori, Sugita Yuji

    Seibutsu Butsuri   50 ( 2 )   S152 - S153   2010

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    DOI： 10.2142/biophys.50.S152_5

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  • 3P011 STRUCTURAL STUDY OF THERMOSTABLE DIRECT HEMOLYSIN FROM VIBRIO PARAHAEMOLYTICUS(Protein: Structure,The 48th Annual Meeting of the Biophysical Society of Japan)

    HASHIMOTO HIROSHI, NAKAHIRA KUMIKO, YAMANE TSUTOMU, FUKUI TAKASHI, OHNISHI KIYOHISA, SHIMIZU TOSHIYUKI, HONDA TAKESHI, IKEGUCHI MITSUNORI, SATO MAMORU, YANAGIHARA ITARU

    Seibutsu Butsuri   50 ( 2 )   S146   2010

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    DOI： 10.2142/biophys.50.S146_5

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  • 2P194 Investigation of the conformational change of the F_1-ATPase (β subunit) via molecular dynamics simulation(The 48th Annual Meeting of the Biophysical Society of Japan)

    Ito Yuko, Oroguchi Tomotaka, Ikeguchi Mitsunori

    Seibutsu Butsuri   50 ( 2 )   S116   2010

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    DOI： 10.2142/biophys.50.S116_5

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  • 1P062 Theoretical Prediction of Hot Spots in Protein-Protein Complexes(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan)

    Oshima Hiraku, Yasuda Satoshi, Yoshidome Takashi, Ikeguchi Mitsunori, Kinoshita Masahiro

    Seibutsu Butsuri   50 ( 2 )   S30   2010

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    DOI： 10.2142/biophys.50.S30_1

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  • Free-energy function based on an all-atom model for proteins Reviewed

    Takashi Yoshidome, Koji Oda, Yuichi Harano, Roland Roth, Yuji Sugita, Mitsunori Ikeguchi, Masahiro Kinoshita

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   77 ( 4 )   950 - 961   2009.12

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    DOI： 10.1002/prot.22520

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  • Linear Response Theory in Dihedral Angle Space for Protein Structural Change Upon Ligand Binding Reviewed

    Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

    JOURNAL OF COMPUTATIONAL CHEMISTRY   30 ( 16 )   2602 - 2608   2009.12

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    DOI： 10.1002/jcc.21269

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  • Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis Reviewed

    Tomotaka Oroguchi, Hiroshi Hashimoto, Toshiyuki Shimizu, Mamoru Sato, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   96 ( 7 )   2808 - 2822   2009.4

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    DOI： 10.1016/j.bpj.2008.12.3914

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  • Water transport in aquaporins: Molecular dynamics simulations Reviewed

    Mitsunori Ikeguchi

    Frontiers in Bioscience   14 ( 4 )   1283 - 1291   2009.1

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    DOI： 10.2741/3308

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  • Structure Analysis of F-1-ATPase via Molecular Dynamics Reviewed

    Ito Yuko, Ikeguchi Mitsunori

    Biophysical Journal   96 ( 3 )   144A   2009

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  • 2P-004 Solution structures of DNA recombination mediators Swi5 and Sfr1 in fission yeast studied by small-angle x-ray scattering(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan)

    Kokabu Yuichi, Oroguchi Tomotaka, Murayama Yasuto, Kuwabara Naoyuki, Yamane Tsutomu, Hashimoto Hiroshi, Unzai Satoru, Shimizu Toshiyuki, Iwasaki Hiroshi, Ikeguchi Mitsunori

    Seibutsu Butsuri   49   S106   2009

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    DOI： 10.2142/biophys.49.S106_4

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  • 1P-121 Structural fluctuation and cooperativity in F_1-ATPase : a molecular dynamics study(Molecular motor, The 47th Annual Meeting of the Biophysical Society of Japan)

    Ito Yuko, Ikeguchi Mitsunori

    Seibutsu Butsuri   49   S82   2009

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    DOI： 10.2142/biophys.49.S82_4

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  • 1P-023 Molecular Dynamics Simulation Study of Diubiquitins with Different Linkages(Protein:Structure & Function, The 47th Annual Meeting of the Biophysical Society of Japan)

    Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   49   S67   2009

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    DOI： 10.2142/biophys.49.S67_1

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  • Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3. Reviewed International journal

    Naotaka Sekiyama, Takahisa Ikegami, Tsutomu Yamane, Mitsunori Ikeguchi, Yasuhiro Uchimura, Daichi Baba, Mariko Ariyoshi, Hidehito Tochio, Hisato Saitoh, Masahiro Shirakawa

    The Journal of biological chemistry   283 ( 51 )   35966 - 75   2008.12

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    Post-translational modification by small ubiquitin-like modifier (SUMO) proteins has been implicated in the regulation of a variety of cellular events. The functions of sumoylation are often mediated by downstream effector proteins harboring SUMO-interacting motifs (SIMs) that are composed of a hydrophobic core and a stretch of acidic residues. MBD1-containing chromatin-associated factor 1 (MCAF1), a transcription repressor, interacts with SUMO-2/3 and SUMO-1, with a preference for SUMO-2/3. We used NMR spectroscopy to solve the solution structure of the SIM of MCAF1 bound to SUMO-3. The hydrophobic core of the SIM forms a parallel beta-sheet pairing with strand beta2 of SUMO-3, whereas its C-terminal acidic stretch seems to mediate electrostatic interactions with a surface area formed by basic residues of SUMO-3. The significance of these electrostatic interactions was shown by mutations of both SUMO-3 and MCAF1. The present structural and biochemical data suggest that the acidic stretch of the SIM of MCAF1 plays an important role in the binding to SUMO-3.

    DOI： 10.1074/jbc.M802528200

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  • [Comparative molecular simulations of water permeation in aquaporins]. Reviewed

    Kidera A, Ikeguchi M

    Seikagaku. The Journal of Japanese Biochemical Society   80 ( 10 )   940 - 947   2008.10

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  • Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment Reviewed

    Tsutomu Yamane, Hideyasu Okamura, Mitsunori Ikeguchi, Yoshifumi Nishimura, Akinori Kidera

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   71 ( 4 )   1970 - 1983   2008.6

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    DOI： 10.1002/prot.21874

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  • 2P-052 Analysis of side-chain dynamics of PhoB DNA binding/transactivation domain using molecular dynamics simulations(The 46th Annual Meeting of the Biophysical Society of Japan)

    Yamane Tsutomu, Okamura Hideyasu, Nishimura Yoshifumi, Kidera Akinori, Ikeguchi Mitsunori

    Seibutsu Butsuri   48   S83   2008

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    DOI： 10.2142/biophys.48.S83_2

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  • 1P-026 Structure and Function Analysis of F1-ATPase by Molecular Dynamics(The 46th Annual Meeting of the Biophysical Society of Japan)

    Ito Yuko, Ikeguchi Mitsunori

    Seibutsu Butsuri   48   S24   2008

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    DOI： 10.2142/biophys.48.S24_6

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  • 1P-264 The HAMP domain model of sensory rhodopsin / cognate transducer complex : Molecular dynamics study(The 46th Annual Meeting of the Biophysical Society of Japan)

    NISHIKATA Koro, FUCHIGAMI Sotaro, IKEGUCHI Mitsunori, KIDERA Akinori

    Seibutsu Butsuri   48   S63   2008

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    DOI： 10.2142/biophys.48.S63_1

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  • 2P-010 Solution structure of Schizosaccharomyces pombe Swi5 studied by small-angle X-ray scattering and molecular dynamics simulations(The 46th Annual Meeting of the Biophysical Society of Japan)

    Kokabu Yuichi, Oroguchi Tomotaka, Yamane Tsutomu, Hashimoto Hiroshi, Shimizu Toshiyuki, Iwasaki Hiroshi, Ikeguchi Mitsunori

    Seibutsu Butsuri   48   S76   2008

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    DOI： 10.2142/biophys.48.S76_4

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  • Unfolding pathways of goat alpha-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories Reviewed

    Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera

    JOURNAL OF MOLECULAR BIOLOGY   371 ( 5 )   1354 - 1364   2007.8

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    DOI： 10.1016/j.jmb.2007.06.023

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  • Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations Reviewed

    Masanori Hashido, Akinori Kidera, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   93 ( 2 )   373 - 385   2007.7

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    DOI： 10.1529/biophysj.107.101170

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  • Physical basis for characterizing native structures of proteins Reviewed

    Harano Yuichi, Roth Roland, Sugita Yuji, Ikeguchi Mitsunori, Kinoshita Masahiro

    CHEMICAL PHYSICS LETTERS   437 ( 1-3 )   112 - 116   2007.3

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  • Fission yeast Swi5/Sfr1 and Rhp55/Rhp57 differentially regulate Rhp51-dependent recombination outcomes Reviewed

    Yufuko Akamatsu, Yasuhiro Tsutsui, Takashi Morishita, M. D. Shahjahan P. Siddique, Yumiko Kurokawa, Mitsunori Ikeguchi, Fumiaki Yamao, Benoit Arcangioli, Hiroshi Iwasaki

    EMBO JOURNAL   26 ( 5 )   1352 - 1362   2007.3

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    DOI： 10.1038/sj.emboj.7601582

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  • Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography Reviewed

    Christine Addy, Masato Ohara, Fumihiro Kawai, Akinori Kidera, Mitsunori Ikeguchi, Sotaro Fuchigami, Masanori Osawa, Ichio Shimada, Sam-Yong Park, Jeremy R. H. Tame, Jonathan G. Heddle

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   63   221 - 229   2007.2

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    Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wildtype NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.

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  • Nickel binding to NikA: An additional binding site reconciles spectroscopy, calorimetry and crystallography Reviewed

    Christine Addy, Masato Ohara, Fumihiro Kawai, Akinori Kidera, Mitsunori Ikeguchi, Sotaro Fuchigami, Masanori Osawa, Ichio Shimada, Sam-Yong Park, Jeremy R. H. Tame, Jonathan G. Heddle

    Acta Crystallographica Section D: Biological Crystallography   63 ( 2 )   221 - 229   2007.2

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    Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed. © International Union of Crystallography, 2007.

    DOI： 10.1107/S0907444906048712

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  • 1P074 Dynamical process of protein conformational change upon ligand binding : Linear response theory with time-dependent perturbation(Proteins-functions, methodology, and protein enigineering,Oral Presentations)

    Naritomi Yusuke, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S42   2007

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    DOI： 10.2142/biophys.47.S42_1

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  • 2P003 Database analysis of the protein structural change by the linear response theory(Proteins-structure and structure-function relationship,Oral Presentations)

    Amemiya Takayuki, Koike Ryotaro, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S113   2007

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    DOI： 10.2142/biophys.47.S113_4

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  • 1P006 Molecular dynamics simulation of 3α-hydroxysteroid dehydrogenase with NADH : Structural changes in the substrate-binding loop(Proteins-structure and structure-function relationship,Oral Presentations)

    Nakamura Shota, Oroguchi Tomotaka, Yamane Tsutomu, Ikeguchi Mitsunori, Kataoka Sachiyo, Koga Maiko, Oda Masayuki, Kobayashi Yuji, Ohkubo Tadayasu

    Seibutsu Butsuri   47   S25   2007

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    DOI： 10.2142/biophys.47.S25_1

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  • 1P247 Diversity of protein-protein interactions viewed from conformational changes(Bioinformatics-structural genomics,Poster Presentations)

    Kayama Hiroaki, Amemiya Takayuki, Koike Ryotaro, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S85   2007

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    DOI： 10.2142/biophys.47.S85_2

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  • 3P239 Molecular Dynamics Study of the HAMP domain of Halobacterial Transducer of Rhodopsin II (HtrII)(Photobiology- vision and photoreception. Actinobiology,Oral Presentations)

    Nishikata Koro, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S262   2007

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    DOI： 10.2142/biophys.47.S262_4

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  • 3P168 How many phospholipids plug a central cavity of c-ring in F-type ATP synthase? : a molecular dynamics simulation approach(Molecular motors,Poster Presentations)

    Fuchigami Sotaro, Nakajima Kyoko, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S245   2007

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    DOI： 10.2142/biophys.47.S245_1

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  • 1P003 Molecular dynamics simulations of the ligand-binding core of the inositol 1,4,5-trisphosphate receptor in the ligand-free slate(Proteins-structure and structure-function relationship,Oral Presentations)

    Ida Yoichi, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   47   S24   2007

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    DOI： 10.2142/biophys.47.S24_2

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  • 2P056 Dynamics and hydration structure of Eco109I studied by small-angle X-ray scattering experiment and molecular dynamics simulation(Proteins-structure and structure-function relationship,Poster Presentations)

    Oroguchi Tomotaka, Sato Mamoru, Ikeguchi Mitsunori

    Seibutsu Butsuri   47   S127   2007

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    DOI： 10.2142/biophys.47.S127_1

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  • 3P079 Dynamics of PhoB protein as revealed in the comparison between molecular dynamics simulation and NMR relaxation experiments(Proteins-stability, folding, and other physicochemical properties,Poster Presentations)

    Yamane Tsutomu, Okamura Hideyasu, Ikeguchi Mitsunori, Nishimura Yoshifumi, Kidera Akinori

    Seibutsu Butsuri   47   S222   2007

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    DOI： 10.2142/biophys.47.S222_4

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  • Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: A molecular dynamics study Reviewed

    Yuji Sugita, Naoyuki Miyashita, Takao Yoda, Mitsunori Ikeguchi, Chikashi Toyoshima

    BIOCHEMISTRY   45 ( 39 )   11752 - 11761   2006.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/bi061071z

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  • Theory of Structural Changes in Proteins : Equilibrium Fluctuation and Linear Response Theory

    IKEGUCHI Mitsunori, KIDERA Akinori

    Seibutsu Butsuri   46 ( 5 )   275 - 278   2006.9

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    DOI： 10.2142/biophys.46.275

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    Other Link： https://jlc.jst.go.jp/DN/JALC/00284355193?from=CiNii

  • [Conformational changes in proteins are originated from fluctuation: theory of conformational changes in proteins upon ligand binding]. Reviewed

    Ikeguchi M, Kidera A

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   51 ( 3 )   268 - 273   2006.3

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  • 2P157 Molecular dynamics simulation of c-ring of F-type ATP synthase in explicit membrane(34. Membrane protein,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Nakajima Kyoko, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S335   2006

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.46.S335_1

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  • 2P084 Structural change of protein described by linear response theory : internal coordinates(30. Protein function (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Omori Satoshi, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S316   2006

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.46.S316_4

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  • 2P451 Database analyses of protein structural changes induced by ligand binding(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Amemiya Takayuki, Koike Ryotaro, Imamura Yuki, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S408   2006

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    DOI： 10.2142/biophys.46.S408_3

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  • 1P564 All-Atom Molecular Dynamics Simulation of Conformational Changes in Adenylate Kinase(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S287   2006

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    DOI： 10.2142/biophys.46.S287_4

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  • 1P099 A novel method for predicting the native structure of a protein(3. Protein folding and misfolding (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Harano Yuichi, Roth Roland, Sugita Yuji, Ikeguchi Mitsunori, Kinoshita Masahiro

    Seibutsu Butsuri   46 ( 2 )   S171   2006

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    DOI： 10.2142/biophys.46.S171_3

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  • 1P044 Ligand-dissociation increases protein flexibility in trp RNA-binding attenuation protein (TRAP) : Molecular dynamics simulation study(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Araki Hidemi, Fuchigami Sotaro, Ikeguchi Mitsunori, Heddle Jonathan G., Tame Jeremy R. H., Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S157   2006

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    DOI： 10.2142/biophys.46.S157_4

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  • 2P051 Differences between solution and crystal structures of a DNA binding protein(29. Protein structure and dynamics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Yamane Tsutomu, Okamura Hideyasu, Ikeguchi Mitsunori, Kidera Akinori, Nishimura Yoshifumi

    Seibutsu Butsuri   46 ( 2 )   S308   2006

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    DOI： 10.2142/biophys.46.S308_3

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  • A novel magnetic resonance-based method to measure gene expression in living cells Reviewed

    S Ki, F Sugihara, K Kasahara, H Tochio, A Okada-Marubayashi, S Tomita, M Morita, M Ikeguchi, M Shirakawa, T Kokubo

    NUCLEIC ACIDS RESEARCH   34 ( 6 )   e51   2006

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/nar/gkl135

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  • 2P329 Molecular Dynamics Study of Sensory Rhodopsin II Complex with Cognate Transducer(42. Sensory signal transduction,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Nishikata Koro, Hashido Masanori, Fuchigami Sotaro, Ikeguchi Mitsunori, Kidera Akinori

    Seibutsu Butsuri   46 ( 2 )   S378   2006

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    DOI： 10.2142/biophys.46.S378_1

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  • Atomically detailed description of the unfolding of alpha-lactalbumin by the combined use of experiments and simulations Reviewed

    T Oroguchi, M Ikeguchi, K Saeki, K Kamagata, Y Sawano, M Tanokura, A Kidera, K Kuwajima

    JOURNAL OF MOLECULAR BIOLOGY   354 ( 1 )   164 - 172   2005.11

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    DOI： 10.1016/j.jmb.2005.09.061

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  • Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF Reviewed

    M Hashido, M Ikeguchi, A Kidera

    FEBS LETTERS   579 ( 25 )   5549 - 5552   2005.10

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    DOI： 10.1016/j.febslet.2005.09.018

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  • Protonation of the acidic residues in the transmembrane cation-binding sites of the Ca2+ pump Reviewed

    Y Sugita, N Miyashita, M Ikeguchi, A Kidera, C Toyoshima

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   127 ( 17 )   6150 - 6151   2005.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/ja0427505

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  • Protein structural change upon ligand binding: Linear response theory Reviewed

    M Ikeguchi, J Ueno, M Sato, A Kidera

    PHYSICAL REVIEW LETTERS   94 ( 7 )   078102   2005.2

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    DOI： 10.1103/PhysRevLett.94.078102

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  • 2P062 What is the determinant of the folding and non-folding trajectories in Trp-cage?

    Ota M., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   45   S135   2005

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    DOI： 10.2142/biophys.45.S135_2

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  • 3P118 Molecular Dynamics Simulation of Phoborhodopsin/Transducer Complex

    Nishikata N., Hashido M., Fuchigami S., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   45   S233   2005

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    DOI： 10.2142/biophys.45.S233_2

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  • 3P117 Molecular dynamics simulation of water channel protein Aquaporin family

    Hashido M., Ikeguchi M, Kidera A.

    Seibutsu Butsuri   45   S233   2005

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    DOI： 10.2142/biophys.45.S233_1

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  • 3P160 Molecular dynamic simulations of isolated beta-subunit of F_1-ATP synthase

    Nakao M., Fuchigami S., Kidera A., Ikeguchi M.

    Seibutsu Butsuri   45   S243   2005

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    DOI： 10.2142/biophys.45.S243_4

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  • 1SD03 Protein function is driven by the intrinsic dynamics

    Fuchigami S., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   45   S6   2005

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    DOI： 10.2142/biophys.45.S6_1

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  • 1P026 Structural analysis of proteins in aqueous solution by distance geometry method: structural refinement by simulated annealing

    Yamane T., Ikeguchi M., Kidera A., Okamura H., Nishimura Y.

    Seibutsu Butsuri   45   S38   2005

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    DOI： 10.2142/biophys.45.S38_2

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  • 1P040 Conformational change dynamics in adenylate kinase : Ligand binding induces the intrinsic dynamics

    Fuchigami S., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   45   S41   2005

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    DOI： 10.2142/biophys.45.S41_4

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  • 2P035 Database of protein structural changes

    Amemiya T., Koike R., Fuchigami S., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   45   S128   2005

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    DOI： 10.2142/biophys.45.S128_3

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  • Phylogeny of protein-folding trajectories reveals a unique pathway to native structure Reviewed

    M Ota, M Ikeguchi, A Kidera

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   101 ( 51 )   17658 - 17663   2004.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1073/pnas.0407015102

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  • The crystal structure of the tryptophan synthase beta(2) subunit from the hyperthermophile Pyrococcus furiosus - Investigation of stabilization factors Reviewed

    Y Hioki, K Ogasahara, SJ Lee, JC Ma, M Ishida, Y Yamagata, Y Matsuura, M Ota, M Ikeguchi, S Kuramitsu, K Yutani

    EUROPEAN JOURNAL OF BIOCHEMISTRY   271 ( 13 )   2624 - 2635   2004.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1111/j.1432-1033.2004.04191.x

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  • Partial rigid-body dynamics in NPT, NPAT and NP gamma T ensembles for proteins and membranes Reviewed

    M Ikeguchi

    JOURNAL OF COMPUTATIONAL CHEMISTRY   25 ( 4 )   529 - 541   2004.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/jcc.10402

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  • 1P135 Experimental and simulation studies of the unfolding of recombinant and authentic lactalbumin : Effect of an N-terminal methionine residue

    Oroguchi T., Ikeguchi M., Saeki K., Kidera A., Kuwajima K.

    Seibutsu Butsuri   44   S63   2004

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.44.S63_3

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  • 1P105 The function of the proton-counter transport in Ca^<2+>ATPase of sarcoplasmic reticulm

    Miyashita N., Sugita Y., Ikeguchi M., Toyoshima C.

    Seibutsu Butsuri   44   S56   2004

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    DOI： 10.2142/biophys.44.S56_1

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  • 2P015 Structural analysis of protein by using distance geometry method in aqueous solution

    Yamane T., Ikeguchi M., Kidera A., Okamura H., Nishimura Y.

    Seibutsu Butsuri   44   S113   2004

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.44.S113_3

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  • 3P091 How lipids interact with calcium pump : A molecular dynamics study

    Sugita Y., Ikeguchi M., Kidera A., Toyoshima C.

    Seibutsu Butsuri   44   S212   2004

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.44.S212_3

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  • 3P093 Phytogeny of protein folding trajectories reveals a unique pathway to native structure

    Ota M., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   44   S213   2004

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.44.S213_1

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  • Two different Swi5-containing protein complexes are involved in mating-type switching and recombination repair in fission yeast Reviewed

    Y Akamatsu, D Dziadkowiec, M Ikeguchi, H Shinagawa, H Iwasaki

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   100 ( 26 )   15770 - 15775   2003.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1073/pnas.2632890100

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  • Folding simulation of TrpCage

    Ota M., Ikeguchi M., Kidera A.

    Seibutsu Butsuri   43   S90   2003

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    DOI： 10.2142/biophys.43.S90_2

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  • Dynamical analysis of tRNA(Gln)-GlnRS complex using normal mode calculation

    S. Nakamura, M. Ikeguchi, K. Shimizu

    Chem. Phys. Lett.   372 ( 3/4 )   423 - 431   2003

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  • Analysis of the unfolding of authentic and recombinant a -lactalbumin : experiments and simulations

    Oroguchi T., Ikeguchi M., Kidera A., Kuwajima K.

    Seibutsu Butsuri   43   S62   2003

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.43.S62_2

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  • [Protein structural dynamics]. Reviewed

    Kidera A, Ikeguchi M

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   47 ( 8 Suppl )   1052 - 1057   2002.6

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  • New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates Reviewed

    S Nakamura, D Kyono, M Ikeguchi, K Shimizu

    JOURNAL OF COMPUTATIONAL CHEMISTRY   23 ( 4 )   463 - 469   2002.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1002/jcc.10039

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  • Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1 Reviewed

    JG Jee, T Ikegami, M Hashimoto, T Kawabata, M Ikeguchi, T Watanabe, M Shirakawa

    JOURNAL OF BIOLOGICAL CHEMISTRY   277 ( 2 )   1388 - 1397   2002.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1074/jbc.M109726200

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  • Structural change on molecular recognition and hydration of mono-nucleotide binding proteins

    Ikeguchi M., Kinoshita K., Kidera A.

    Seibutsu Butsuri   41   S105   2001

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    DOI： 10.2142/biophys.41.S105_1

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  • Development of the Parsley Parallel Programming Environment and Application to Molecular Dynamics Simualtion

    Sekijima M., Takasaki S., Nakamura S., Ikeguchi M., Shimizu K.

    Seibutsu Butsuri   41   S38   2001

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    DOI： 10.2142/biophys.41.S38_4

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  • Scheduling Policy and Mechanism of Parsley, A Parallel Programming En vironment Reviewed

    S. Takasaki, M. Sekijima, S. Nakamura, M. Ikeguchi, K Shimizu

    Proceedings of the 12th IASTED International Conference on Parallel and Distributed Comp. and Sys tems   605 - 610   2000

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  • Molecular dynamics simulation of mononucleotide binding proteins

    Ikeguchi M., Nakamura S., Shimizu K.

    Seibutsu Butsuri   40   S92   2000

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    DOI： 10.2142/biophys.40.S92_2

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  • Analysis of relationship between local sequence and distribution of dihedral angles on mainchain

    Nakamura S., Inoue T., Ikeguchi M., Shimizu K.

    Seibutsu Butsuri   40   S171   2000

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.40.S171_1

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  • Theoretical study on denaturants effects.

    Ikeguchi M., Nakamura S., Shimizu K.

    Seibutsu Butsuri   39   S163   1999

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    DOI： 10.2142/biophys.39.S163_4

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  • Prediction of protein structure classes and secondary structures by means of hidden Markov models. Reviewed

    Hiroshi Yoshikawa, Mitsunori Ikeguchi, Shugo Nakamura, Kentaro Shimizu, Junta Doi

    Systems and Computers in Japan   30 ( 13 )   13 - 22   1999

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  • Analysis of the Dynamics of ARS-tRNA Complex.

    Nakamura S., Ikeguchi M., Shimizu K.

    Seibutsu Butsuri   39   S178   1999

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    DOI： 10.2142/biophys.39.S178_2

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  • Hydrophobic effects: Roles of water and denaturants Reviewed

    M Ikeguchi, S Nakamura, K Shimizu

    OLD AND NEW VIEWS OF PROTEIN FOLDING   1194   195 - 204   1999

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  • Parsley: a Scalable Framework for Dependence-Driven Task Scheduling in Distributed-Memory Multiprocessor Systems Reviewed

    M. Sekijima, S. Takasaki, S. Nakamura, M. Ikeguchi, K. Shimizu

    Proceedings of the eleventh IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS '99)   800 - 805   1999

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  • Roles of hydrogen bonding and the hard core of water on hydrophobic hydration Reviewed

    M Ikeguchi, S Shimizu, S Nakamura, K Shimizu

    JOURNAL OF PHYSICAL CHEMISTRY B   102 ( 30 )   5891 - 5898   1998.7

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  • An off-lattice theory of solvation: extension of the Flory chi parameter into continuum space Reviewed

    S Shimizu, M Ikeguchi, K Shimizu

    CHEMICAL PHYSICS LETTERS   282 ( 1 )   79 - 90   1998.1

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  • Sequence Analysis of the IRES-Loop III Region of Hepatitis C Virus

    Sasano Takayoshi, Sagara Jun-Ichi, Nakamura Shugo, Ikeguchi Mitsunori, Shimizu Kentaro

    GI   9   395 - 396   1998

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    Language：English   Publisher：Japanese Society for Bioinformatics  

    DOI： 10.11234/gi1990.9.395

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  • Parallel algorithm for efficient calculations of second derivatives of conformational energy function in internal coordinates

    S. Nakamura, M. Ikeguchi, K. Shimizu

    J. Comput. Chem.   19 ( 15 )   1716 - 1723   1998

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  • A Study Using Sequence Comparison to Investigate the Molecular Evolution of Mitochondrial tRNA Genes

    Sagara Jun-Ichi, Nakamura Shugo, Ikeguchi Mitsunori, Shimizu Kentaro

    GI   9   353 - 354   1998

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    DOI： 10.11234/gi1990.9.353

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  • Parallel programming environment with dynamic resource management services: Design and application to molecular dynamics simulation Reviewed

    K Shimizu, A Oishi, H Ashihara, M Ikeguchi, S Nakamura

    COMPUTERS AND THEIR APPLICATIONS   226 - 231   1997

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  • A Novel Method to Detect <I>Identities</I> in tRNA Genes Using Sequence Comparison

    Sagara Jun-Ichi, Shimizu Seishi, Kawabata Takeshi, Nakamura Shugo, Ikeguchi Mitsunori, Shimizu Kentaro

    GI   8   330 - 331   1997

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    Language：English   Publisher：Japanese Society for Bioinformatics  

    We developed a computational method to detect identities in tRNA genes. The method uses the multidimensional scaling method to classify the sequences of tRNA genes into multiple groups of similar sequences, and also to extract characteristic bases that are conserved within a group but differ from other groups. This procedure was applied recursively to classify the sequences into hierarchical groups so that characteristic sites can be detected more precisely. We were able to detect many characteristic sites in T and D domains of tRNAs as well as the characteristic sites that have been detected experimentally. This suggests that the preservation of L-shape structure in tRNAs is important to the tRNA-ARS recognition.

    DOI： 10.11234/gi1990.8.330

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  • Conformational Energy Minimization Using A Two-Stage Method

    S. Nakamura, H. Hirose, M. Ikeguchi, J. Doi

    J. Phys. Chem.   99 ( 20 )   8374 - 8378   1995

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Books

  • 実験医学増刊 構造生命科学で何がわかるのか何ができるのか

    池口満徳, 山根努（ Role： Contributor生体系の分子シミュレーションと多剤排出トランスポーターへの応用）

    羊土社  2014 

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  • Protein Conformational Dynamics

    Y. Ito, M. Ikeguchi（ Role： ContributorMolecular dynamics simulations of F1-ATPase）

    Springer Cham Heidelberg New York Dordrecht London  2014 

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  • 1分子ナノバイオ計測

    伊藤祐子, 池口満徳（ Role： Contributor全原子分子動力学計算が解き明かす回転分子モーターの作用機構）

    化学同人  2014 

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  • 最新分子マシン ナノで働く“高度な機械”を目指して

    池口満徳（ Role： Contributor水を輸送する分子マシン アクアポリンの分子シミュレーション）

    化学同人  2008 

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MISC

  • Interaction study of NGF receptor TrkA domain 5 and a binding peptide derived from phage display.

    鈴木里佳, 登坂綺水, 浴本亨, 高橋真帆, 山根努, 坂倉正義, 水越弓子, 竹内恒, 嶋田一夫, 池口満徳, 池口満徳, 高橋栄夫

    日本薬学会年会要旨集(Web)   141st   2021

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  • STRUCTURAL AND PHYSICAL BASIS FOR THE HIGHER AFFINITY TO ONCOPROTEIN MDM2 OF A PEPTIDE SELECTED WITH MRNA DISPLAY OVER TUMOR SUPPRESSOR P53

    Nagata T, Yamada T, Hayashi T, Hikiri S, Kobayashi N, Ikeguchi M, Katahira M, Kinoshita M, Yanagawa H

    64th Annual Meeting of the Biophysical Society, San Diego, 2020.2.15-19   2020.2

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  • X線小角散乱と分子動力学シミュレーションを組み合わせた生体分子の溶液構造解析

    浴本亨, 小甲裕一, 苙口友隆, 池口満徳, 池口満徳

    アンサンブル   22 ( 3 )   2020

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  • Research on pocket prediction using 3D-CNN

    馬場剛史, 小甲裕一, 佐藤美和, 中川寛之, 宮口郁子, MA Biao, 松本篤幸, 徳久淳師, 大田雅照, 池口満徳, 池口満徳

    構造活性相関シンポジウム講演要旨集   47th (CD-ROM)   2019

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  • In vitroとin silicoの融合によるセマフォリン-プレキシンペアの結合特異性決定因子の探索

    田中翼, 下地恵令奈, 永友芽里, 山根努, 浴本亨, 根谷崎牧子, 大井里香, 池口満徳, 禾晃和

    日本細胞生物学会大会(Web)   71st   2019

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  • 深層学習による低解像度電子密度データからの構造予測

    佐藤美和, 中川寛之, 小甲裕一, 宮口郁子, 鹿島亜希子, 馬彪, 徳久淳師, 大田雅照, 池口満徳, 池口満徳

    日本細胞生物学会大会(Web)   71st   2019

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  • AI用学習データ作成のための高・低分解能の蛋白質結晶構造比較

    宮口郁子, 鹿島亜季子, 佐藤美和, 中田一人, 馬彪, 松本篤幸, 徳久淳師, 大田雅照, 池口満徳

    日本細胞生物学会大会(Web)   71st   2019

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  • シグナル分子セマフォリンと受容体プレキシンの結合特異性に関する構造生物学的解析

    田中翼, 永友芽里, 根谷崎牧子, 大井里香, 下地恵令奈, 山根努, 浴本亨, 池口満徳, 禾晃和

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018

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  • Reconstruction of Three-Dimensional Structures of a Protein with Software ENMA and EMC Algorithm: A Simulation for XFEL-CXDI Experiment

    Takashi Yoshidome, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   112 ( 3 )   288A - 288A   2017.2

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  • Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by a Combination Andlysis of MD Simulations and SAXS Experiments

    Yasuaki Anami, Nobutaka Shimizu, Toru Ekimoto, Daichi Egawa, Toshimasa Itoh, Mitsunori Ikeguchi, Keiko Yamamoto

    BIOPHYSICAL JOURNAL   112 ( 3 )   48A - 48A   2017.2

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  • Determination of the Solution Structure of Isolated Histone H2A-H2B Heterodimer by using CS-Rosetta

    Tsutomu Yamane, Yoshihito Moriwaki, Hideaki Ohtomo, Mitsunori Ikeguchi, Jun-ichi Kurita, Masahiko Sato, Aritaka Nagadoi, Hideaki Shimojo, Yoshifumi Nishimura

    BIOPHYSICAL JOURNAL   112 ( 3 )   488A - 488A   2017.2

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  • 神経軸索ガイダンス分子セマフォリンと受容体の相互作用のin silico解析

    下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

    日本蛋白質科学会年会プログラム・要旨集   17th   2017

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  • SAXS-MD解析を用いたビタミンD受容体のアポ型及びアンタゴニスト結合型構造の解析

    山本恵子, 穴見康昭, 清水伸隆, 浴本亨, 江川大地, 伊藤俊将, 池口満徳

    日本薬学会年会要旨集(CD-ROM)   137th   2017

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  • Water Pathway Analysis of Multi-Drug Efflux Transporter AcrB

    Tsutomu Yamane, Ryotaro Koike, Motonori Ota, Satoshi Murakami, Akinori Kidera, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   110 ( 3 )   631A - 631A   2016.2

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  • CS-Rosettaを用いたヒストンH2A-H2B複合体の溶液構造解析

    山根努, 森脇義仁, 佐藤昌彦, 大友秀明, 池口満徳, 栗田順一, 長土居有隆, 下條秀朗, 西村善文

    日本蛋白質科学会年会プログラム・要旨集   16th   2016

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  • 神経軸索伸長ガイダンス分子セマフォリンと受容体プレキシンのタンパク質複合体の分子モデリング

    下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

    日本蛋白質科学会年会プログラム・要旨集   16th   2016

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  • X線小角散乱(SAXS)と分子動力学計算(MD)を組み合わせたSAXS-MD法によるビタミンD受容体リガンド結合領域の相関構造解析

    穴見康昭, 清水伸隆, 浴本亨, 江川大地, 伊藤俊将, 池口満徳, 山本恵子

    日本薬学会関東支部大会講演要旨集   59th   2015

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  • 7aAM-5 Imaging analysis using a new classification protocol of projection images based on the manifold

    Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M.

    Meeting abstracts of the Physical Society of Japan   69 ( 2 )   188 - 188   2014.8

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  • Structural Characterization of the Histone Multimers in the Gas Phase using Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

    Kazumi Saikusa, Sotaro Fuchigami, Kyohei Takahashi, Yuuki Asano, Aritaka Nagadoi, Hiroaki Tachiwana, Hitoshi Kurumizaka, Mitsunori Ikeguchi, Yoshifumi Nishimura, Satoko Akashi

    BIOPHYSICAL JOURNAL   106 ( 2 )   464A - 464A   2014.1

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  • Classification Protocol of Projection Images by Manifold: Toward Analysis of Dynamics of Particles with Coherent X-Ray Diffraction Imaging

    Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   106 ( 2 )   384A - 384A   2014.1

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  • イオンモビリティ質量分析と分子動力学シミュレーションを用いたヒストン多量体の構造解析

    七種和美, 渕上壮太郎, 浅野裕輝, 高橋恭平, 長土居有隆, 立和名博昭, 胡桃坂仁志, 池口満徳, 西村善文, 明石知子

    質量分析総合討論会講演要旨集   61st   93   2013.9

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  • A novel computation method of hydration free energy: A hybrid of the method of energy representation and the morphometric approach

    T. Yoshidome, T. Ekimoto, N. Matubayasi, R. Roth, Y. Harano, M. Kinoshita, M. Ikeguchi

    7th Mini-Symposium on Liquids   2013.7

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  • コヒーレントX線回折イメージング構造解析理論の開発と展望

    中迫雅由, 苙口友隆, 高山裕貴, 小林周, 児玉渉, 坂本啓太, 吉留崇, 池口満徳

    放射光   26   11 - 25   2013.1

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  • Molecular analysis of the Schizosaccharomyces pombe Rad51 recombinase mutant with a mutation of H315 residue

    Kentaro Ito, Yasuhiro Tsutsui, Kota Mayanagi, Yumiko Kurokawa, Yuichi Kokabu, Mitsunori Ikeguchi, Fumiaki Yamao, Hiroshi Iwasaki

    GENES & GENETIC SYSTEMS   87 ( 6 )   436 - 436   2012.12

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  • 分裂酵母Rad51リコンビナーゼのHis‐315ミュータントの解析

    伊藤健太郎, 筒井康博, 真柳浩太, 黒川裕美子, 小甲裕一, 池口満徳, 山尾文明, 岩崎博史

    日本遺伝学会大会プログラム・予稿集   84th   125   2012.8

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  • All-Atom Molecular Dynamics Simulation of Multidrug Efflux Transporter AcrB

    Tsutomu Yamane, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   102 ( 3 )   660A - 660A   2012.1

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  • サブユニットの16度回転前後におけるイーストF1-ATPase の構造特性：水のエントロピー効果に焦点をあてた理論解析

    吉留崇, 伊藤祐子, 松林伸幸, 池口満徳, 木下正弘

    新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議，岩沼屋，仙台，2012.3.7-9   2012

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  • 白質複合体におけるホットスポットの理論的予測

    尾嶋拓, 安田賢司, 吉留崇, 池口満徳, 木下正弘

    新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議，岩沼屋，仙台，2012.3.7-9   2012

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  • 相同組換えに関わるSwi5‐Sfr1複合体の構造機能解析

    桑原直之, 橋本博, 小甲裕一, 池口満徳, 佐藤衛, 真柳浩太, 村山泰人, 岩崎博史, 清水敏之

    日本蛋白質科学会年会プログラム・要旨集   11th   89   2011.5

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  • All-Atom Molecular Dynamics Simulation of Multidrug Efflux Transporter AcrB

    Tsutomu Yamane, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   100 ( 3 )   544 - 544   2011.2

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  • A Theoretical Analysis on Water-Entropy Change in Yeast F1-ATPase during 16 Degrees Rotation of Gamma Subunit

    吉留崇, 池口満徳, 木下正弘

    第49回日本生物物理学会年会，兵庫県立大学，2011.9.16   2011

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  • Theoretical Analysis for Hot Spots in Protein-Protein Complexes: Critical Importance of Water Entropy

    H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, M. Kinoshita

    8th Liquid Matter Conference，Universität Wien, Austria，2011.9.9   2011

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  • 実験で得られた蛋白質天然構造モデルのキャラクタリゼーション

    三嶋浩和, 安田哲司, 吉留崇, 池口満徳, 木下正弘

    第34 回溶液化学シンポジウム，名古屋大学ES総合館ESホール，2011.11.15-17   2011

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  • On the Physical Mechanism of Rotation of F1-ATPase:Crucial Importance of the Water Entropy Effect

    T. Yoshidome, Y. Ito, M. Ikeguchi, M. Kinoshita

    8th Liquid Matter Conference，Universität Wien, Austria，2011.9.9   2011

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  • イオンモビリティ質量分析とX線小角散乱による基本転写因子TFIIEの構造解析

    七種和美, 小田隆, 奥田昌彦, 池口満徳, 佐藤衛, 西村善文, 明石知子

    質量分析総合討論会講演要旨集   59th   2011

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  • 24pTG-8 On the Rotational Mechanism of F_1-ATPase : Crucial Importance of Water-Entropy Effect

    Yoshidome T., Ito Y., Ikeguchi M., Kinoshita M.

    Meeting abstracts of the Physical Society of Japan   65 ( 2 )   327 - 327   2010.8

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  • 22pEC-9 On the rotation mechanism of F_1-ATPase : Importance of the water entropy

    Yoshidome T., Ito Y., Ikeguchi M., Kinoshita M.

    Meeting abstracts of the Physical Society of Japan   65 ( 1 )   390 - 390   2010.3

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  • Ionic Effect on MD-SAXS Profile

    Tomotaka Oroguchi, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   98 ( 3 )   738A - 738A   2010.1

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  • All-Atom Molecular Dynamics Simulation of Bacterial Multidrug Efflux Transporters AcrB

    Tsutomu Yamane, Mitsunori Ikeguchi

    BIOPHYSICAL JOURNAL   98 ( 3 )   685A - 685A   2010.1

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  • F1-ATPaseの回転のメカニズムに関する一考察

    吉留崇, 伊藤祐子, 池口満徳, 木下正弘

    水のエントロピーの重要性，日本物理学会第65回年次大会，岡山大学，2010.3.22   2010

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  • F1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性

    吉留崇, 伊藤祐子, 池口満徳, 木下正弘

    日本物理学会2010 年秋季大会，大阪府立大学，2010.9.23-25   2010

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  • 非天然アミノ酸を導入したF<sub>1</sub>‐ATPaseにおけるATP加水分解反応のエナジェティクスの理論予測

    神谷基司, 梅村舞子, 伊藤祐子, 池口満徳, 林重彦

    日本生体エネルギー研究会討論会講演要旨集   36th   58 - 59   2010

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  • 相同組換えに関わるSwi5‐Sfr1複合体の構造機能解析

    桑原直之, 橋本博, 小甲裕一, 池口満徳, 佐藤衛, 真柳浩太, 村山泰斗, 岩崎博史, 清水敏之

    生化学   ROMBUNNO.1T16-1   2010

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  • Development of a free-energy function toward predicting the native structure of a protein

    S. Yasuda, T. Yoshidome, Y. Harano, R. Roth, Y. Sugita, M. Ikeguchi, M. Kinoshita

    The 2nd GCOE International Symposium (Zero-Carbon Energy Kyoto2010), Obaku Plaza, Kyoto University, Uji, Japan,2010.8.19-20   2010

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  • Dynamics and conformational changes in DNA-binding proteins

    Mitsunori Ikeguchi

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   238   2009.8

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  • 全原子モデルに基づいた蛋白質用の自由エネルギー関数

    木下正弘, 吉留崇, 安田賢司, 原野雄一, Roland Roth, 杉田有冶, 池口満徳

    次世代ナノ統合シミュレーションソフトウェアの研究開発第3回公開シンポジウム，岡崎コンファレンスセンター，2009.3.4-5   2009

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  • 3P-164 Molecular mechanism of ATP hydrolysis reaction in F_1-ATPase molecular motor(The 46th Annual Meeting of the Biophysical Society of Japan)

    Shaikh Abdul Rajjak, Ito Yuko, Ikeguchi Mitsunori, Ueno Hiroshi, Noji Hiroyuki, Hayashi Shigehiko

    Seibutsu Butsuri   48 ( 0 )   2008

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  • タンパク質の立体構造予測に向けた新規スコア関数

    原野雄一, 吉留崇, Roland Roth, 杉田有治, 池口満徳, 木下正弘

    第46回日本生物物理学会年会，福岡国際会議場，2008.12.3-5   2008

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  • Novel Scoring Function for Discriminating the Native Fold of a Protein from Misfolded Decoys

    Y Harano, T Yoshidome, R Roth, Y Sugita, M Ikeguchi, M Kinoshita

    1st International Conference of the Grand Challenge to Next-Generation Integrated Nanoscience, Tokyo, Japan, 2008. 6.3-7   2008

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  • 天然構造を特徴づける蛋白質内水素結合パラメータ

    小田晃司, 原野雄一, 吉留崇, 杉田有治, 池口満徳, 木下正弘

    第46回日本生物物理学会年会，福岡国際会議場，2008.12.3-5   2008

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  • Detecting domain motions of proteins in molecular dynamics simulations and normal mode analyses

    Mitsunori Ikeguchi, Sotaro Fuchigami, Akinori Kidera

    BIOPHYSICAL JOURNAL   409A - 409A   2007.1

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  • A Novel Method for Predicting the Native Structure of a Protein

    Y. Harano, R. Roth, Y. Sugita, M. Ikeguchi, M. Kinoshita

    Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, Symposium: Hydration Effects on the Structure and Thermodynamics of Proteins，Okinawa Convention Center, Okinawa, Japan，2006.11.13-16   2006.11

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  • 蛋白質構造変化の源はゆらぎ--分子結合に伴う蛋白質立体構造変化の理論

    池口 満徳, 木寺 詔紀

    蛋白質核酸酵素   51 ( 3 )   268 - 273   2006.3

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  • 物理化学に基づくタンパク質立体構造予測に向けた斬新な方法

    原野雄一, Roland Roth, 杉田有治, 池口満徳, 木下正弘

    生体機能関連化学部会，バイオテクノロジー部会，生命化学研究会合同シンポジウム，京都大学桂キャンパス，2006.9   2006

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  • Theory of conformational change in proteins upon ligand binding

    M Ikeguchi, J Ueno, M Sato, A Kidera

    BIOPHYSICAL JOURNAL   88 ( 1 )   556A - 556A   2005.1

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  • 15pTA-10 Molecular Dynamics Simulations of Calcium Pump in a Lipid Bilayer

    Sugita Yuji, Ikeguchi Mitsunori, Kidera Akinori, Toyoshima Chikashi

    Meeting abstracts of the Physical Society of Japan   59 ( 2 )   313 - 313   2004.8

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  • 29pWE-11 Molecular Dynamics Simulations of Calcium Pump in a Lipid Bilayer

    Sugita Yuji, Ikeguchi Mitsunori, Toyoshima Chikashi

    Meeting abstracts of the Physical Society of Japan   59 ( 1 )   377 - 377   2004.3

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  • 29pWE-10 The function of the proton-counter transport in Ca^<2+> ATPase of sarcoplasmic reticulm

    Miyashita Naoyuki, Sugita Yuji, Ikeguchi Mitsunori, Toyoshima Chikashi

    Meeting abstracts of the Physical Society of Japan   59 ( 1 )   376 - 376   2004.3

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  • Molecular dynamics methods for membrane and protein-membrane systems

    M Ikeguchi, A Kidera

    BIOPHYSICAL JOURNAL   84 ( 2 )   461A - 462A   2003.2

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  • Molecular dynamics study on hydrophobic effects in aqueous urea solutions

    M. Ikeguchi, S. Nakamura, K. Shimizu

    J. Am. Chem. Soc.   123 ( 4 )   677 - 682   2001

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  • Parsley : A Scalable Framework for Dependence - driven Subtask Scheduling in Distributed - memory Multiprocessor Systems

    41 ( SIG02(PRO6) )   65 - 77   2000.3

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  • A parallel programming environment with dependence-driven task scheduling in distributed-memory multiprocessor systems

    M Sekijima, S Takasaki, S Nakamura, M Ikeguchi, K Shimizu

    PARALLEL AND DISTRIBUTED COMPUTING SYSTEMS   348 - 354   2000

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  • 分子動力学法を用いた自由エネルギーの効率的計算手法の開発

    村田達也, 中村周吾, 池口満徳, 清水謙多郎

    タンパク質構造討論会講演要旨集   50th   161   1999.6

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  • 水/尿素混合系における疎水性相互作用

    池口満徳, 中村周吾, 清水謙多郎

    タンパク質構造討論会講演要旨集   50th   140   1999.6

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  • Decomposition Methods for Parallel Molecular Dynamics Simulation.

    西村健, 中村周吾, 池口満徳, 清水謙多郎

    情報処理学会研究報告   99 ( 21(ARC-132 OS-80 HPC-75) )   61 - 66   1999.3

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  • Size dependence of transfer free energies: A hard-sphere-chain-based formalism

    S. Shimizu, M. Ikeguchi, S. Nakamura, K. Shimizu

    J. Chem. Phys.   110 ( 6 )   2971 - 2982   1999

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  • Structural modeling of DNA mini-hairpin molecules with various loop sequences

    S. Nakamura, K. Tazaki, M. Ikeguchi, K. Shimizu

    Chem. Phys. Lett.   308 ( 3/4 )   267 - 273   1999

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  • Prallel Programming Environment with Dependence-Driven Subtask Scheduling: Design and Application to Molecular Dynamics Simulation.

    関嶋政和, 村田達也, 正木宏和, 中村周吾, 池口満徳, 清水謙多郎

    情報処理学会全国大会講演論文集   57th ( 1 )   113.-1.14   1998.10

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  • Theoretical analysis of effects of denaturants on protein unfolding.

    池口満徳, 清水青史, 中村周吾, 清水謙多郎

    溶液化学シンポジウム講演要旨集   21st   58 - 59   1998.10

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  • 分子動力学法の並列アルゴリズムの開発

    関嶋政和, 村田達也, 正木宏和, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   36th   S154   1998.9

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  • tRNA‐ARS複合体の動特性解析

    中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   36th   S118   1998.9

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  • 主成分分析法を用いたtRNA遺伝子の分子進化に関する研究

    相良純一, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   36th   S121   1998.9

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  • Parallelization f molecular dynamics simulation using subtask division.

    村田達也, 関嶋政和, 正木宏和, 宮田忠明, 中村周吾, 池口満徳, 清水謙多郎

    情報処理学会全国大会講演論文集   56th ( 1 )   1.404-1.405   1998.3

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  • The use of sequence comparison to detect 'identities' in tRNA genes

    J. I. Sagara, S. Shimizu, T. Kawabata, S. Nakamura, M. Ikeguchi, K. Shimizu

    Nucleic Acids Res.   26 ( 8 )   1974 - 1979   1998

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  • Molecular volume, surface area, and curvature dependence of the configurational entropy change upon solvation: Effects of molecular bonding

    S. Shimizu, M. Ikeguchi, S. Nakamura, K. Shimizu

    Chem. Phys. Lett.   284 ( 3/4 )   235 - 246   1998

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  • 隠れマルコフモデルによるタンパク質構造クラスの解析

    吉川裕, 池口満徳, 中村周吾, 清水謙多郎, 土井淳多

    電子情報通信学会論文誌   J81-D-II ( 7 )   1656 - 1665   1998

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  • Roles of hydrogen bonding and the hard core of water on hydrophobic hydration

    M. Ikeguchi, S. Shimizu, S. Nakamura, K. Shimizu

    J. Phys. Chem.   102 ( 30 )   5891 - 5898   1998

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  • Calculation of temperature dependence of free energy caused by potential function changes

    M. Ikeguchi, S. Shimizu, K. Tazaki, S. Nakamura, K. Shimizu

    Chem. Phys. Lett.   288 ( 2/4 )   333 - 337   1998

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  • Statistical thermodynamical theory of chain molecular solution

    SHIMZU S., IKEGUCHI M., SHIMIZU K.

    Biophysics   37   S66   1997.10

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    Language：Japanese   Publisher：The Biophysical Society of Japan General Incorporated Association  

    CiNii Books

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  • 並列構造探索システムの構築と核酸ミニヘアピン分子への適用

    中村周吾, 池口満徳, 広瀬仁, 清水謙多郎

    日本生物物理学会年会講演予稿集   35th   S37   1997.9

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  • 多変量解析を用いた遺伝子解析手法によるtRNA遺伝子の解析

    相良純一, 清水青史, 川端猛, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   35th   S130   1997.9

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  • 連続空間での蛋白質foldingにおけるfunnel理論の研究

    広瀬仁, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   35th   S31   1997.9

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  • Extracting contact free energy from solubility: Excluded volume effects of polymers in continuum space

    S Shimizu, M Ikeguchi, K Shimizu

    CHEMICAL PHYSICS LETTERS   268 ( 1-2 )   93 - 100   1997.4

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  • Modelling molecule-membrane interactions from partition data: A generalized theory of size effects in solvation.

    S Shimizu, M Ikeguchi, K Shimizu

    PROTEIN ENGINEERING   10   35 - 35   1997

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  • A method of detecting identities in tRNA genes using sequence comparison

    J Sagara, S Shimizu, T Kawabata, S Nakamura, M Ikeguchi, K Shimizu

    PROTEIN ENGINEERING   10   52 - 52   1997

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  • 蛋白質の立体構造予測のための高速大域最小化アルゴリズム

    広瀬仁, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   34th   S90   1996.10

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  • 分子動力学法に基づく水和熱力学量計算法の開発

    池口満徳, 清水青史, 田崎康一, 中村周吾, 清水謙多郎

    日本生物物理学会年会講演予稿集   34th   S9   1996.10

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  • DNAミニヘアピン分子の熱安定性の解析

    中村周吾, 田崎康一, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   34th   S166   1996.10

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  • Mean Field Optimizationによる蛋白質局所構造予測法の開発

    加藤晋一郎, 中村周吾, 池口満徳, 清水謙多郎

    日本生物物理学会年会講演予稿集   34th   S89   1996.10

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  • Modificaiton of diffusion equation method and its application to DNA mini-hairpin structures.

    中村周吾, 広瀬仁, 池口満徳, 土井淳多

    日本生物物理学会年会講演予稿集   33rd   S203   1995.8

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Presentations

  • タンパク質の真のフォールディングファネルは初期トポロジーによって分断されている

    第7回日本蛋白質科学会年会  2007 

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  • 低分子リガンド結合に伴う構造変化のデータベース解析

    第7回日本蛋白質科学会年会  2007 

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  • 分子動力学シミュレーションと基準振動解析におけるタンパク質ドメイン運動の検出

    51st Annual Meeting of Biophysical Society  2007 

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  • タンパク質の一部分の外部自由度を固定した基準振動解析

    第6回日本蛋白質科学会年会  2006 

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  • PhoBのDNA結合ドメインのダイナミクスの解析

    第7回日本蛋白質科学会年会  2007 

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  • タンパク質立体構造変化における経路の多様性とメカニズム：アデニル酸キナーゼの場合

    第7回日本蛋白質科学会年会  2007 

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  • センサリーロドプシンIIトランスデューサーHAMPドメインの分子動力学研究

    第7回日本蛋白質科学会年会  2007 

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  • アクアポリンファミリー、AQP1, AQPZ, AQP0, GlpFの比較分子動力学シミュレーション

    50th Annual Meeting of Biophysical Society  2006 

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  • 線形応答理論による蛋白質構造変化の記述：内部座標系

    第7回日本蛋白質科学会年会  2007 

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  • 蛋白質-蛋白質複合体におけるホットスポットの理論的予測

    日本生物物理学会第48回年会  2010 

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  • リガンド結合によるタンパク質立体構造変化のデータベース解析

    日本生物物理学会第48回年会  2010 

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  • X線小角散乱法による分裂酵母Swi5-Sfr1の溶液構造解析

    日本生物物理学会第48回年会  2010 

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  • MD-SAXS データ及びに溶媒和構造の塩濃度依存性

    日本蛋白質科学会第10回年会  2010 

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  • 独立成分解析によるタンパク質ダイナミクスの解析：長時間スケールの揺らぎ

    日本生物物理学会第48回年会  2010 

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  • F1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性

    日本生物物理学会第48回年会  2010 

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  • タンパク質立体構造予測に向けた自由エネルギー関数の開発

    日本生物物理学会第48回年会  2010 

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  • MD-SAXS法によるジユビキチンの動的構造解析：結合様式による違い

    日本生物物理学会第48回年会  2010 

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  • 多次元レプリカ交換分子動力学法プログラム（REIN）の開発

    日本生物物理学会第48回年会  2010 

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  • 腸内ビブリオの算出する耐熱性溶血毒TDHの構造

    日本生物物理学会第48回年会  2010 

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  • 分子動力学シミュレーションによるF1-ATPase（βサブユニット）の構造変化研究

    日本生物物理学会第48回年会  2010 

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  • 全原子分子動力学シミュレーションによる多剤排出トランスポーターAcrBの解析

    日本生物物理学会第48回年会  2010 

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  • 二面角空間における蛋白質分子の補償的ダイナミクス

    日本生物物理学会第48回年会  2010 

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  • イヌミルクリゾチームのアンフォールディング経路についての理論的研究：ヤギαラクトアルブミンとの比較

    日本生物物理学会第48回年会  2010 

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  • HAMPドメインの分子動力学解析：電子スピン常磁性共鳴のデータを満足する4-helix bundle構造

    日本生物物理学会第47回年会  2009 

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  • タンパク質の長時間シミュレーションにおいて観測された遅い構造緩和

    第3回分子科学討論会  2009 

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  • 多剤排出トランスポーター AcrB の分子動力学シミュレーションによる解析

    日本蛋白質科学会第9回年会  2009 

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  • タンパク質の分子動力学シミュレーションにおける平衡化過程の定量的解析

    日本蛋白質科学会第9回年会  2009 

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  • 球状蛋白質構造ゆらぎの 2 面角系主成分分析

    日本蛋白質科学会第9回年会  2009 

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  • 分子動力学シミュレーションとＸ線散乱を用いたATP結合によるF1-ATPase ε サブユニットの構造変化研究

    53rd Annual Meeting of Biophysical Society  2009 

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  • DNA結合タンパク質のダイナミクスと構造変化

    238th American Chemical Society National Meeting  2009 

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  • 低分子リガンド相互作用に関わるタンパク質立体構造変化のデータベース解析

    日本蛋白質科学会第9回年会  2009 

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  • 分子動力学を用いた F1 ‒ATPase の構造と機能解析

    日本蛋白質科学会第9回年会  2009 

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  • 分裂酵母の相同組換えに機能する Swi5と Sfr1の溶液構造解析

    日本蛋白質科学会第9回年会  2009 

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  • タンパク質の平衡揺らぎの独立成分解析

    日本生物物理学会第47回年会  2009 

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  • MD-SAXSプロファイルにおけるイオン効果

    54th Annual Meeting of Biophysical Society  2010 

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  • 多剤排出トランスポーターAcrBの分子動力学シミュレーション

    日本生物物理学会第47回年会  2009 

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  • 翻訳後修飾を受けるタンパク質の立体構造変化データベース解析

    2009 

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  • 異なる結合様式をもつジユビキチンの分子動力学シミュレーション

    日本生物物理学会第47回年会  2009 

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  • 蛋白質構造ゆらぎの二面角系主成分解析

    日本生物物理学会第47回年会  2009 

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  • バクテリア多剤排出トランスポーターAcrBの全原子分子動力学シミュレーション

    54th Annual Meeting of Biophysical Society  2010 

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  • 分子モーターF1-ATPaseの回転メカニズムについての理論的研究

    International Symposium on Hydration and ATP Energy  2009 

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  • X線小角散乱によるDNA相同組換えのメディエータである分裂酵母Swi5とSfr1の溶液構造解析

    日本生物物理学会第47回年会  2009 

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  • 分子動力学による理論的研究：分子の揺らぎからわかるF1-ATPaseのサブユニット協調性

    日本生物物理学会第47回年会  2009 

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  • イノシトール1,4,5-三リン酸受容体とその変異体のリガンド結合コアのリガンド非結合状態における分子動力学シミュレーション

    日本生物物理学会第46回年会  2008 

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  • 分子動力学によるF1-ATPaseの構造と機能解析

    日本生物物理学会第46回年会  2008 

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  • 蛋白質天然状態を特徴づける分子内水素結合に関するパラメータ

    日本生物物理学会第46回年会  2008 

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  • 変性状態蛋白質の構造デコイ群から天然構造を判別する新規スコア関数

    日本生物物理学会第46回年会  2008 

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  • センサリーロドプシンII/トランスデューサー複合体の分子動力学研究

    日本蛋白質科学会第8回年会  2008 

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  • 低分子リガンド結合に関わるタンパク質構造変化のデータベース解析：結晶場の影響

    日本蛋白質科学会第8回年会  2008 

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  • タンパク質の立体構造変化における運動の階層性

    日本蛋白質科学会第8回年会  2008 

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  • 分子動力学シミュレーションによるPhoB DNA binding/transactivation ドメインの運動性の解析

    日本蛋白質科学会第8回年会  2008 

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  • X 線小角散乱及び分子動力学計算を用いたII 型制限酵素EcoO109I の溶液中ダイナミックスの解析

    日本蛋白質科学会第8回年会  2008 

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  • 蛋白質構造ゆらぎの2面角系主成分分析

    日本蛋白質科学会第8回年会  2008 

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  • 分子動力学シミュレーションを用いたPhoB DNA-binding/transactivationドメインの側鎖ダイナミクスの解析

    53rd Annual Meeting of Biophysical Society  2009 

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  • 分子動力学によるF1-ATPaseの構造解析

    53rd Annual Meeting of Biophysical Society  2009 

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  • F1-ATPase分子モーターにおけるATP加水分解の分子メカニズム

    日本生物物理学会第46回年会  2008 

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  • Ｘ線小角散乱と分子動力学シミュレーションによる分裂酵母Swi5の溶液構造解析

    日本生物物理学会第46回年会  2008 

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  • センソリーロドプシンII／トランスデューサー複合体のHAMPドメインのモデル：分子動力学研究

    日本生物物理学会第46回年会  2008 

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  • アデニル酸キナーゼの構造変化における階層型ダイナミクス

    日本生物物理学会第46回年会  2008 

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  • リガンド結合に伴う蛋白質の構造変化における緩和モード

    日本生物物理学会第46回年会  2008 

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  • 分子動力学シミュレーションとＸ線散乱によるATP結合に伴うF1-ATPaseエプシロンサブユニットの構造変化研究

    日本生物物理学会第46回年会  2008 

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  • 蛋白質多量体化によって誘起される構造変化

    日本生物物理学会第46回年会  2008 

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  • 分子動力学シミュレーションによるPhoB DNA結合／転写活性化ドメインの側鎖ダイナミクスの解析

    日本生物物理学会第46回年会  2008 

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  • 固体NMRを用いたH+-ATP合成酵素βサブユニットに結合したATPの構造解析

    第7回日本蛋白質科学会年会  2007 

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  • K48,K63 および K11 結合型ジユビキチンの分子動力学シミュレーション

    日本蛋白質科学会第10回年会  2010 

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  • 線形応答理論により記述されるタンパク質の構造変化：内部座標系

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • DNA結合タンパク質における溶液構造と結晶構造の相違

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • アデニル酸キナーゼの構造変化の全原子分子動力学シミュレーション

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • 水チャネルアクアポリンの水透過分子シミュレーション

    第6回日本蛋白質科学会年会  2006 

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  • リガンド結合に伴うタンパク質構造変化のデータベース解析

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • センソリーロドプシンIIとトランスデューサー複合体の分子動力学研究

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • 生体膜中におけるF型ATP合成酵素のcリングの分子動力学シミュレーション

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • アデニル酸キナーゼの立体構造変化における局所ダイナミクス

    第6回日本蛋白質科学会年会  2006 

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  • PhoB DNAバインディングプロテインの溶液構造解析

    第6回日本蛋白質科学会年会  2006 

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  • 分子動力学シミュレーションによるAquaporinの水透過機構の解析

    第6回日本蛋白質科学会年会  2006 

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  • タンパク質の天然構造予測の新規方法

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • デザインされたジンクフィンガー様タンパク質の折れたたみシミュレーション

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • リガンド解離がTRAPの柔軟性を増加させる：分子動力学シミュレーション研究

    第5回東アジア生物物理シンポジウム・日本生物物理学会第44回年会  2006 

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  • F1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性

    日本物理学会秋季大会  2010 

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  • 分子シミュレーションで探るDNA結合タンパク質の揺らぎと機能

    日本物理学会秋季大会  2010 

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  • X線小角散乱を用いたタンパク質複合体の構造モデリング

    日本生物物理学会第48回年会  2010 

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  • MD-SAXSプロファイルにおけるイオン効果

    日本生物物理学会第48回年会  2010 

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  • Apo- and antagonist-binding structures of vitamin D receptor ligand-binding domain in solution revealed by MD and SAXS hybrid approach

    浴本亨, 池口満徳

    第17回日本蛋白質科学会年会  2017 

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  • 神経軸索ガイダンス分子セマフォリンと受容体の相互作用のin silico解析

    下地恵令奈, 山根努, 浴本亨, 禾晃和, 池口満徳

    第17回日本蛋白質科学会年会  2017 

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  • ホスホジエステラーゼ(PDE)-10Aのin silicoリガンド結合解析

    湯浅千紗, 浴本亨, 山根努, 池口満徳

    第17回日本蛋白質科学会年会  2017 

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  • X線小角散乱実験と分子動力学計算を組み合わせた相関構造解析による蛋白質の溶液構造解析

    浴本亨, 池口満徳

    第17回日本蛋白質科学会年会  2017 

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  • Apo- and antagonist-binding structures of vitamin D receptor ligand-binding domain elucidated by SAXS experiments and MD simulations

    穴見康昭, 清水伸隆, 浴本亨, 江川大地, 伊藤俊将, 池口満徳, 山本恵子

    第55回日本生物物理学会年会  2017 

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  • Protein dynamics revealed by a combination analysis of molecular dynamics (MD) simulations and small-angle x-ray scattering (SAXS) experiments

    浴本亨, 池口満徳

    第55回日本生物物理学会年会  2017 

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  • Finite-size effect on the charging free energy in the alchemical perturbation and ``warp drive'' method

    浴本亨, 山根努, 池口満徳

    情報計算科学生物学会2017年大会  2017 

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  • Finite-size effect on the charging free energy in the alchemical perturbation and “Warp Drive” method

    浴本亨, 山根努, 池口満徳

    Biophysical society 62th Annual Meeting  2018 

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  • In silico binding affinity analysis for phosphodiesterase-10A inhibitors

    湯浅千紗, 浴本亨, 山根努, 池口満徳

    情報計算科学生物学会2017年大会  2017 

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  • In silico protein design for functional modification of the photoactivated adenylate cyclase

    田中真結, 浴本亨, 大木規央, 山根努, 朴三用, 池口満徳

    情報計算科学生物学会2017年大会  2017 

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  • 多剤排出トランスポーター AcrB の全原子分子動力学シミュレーションによる解析

    日本蛋白質科学会第10回年会  2010 

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  • F1-ATPaseの回転のメカニズムに関する一考察：水のエントロピーの重要性

    日本物理学会春季大会  2010 

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  • タンパク質平衡揺らぎの動的性質:独立成分分析による解析

    日本蛋白質科学会第10回年会  2010 

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  • X 線小角散乱法による分裂酵母 Swi5-Sfr1 の溶液構造解析

    日本蛋白質科学会第10回年会  2010 

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  • X 線小角散乱を用いたタンパク質複合体の構造モデリングを目指して

    日本蛋白質科学会第10回年会  2010 

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Research Projects

  • 生体発動分子の機能発現に関する構造ダイナミクス研究

    Grant number：18H05426  2018.6 - 2023.3

    日本学術振興会  科学研究費助成事業  新学術領域研究(研究領域提案型)

    池口 満徳, 高橋 栄夫

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    Grant amount：\93340000 （ Direct Cost: \71800000 、 Indirect Cost：\21540000 ）

    本研究は、スーパーコンピュータ等を用いた分子動力学(MD)シミュレーションとNMR実験を活用し、理論・計測の統合によって発動分子の構造ダイナミクスと機能発現を結びつけ、新規機能獲得に向けた合理的分子設計法を確立することを目的としている。具体的な標的として、TrkAd5という生体発動分子を選択し、MD計算とNMR実験の双方からの研究を推進している。2021年度には、TrkAd5を制御する結合ペプチド（TP1）のアミノ酸置換体のデザインを行った。前年度までに実施したMD計算により推定された結合構造とNMR実験の情報に基づき、相互作用が向上すると期待されるペプチドのアミノ酸置換体を10個程度予測し、NMR実験を行った。その結果、若干ではあるがTP1より親和性が向上する置換体が見つかった。その置換体についてMD計算を実施し、その親和性向上のメカニズムを考察した。また、主要な結合要素を抽出し構造を固定化する改変体をデザインしたところ、TP1を超える結合能を示したことから、エントロピーの制御が親和性増大に有効であることが示された。
    次に、A01班と連携し、人工発動分子イオンチャネルのQM/MM-MD研究を実施した。その結果、人工発動分子イオンチャネルのフッ素原子とカリウムイオンの相互作用が、イオンチャネルの選択性に寄与しているということが明らかになった。また、B01-2班と連携し、微小管を構成するチューブリン・キネシン複合体の分子シミュレーションも継続している。また、C01班、A01班との連携研究により、好熱細菌由来ロドプシンを対象としたNMR解析を進め、9割を超える主鎖由来シグナル帰属を完了するとともに、光反応サイクルを進めるための動的構造特性について考察した。また、光照射NMR実験により、光反応後期中間体に関する構造情報の取得が可能となった。

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  • Molecular simulation study on the rotation mechanism of V-ATPase

    Grant number：25291036  2013.4 - 2016.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    IKEGUCHI Mitsunori, MURATA Takeshi

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    Grant amount：\18070000 （ Direct Cost: \13900000 、 Indirect Cost：\4170000 ）

    The rotation mechanism of molecular motor V-ATPase, which transports ions utilizing ATP-hydrolysis energies, was studied using molecular dynamics (MD) simulations. Multiscale MD simulations employing both an all-atom model involving hydrogen atoms and a coarse-grained model approximating amino acids as particles successfully reproduced the rotation of a central stalk in V-ATPase. From analyses of the trajectories, the rotation mechanism of V-ATPase was elucidated structurally.

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  • Ｐループ型ＡＴＰ加水分解酵素の機能発現機構の解明

    Grant number：23118713  2011.4 - 2013.3

    日本学術振興会  科学研究費助成事業  新学術領域研究(研究領域提案型)

    池口 満徳

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    Grant amount：\16120000 （ Direct Cost: \12400000 、 Indirect Cost：\3720000 ）

    本研究は，Pループ型ATP加水分解酵素の機能発現機構について，分子シミュレーション等の計算科学的手法を用いて解析することを目的としている．
    平成24年度には，DNA相同組換えで働くPループ型ATP加水分解酵素であるRad51について，分子構造モデリングと分子動力学シミュレーションを行い，論文として，Biophysical Journal誌に出版することができた．Rad51の原子レベルの立体構造はX線結晶解析により得られているが，モノマー間の界面にはATPは存在せず，電子顕微鏡研究などで得られている活性型の構造とは言えない．そこで，まず，フィラメントの最小単位である２量体について，古細菌の類縁タンパク質であるRadAの結晶構造を参照して分子構造モデリングを行い，全原子分子動力学シミュレーションを遂行した．その結果，ATPのγリン酸部位では，安定な活性型構造を維持するのに，カリウムイオンが必須であり，隣接モノマーのH352, D374と相互作用ネットワークを形成していることを見出した．このようなカリウムイオンの相互作用は，他のPループ型ATP加水分解酵素におけるアルギニンフィンガーと類似の機能を果たしているように示唆された．さらに，もうひとつの活性型構造を維持するメカニズムとして，ATPのアデニン環が，R228と, 隣接モノマーにあるP379に挟まれるように相互作用することも見出した．このように，ATPがモノマー間の「糊」として働いており，活性型構造を安定化していることを明らかにした．
    また，領域内の液体統計力学解析の専門家と共同研究を行い，溶媒効果，特に水のエントロピー解析を発展させ，他のPループ型ATP加水分解酵素であるF1-ATPaseについて，分子動力学シミュレーションと統計力学解析を基に動作メカニズムを提案した．

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  • Structure-function relationships of Rad51-Swi5-Sfr1 complex for homologous recombination

    Grant number：23770105  2011 - 2012

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (B)

    KUWABARA Naoyuki, SATO Mamoru, IKEGUCHI Mitsunori, IWASAKI Hiroshi, SHIMIZU Toshiyuki

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    Grant amount：\4680000 （ Direct Cost: \3600000 、 Indirect Cost：\1080000 ）

    In this study, I made focus on the structure-function relationships of Swi5-Sfr1 complex that interacts Rad51. I revealed the complex structure of Swi5 and C-terminal region of Sfr1 by X-ray crystallography and found that this protein complex is essential for Rad51 activation. Furthermore, we showed that Swi5-Sfr1 complex enters the groove of Rad51 filament in the activation process, and intrinsically disorder regions of Sfr1 is important in the process. From these results, I proposed a model of Rad51 activating mechanism by Swi5-Sfr1.

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  • Study on rotation mechanisms of F1 molecular motor using molecular simulations

    Grant number：22300102  2010 - 2012

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    IKEGUCHI Mitsunori

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    Grant amount：\17550000 （ Direct Cost: \13500000 、 Indirect Cost：\4050000 ）

    In this study, the rotation mechanism of the F1 molecular motor was investigated using molecular simulations. Conformational changes in the B subunit, an engine of the F1 molecular motor, were analyzed using equilibrium and free-energy MD simulations. Further, based on the results of MD simulations and statistical thermodynamics theory applied for the XBR complex, the packing exchange model, in which the exchange of inter-subunit packing induces the rotational motion of the molecular motor, was proposed.

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  • Pループ型ATP加水分解酵素の機能発現機構の解明

    Grant number：21118519  2009 - 2010

    日本学術振興会  科学研究費助成事業  新学術領域研究(研究領域提案型)

    池口 満徳

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    Grant amount：\5200000 （ Direct Cost: \4000000 、 Indirect Cost：\1200000 ）

    本研究は,Pループ型ATP加水分解酵素の機能発現機構について,分子シミュレーション及び,統計力学解析を用いて解析することを目的としている.本年度は,DNA相同組換えで働く,Pループ型ATP加水分解酵素であるRad51について,分子構造モデリングと分子動力学シミュレーションを行った.Rad51は,DNAの周囲にらせん状のフィラメントを形成する.酵母のRad51に対する結晶構造が決定されているが,そのらせんピッチは130Aであり,電子顕微鏡などの実験値である90～100Aと比較すると若干大きかった.その結晶構造を元に,分子動力学シミュレーションを遂行したが,らせんピッチは増加する一方で実験値に近くはならなかった.そこで,らせんピッチが90A程度とほぼ実験値に近い古細菌のホモログであるRadAの結晶構造を元にして,Rad51のモデリングを行ったところ,ATP塩基のパッキングが,ピッチ130Aの構造と90-100Aの構造で大きく異なることが判明した.ピッチ130Aの構造ではATPが結合していないので,塩基パッキングの影響でATPの安定的結合が形成されなかったと考えられる.
    また,統計力学理論に基づく水のエントロピー解析を,やはりPループ型ATP加水分解酵素であるF1-ATPaseについて適用した.水のエントロピーは,タンパク質の密なパッキングをもたらす駆動力として効くことが知られている.水のエントロピー解析をF1-ATPaseに適用した結果,サブユニット間インターフェースのパッキングが場所によって,大きく異なっていることが明らかになり,ATP加水分解に付随して起こるγサブユニットの回転の際,大規模なパッキングの移動が起こっており,回転機構に重要な役割を果たしていることが明らかになった.

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  • トランスポーチンによるタンパク質の核内輸送の構造生物学

    Grant number：20051020  2008 - 2009

    日本学術振興会  科学研究費助成事業  特定領域研究

    佐藤 衛, 池口 満徳

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    Grant amount：\6400000 （ Direct Cost: \6400000 ）

    これまでわれわれは核内輸送受容体トランスポーチン(TRN1)とhnRNP D、JKTBPおよびTAPとの複合体の結晶構造を3.5A分解能で明らかにした。今年度はTRN1と転写因子c-fos,c-junおよびRevとの複合体のX線結晶構造解析を行った。c-fosのTRN1結合部位は以前知られているような核内輸送シグナルは存在しないが、c-junおよびREVのTRN1結合部位にはクラシカルな核内輸送シグナルが存在する。これまで知られているTRN1とリガンドとの結合とは違うメカニズムで複合体を形成していることが予想される。TRN1は前回同様全長890残基を用いた。リガンドには化学合成したペプチドを用いた。実験の結果、TRN1とc-fosおよびTRN1とREVの複合体で200から400μmの単結晶が得られ、PF-ARでX線回折実験を行ったところ、5.6A分解能の回折データを得ることができた。しかし、得られた回折データは低分解能で分子置換法による構造解析はできなかった。TRN1は柔軟な分子である高い分解能が得ることが難しかったと思われ、TRN1分子の不安定なループを削除するなどの工夫が必要と思われる。
    次に、TRN1の全原子分子動力学シミュレーションを行った。まず、分子動力学シミュレーションに用いたTRN1の初期構造を構築した。結晶構造では機能に重要なH8ループの電子密度が柔軟性のため観察されていなかったので、H8ループのモデリングを行い、さらに周囲に水を配置して分子動力学シミュレーションを行った。その結果、H8ループの初期構造は伸長した状態であったが、分子動力学シミュレーションの結果、コンパクトな構造に遷移した。しかし、シミュレーション中にある特定の構造に安定化したわけではなく、運動性の高い状態であった。また、TRN1の全体構造においても、通常の球状タンパク質と比べて柔軟性が高いことがわかった。TRN1はヘリックス-ターンヘリックスモチーフが繰り返されるHEATリピート構造を持つが、それぞれのモチーフの運動が一様でなく、運動性に個性が存在することが明らかになった。

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  • Protein folding simulation on the large scale computer system

    Grant number：19300101  2007 - 2009

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    OTA Motonori, IKEGUCHI Mitsunori

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    Grant amount：\18720000 （ Direct Cost: \14400000 、 Indirect Cost：\4320000 ）

    Because of the progress of computational technology, a large scale calculation that would be unrealistic a couple of years ago, becomes realistic nowadays. In this study, we conducted protein folding simulations on the large scale computers, and analyzed large amount of data produced by the simulations, using newly developed techniques. We simulated folding of Trp-Cage and λrepressor, and developed the multiple trajectory alignment, the partial order trajectory alignment, the itinerary profile.

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  • 分子シミュレーションによる膜タンパク質の機能的ダイナミクスの研究

    Grant number：19036028  2007 - 2008

    日本学術振興会  科学研究費助成事業  特定領域研究

    木寺 詔紀, 池口 満徳, 渕上 壮太郎

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    Grant amount：\6900000 （ Direct Cost: \6900000 ）

    分子動力学シミュレーションを用いて、膜インタフェイスに関わるタンパク質を計算機中で運動させることによって、それらタンパク質の機能発現の動的過程を明らかにすることを目的として、以下の課題の研究を行った。
    (1)Sensory Rhodopsin II/Transducer複合体の脂質2重膜中のシミュレーション : この複合体は高度好塩菌の細胞膜にあり、負の走光性をもたらす信号伝達複合体である。この系の基底状態における脂質2重膜中の分子動力学計算を行うことによって、信号伝達の機構を推定する。TransducerのHAMPドメインを付加した複合体モデルの構築とそのシミュレーションを行いその安定性とEPR実験との整合性を確認した。
    (2)IP3受容体のIP3結合ドメインの構造変化のシミュレーション : IP3受容体は小胞体膜上に存在し、IP3とCa2+の結合により細胞質にCa2+を放出するチャンネルである。その中で結晶構造の解かれているIP3結合型IP3結合ドメインについて、IP3非結合型の立体構造をシミュレーションで作り出した。その構造は、ドメイン間の多くの極性残基間の水素結合によって安定化される多様な構造アンサンブルからなる比較的閉じた構造であることが分かった。

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  • Molecular mechanism of chemical-mechanical energy conversion of F1 molecular motor studied by molecular simulations

    Grant number：18074004  2006 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Priority Areas

    HAYASHI Shigehiko, IKEGUCHI Mitsunori

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    Grant amount：\119400000 （ Direct Cost: \119400000 ）

    Molecular mechanism of chemical-mechanical conversion of a reversible rotary motor protein, F1-ATPase, was revealed in electronic and atomic details through molecular simulations. Molecular mechanisms of catalysis of ATP hydrolysis and its regulation were elucidated by means of a hybrid quantum mechanical/molecular mechanical method. Based on the reaction profile revealed, a mutant enzyme with increased catalytic activity was designed theoretically. Molecular dynamics simulations unveiled in an atomic detail protein structural changes responsible for the motor motion.

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  • 分子シミュレーションによる膜タンパク質の機能的ダイナミクスの研究

    Grant number：17048024  2005 - 2006

    日本学術振興会  科学研究費助成事業  特定領域研究

    木寺 詔紀, 池口 満徳, 渕上 壮太郎

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    Grant amount：\7100000 （ Direct Cost: \7100000 ）

    SRII-HtrII(2:2)複合体は高度好塩菌の細胞膜にあり、光受容体SRIIとその情報を下流に伝え、最終的には負の走光性をもたらす伝達タンパク質HtrIIの2x2の複合体である。その複合体の基底状態の結晶構造(1H2S ; Natronomonas pharaonis)は、多くの欠失部分を含む。SRIIでC端226-239、HtrIIでN端1-22、C端83-114は結晶中でモデルが存在しない。まず、膜中で安定なシミュレーションを行う基盤を作るために、SRII 226-239、HtrII 1-22、83-101のモデリングを行った。ここで、実験情報として、常磁性共鳴分光の距離情報等を拘束条件として用いた。このモデル部分はフレキシプルであることが予想されるので、複数のモデルを構築し、それらを初期構造として脂質2重膜中環境下での10nsの分子動力学シミュレーションを複数回行った。その結果、膜貫通部位における結晶構造からのずれが、2-10nsの間安定的に、1Åを切り、モデル部分に関しても常磁性共鳴分光の実験結果を満たす良好なモデル得ることに成功した。その後、HtrIIについて、単純にコイルドコイル構造を延長することでHAMPドメインまでを含むモデル構築を行っていたが、その間に相同なタンパク質のHAMPドメインの立体構造が解かれた(2ASW ; Af1503)。この立体構造は、単純なコイルドコイル構造の延長ではなく、長いループ部分を含む折り返し構造を持つものであった。そこで、それまでのHAMPドメインを含むモデルを破棄し、新たに2ASWに基づいたモデリングを開始した。まず、2ASW自体の水溶旅中の分子動力学シミュレーションを10ns行った。10ns後の構造のNMR構造からのずれがコア部分で1.3Å程度となり、NMR構造の信頼性が実証された。そこで、2ASWの構造をもとに、コイルドコイル構造の制約の下でAfl5QSとNatronomonas PharaonisのHAMPドメイン部分の配列アラインメントを行い、ホモロジーモデリングを行った。

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  • 分子シミュレーションによる蛋白質フォールディング・分子認識機構の解明

    Grant number：15076209  2003 - 2007

    日本学術振興会  科学研究費助成事業  特定領域研究

    池口 満徳, 木寺 詔紀, 渕上 壮太郎

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    Grant amount：\44200000 （ Direct Cost: \44200000 ）

    蛋白質のフォールディングや機能発現は,水との相互作用によって実現されている物理化学的現象である。本研究では,独自に開発している分子シミュレーションシステムMARBLEを用いて,蛋白質と水の関わりについての研究を行った。
    平成19年度には,蛋白質αラクトアルブミンのアンフォールディングシミュレーションに関する成果を論文としてまとめることができた。この論文では,新たな解析法として,シミュレーション軌道のマルチプルアライメント法を開発し,それをαラクトアルブミンのアンフォールディングシミュレーションに適用することで,特定研究代表である桑島らによるφ値実験とよく一致した結果を得ることができた。さらに,このアンフォールディング軌道の構造を,特定計画研究班員である松林らによるエネルギー表示の積分方程式法に適用することで,アンフォールディング過程での水の役割について,水和自由エネルギー変化の観点から見積もることができた。
    また,分子認識機構については,NMR実験情報による分子シミュレーションを用いて,DNA結合蛋白質PhoBに関して,DNA結合型,非結合型の双方の立体構造を決定した。この論文では,通常真空中でおこなれる構造決定を,水を含めた形で行うことでより精度の良い構造決定を行うことができた。その結果,DNA-PhoB間に,水を介した相互作用を多く見つけることができ,蛋白質PhoBのDNA認識機構における,水の役割の重要性を明らかにした。
    さらに,生体膜中で,水を透過させる水チャネルアクアポリンについての分子動力学シミュレーションを行い,pf-matrix法を新たに開発し,浸透圧による水透過の分子メカニズムを解明した。

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  • Study of Vibrational Energy Transfer in Proteins

    Grant number：14540474  2002 - 2003

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    KIDERA Akinori, IKEGUCHI Mitsunori

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    Grant amount：\3400000 （ Direct Cost: \3400000 ）

    Anharmonic dynamics of a protein molecule was studied by molecular dynamics simulations, (1)in terms of the intramolecular vibrational energy transfer, and (2)second through moving normal mode coordinates.
    (1)A small excess kinetic energy was added to a specified normal mode, and the process of the energy transfer to other modes was observed. It was found that the vibrational energy was transferred by two distinct mechanisms depending on temperature. At near zero temperature, the vibrational energy is transferred ass a process of the Fermi resonance. As the temperature increases, the resonance type transfer is dominated by the off-resonance energy transfer through various mode coupling terms.
    (2)A set of normal mode coordinates is defined at each time instant of the trajectory by principal component analysis (PCA) with a small time window. The time evolution of the normal mode coordinates defines the moving normal mode coordinates. Translation of he origin of he coordinates was decomposed into diffusion and vibrational motions. Significant parts of both types of motions occur in the large-amplitude normal mode space. Rotation of the large-amplitude normal mode space was characterized by fast relaxation completed within the time window of PCA, but was confined in a small space spanned by a limited number of large-amplitude normal modes.

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  • Prediction of structure and function of protein complexes

    Grant number：13208010  2001 - 2004

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Priority Areas

    KIDERA Akinori, IKEGUCHI Mitsunori, AKIO Kitao

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    Grant amount：\64400000 （ Direct Cost: \64400000 ）

    Database analyses of protein structures
    (1)Structural classification of all B-proteins: A novel structural classification of all B-proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on the fact that 92% and 60% of B proteins have the ring topology and the zippered contact pattern, respectively.
    (2)Probabilistic alignment method: We developed a method of generating probabilistic alignments for sequences and structures, by which the correspondence between pairs of residues is evaluated in a probabilistic manner. This method was applied to TIM-barrel and β-trefoil proteins.
    Simulation analyses of protein functions
    (1)Development of a molecular dynamics program on parallel computer: A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT and NPyT ensembles.
    (2)Molecular dynamics simulations of aquaporins: Molecular dynamics simulations were performed for four members of the aquaporin family (AQPl, AQPZ, AQPO, and GlpF) in the explicit membrane environment. The single channel water permeability was evaluated to be GlpF AQPZ > AQPl≫AQPO.
    (3)Linear response theory of protein structural change upon ligand binding: A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. The results for three protein systems of various sizes are consistent with the observations in the crystal structures.
    Experimental analyses of protein dynamics
    (1)Development of analysis method for neutron scattering spectra: The origin of the Boson peak in the inelastic neutron scattering was clarified based on the dynamic structural transition of proteins at low temperature.

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  • 蛋白質化学機能の立体構造からの第一原理的予測法の開発

    Grant number：13208004  2001

    日本学術振興会  科学研究費助成事業  特定領域研究(C)

    池口 満徳, 木下 賢吾

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    Grant amount：\6000000 （ Direct Cost: \6000000 ）

    本研究では、構造ゲノムプロジェクトの進展を念頭において、タンパク質の立体構造情報からその機能を予測する「第一原理的機能予測法」の開発を目指した。そこでは、従来行われていたような進化的類縁関係(配列の類似性)からの機能の類推ではなく、タンパク質の立体構造-機能相関というタンパク質の機能を直接決めているメカニズムを解明し利用することを目指す。このために(1)構造および機能がわかっているタンパク質のデータベースを構築し、(2)このデータベースから構造機能相関の経験的ルールを導き出し、(3)分子シミュレーションを使って経験的ルールの物理化学的な基礎付けと一般化を狙った。本研究では、立体構造の蓄積のあるモノヌクレオチド結合タンパク質を取り上げた。
    本年度は、モノヌクレオチド結合蛋白質データベースの整備を行い、結合部位の立体構造の分類、代表決定を行った。その結果、103スーパーファミリー内に1137種の認識構造を同定した。本研究は、タンパク質のモノヌクレオチド結合について体系的に整理、解析した初めてのものである。
    また、分子認識に対する動的揺らぎの影響を調べるため、高精度で高効率な分子動力学シミュレーションソフトウエアの開発を行った。このソフトウエアの並列化効率、精度は、世界的に高いレベルにある。さらに、このソフトウエアを適用して、モノヌクレオチド結合タンパク質である酵素HPPKに対する分子動力学計算を行い、モノヌクレオチド結合部位周辺の動きの解析を行った。その結果、非結合状態での蛋白質の熱揺らぎの中に、分子認識によって誘起される構造変化が内在していることが分かった。

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  • 蛋白質のレアイベントに対する準平衡論的分子シミュレーション法の開発

    Grant number：12780488  2000 - 2001

    日本学術振興会  科学研究費助成事業  奨励研究(A)

    池口 満徳

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    Grant amount：\1900000 （ Direct Cost: \1900000 ）

    本研究の目的は、蛋白質の構造変化のような、現実にはミリ秒以上かかる蛋白質のレアイベントを捉えることができる分子シミユレーション法の開発である。通常の分子動力学法では、長くても数十nsの座標履歴を計算できる程度で、蛋白質の機能に関わる運勲の時間スケール(μs〜s)とは差が大きい。このような困難を克服するため、本研究では、二つの方向から研究を行った。(1)実時間のサンプリングではなく、人工的に幅広い構造空間をサンプリングするための拡張アンサンブル法の開発と(2)大量計算を効率的に行うための超並列計算機用分子シミュレーションシステムの開発である。拡張アンサンブル法として、多数の分子シミュレーションの結果を統計誤差最小になるように重ね合わせることで自由エネルギーランドスケープを得ることのできるWeighted Histogram Analysis Method(WHAM)と、分子種の違いに対応する自由エネルギー変化を精度よく求めることのできるλダイナミクス法を組み合わせた分子シミュレーションシステムを開発した。一方、分子動力学シミュレーションの並列計算では、計算対象のシステムが巨大になったときにも効率がよい空間分割法を適用し、この方法の問題点である負荷の不均一性による効率低下の問題を、CPUの負荷を実行時に判定し、通信を少なく抑えながら、次第に高速になっていく動的負荷分散法の開発により解決した。

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  • 蛋白質化学機能の立体構造からの第一原理的予測法の開発

    Grant number：12208016  2000

    日本学術振興会  科学研究費助成事業  特定領域研究(C)

    池口 満徳, 木下 賢吾

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    ゲノム配列決定の次の課題は、遺伝子機能の特定である。特に創薬への応用を考える際、遺伝子産物である蛋白質の化学的な機能、つまり蛋白質と他分子との間の相互作用を理解することが重要である。そこで本研究では、データベース解析と分子シミュレーションの互いの利点を生かした解析法を開発することにより、立体構造に基づいた化学機能の予測法の開発を目指した。当面の対象として、すでに多くの立体構造が明らかにされているモノヌクレオチド結合蛋白質を扱った。まず、2000年4月のPDBから,モノヌクレオチド結合蛋白質667個,1190結合部位を同定した。これらの結合部位はそのままでは統計処理に適さない冗長性を含んでいるので、原子の空間配置の類似度に基づき代表構造425個を選別した。これら代表構造に対して、分子シミュレーションと連携しやすい物性として、分子表面、静電ポテンシャル分布を計算しデータベース化を行った。PDBの記述は必ずしも完全ではなく、系統的な構造-機能相関の解析の妨げとなってきた。これに対して、モノヌクレオチド結合蛋白質立体構造データベースを構築し、インターネット上に公開できたことは今年度の重要な成果である。また、近年の超並列計算機を念頭においた並列計算技術を開発し、分子動力学計算システムに応用した。このシステムを、代表構造の一つであるRas蛋白質に適用し、結合部位の表面形状,電場揺らぎ及び結合自由エネルギーの解析を行った.この結果、静的な立体構造を対象とするだけでは不十分であり、立体構造の柔らかさ、特に結晶が得られにくい基質非結合状態が重要であることがわかってきた。機能予測における非結合状態の構造の重要性は、動的構造まで含めた解析手法の構築により初めて得られる知見である。

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  • Development of a Parallel Programming Environment with Dynamic Resource Management Facilities

    Grant number：11558029  1999 - 2001

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    SHIMIZU Kentaro, NAKAURA Shugo

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    Grant amount：\6500000 （ Direct Cost: \6500000 ）

    We designed and implemented a new parallel programming environment called Parsley, which provides fine-grained scheduling services based on the structures of application programs. In Parsley, application programs are divided into subtasks that can run serially or in parallel. It provides a programming interface that allows a user to define subtasks and to easily specify precedence constraints among them. Parsley uses these constraints to schedule subtasks at run time. The scheduling' policy. is automatically improved to reflect the hardware environment and resource usage. The basic 'scheduling policy is an incremental scheduling algorithm based on the critical path method. In this algorithm, subtask priorities are dynamically determined by using the execution time of each subtask, as monitored by the resource management facilities of Parsley. We developed a parallel molecular dynamics (MD) simulation program on the Parsley system and' executed it on three scalable multiprocessor systems. We found that Parsley is efficient for large-scale MD simulation and that load balancing facilities of Parsley can be adopted to the scalable multiprocessor systems of different architectures. The MD simulation on Parsley is 3.5 times faster than the conventional parallel algorithm. The Parsley's automatic improvement of scheduling policies further enhances processor utilization by 35 to 55 %. In addition, Parsley is useful in the heterogeneous environment (e.g. a network of different workstations and clusters) as well as the homogeneous environment. Users need not be aware of the individual performance of the computers and networks, because of the dynamic processor allocation facilities of Parsley.

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  • Efficient Processor Allocation Policies for Massively Parallel Systems

    Grant number：10680336  1998 - 2000

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    SHIMIZU Kentaro, NAKAMURA Shugo

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    Grant amount：\3200000 （ Direct Cost: \3200000 ）

    We designed and implemented a new parallel programming environment called Parsley, which provides fine-grained scheduling services based on the structures of application programs. In Parsley, application programs are divided into subtasks that can run serially or in parallel. It provides a programming interface that allows a user to define subtasks and to easily specify precedence constraints among them. Parsley uses these constraints to schedule subtasks at run time. In this research project, we developed the scheduling policy and mechanism for Parsley and applied them to parallel molecular dynamics simulation program on distributed memory multiprocessor systems. The scheduling policy is automatically improved to reflect the hardware environment and resource usage. The basic policy is an incremental scheduling algorithm based on the critical path method. In this algorithm, subtask priorities are dynamically determined by using the execution time of each subtask, as monitored by the resource management facilities of Parsley. This policy improves processor utilization by 35 to 55 % compared with the FIFO scheduling policy. In addition, Parsley is useful in the heterogeneous environment (e.g. a network of different workstations and clusters) as well as the homogeneous environment. Users need not be aware of the individual performance of the computers and networks, because of the dynamic processor allocation facilities of Parsley. We have developed several resource management policies for Parsley on heterogeneous environment and evaluated the performance for molecular dynamics simulation.

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  • 蛋白質の安定性・折れたたみ機構における水・変性剤の分子メカニズム

    Grant number：10157203  1998

    日本学術振興会  科学研究費助成事業  特定領域研究(A)

    池口 満徳, 中村 周吾, 清水 謙多郎

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    Grant amount：\1400000 （ Direct Cost: \1400000 ）

    本研究では,蛋白質の安定性・折れたたみ機構において,特に水や変性剤のもたらす溶媒効果に焦点をあて,コンピュータシミュレーションにより,その分子メカニズムを解明することを目的とした.そのために,(1)これからのスーパーコンピュータの潮流である超並列スーパーコンピュータ用の分子シミュレーションソフトウエアの開発,(2)溶媒効果,とくに,統計力学的扱いが要求される疎水効果理論の構築,(3)変性剤を導入した分子シミュレーションによる変性剤効果の解明を行った.
    本研究では,通信最適化や負荷分散を効率的に行えるプログラミング環境Parsleyを開発し,それを生体高分子シミュレーション(XYZ系:MARBLE,二面角系:NORMA)に応用した.XYZ系,二面角系とも,本研究により新たな並列化方式が開発された.また,分子動力学ソフトウエアMARBLEは新たに開発したもので,長距離クーロン相互作用をカットオフなしに扱うことのできるFast Multipole Methodなど,近年の分子シミュレーションの最新技術を導入したものとなっている.
    以上のシミュレーション技術を用い,疎水効果の物理的起源を検討した.疎水効果の起源では,従来,相対立する水の構造化説と排除体積効果説が提唱されていた.本研究では,以上の2つの対立する説を統合的に理解する理論を構築し,疎水効果の起源を明らかにした.
    さらに,以上の理論を変性剤(尿素)を導入した系に適用し,変性剤が疎水効果をどう変化させるかを解析した.疎水効果の自由エネルギーは,空孔生成項と溶質-溶媒の分散力項からなるが,尿素は,空孔生成項に対しては疎水効果を強め,分散力項では疎水効果を弱めることがわかった.全体として尿素の効果は,2つの項が微妙なバランスを持って疎水効果に影響していることがわかった.

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  • 計算機を用いた生体分子の構造、機能の理論的解析

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    Grant type：Competitive

    計算機を用い、タンパク質やDNAなどの生体分子の構造、機能についてのシミューレション、および、理論的研究を行っている。生体分子がいかにしてその特異的な立体構造を持つのか、そして、その立体構造がいかにして機能を発現するのか、という問題について物理化学的、および情報科学的な視点から解明していこうと取り組んでいる。

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