Updated on 2025/05/23

All information, except for affiliations, is reprinted from the information registered on researchmap.

写真a

 
Tsuyoshi Konuma
 
Organization
Graduate School of Medical Life Science Department of Medical Life Science Associate Professor
School of Science Department of Science
Title
Associate Professor
External link

Degree

  • 博士(理学) ( 大阪大学 )

Research Interests

  • 分子間相互作用

  • X線結晶構造解析

  • NMR

  • 構造生物学

  • 生化学

  • 分子生物学

  • ネイティブ質量分析

  • 生物物理学

  • ヒストン翻訳後修飾

  • エピジェネティクス

  • 創薬科学

  • 阻害剤開発

Research Areas

  • Life Science / Biophysics

  • Life Science / Molecular biology

  • Life Science / Structural biochemistry

Education

  • 大阪大学大学院博士後期課程   理学研究科   高分子科学専攻

    2007.4 - 2010.3

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  • 大阪大学大学院博士前期課程   理学研究科   高分子科学専攻

    2005.4 - 2007.3

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  • Soka University

    2001.4 - 2005.3

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Research History

  • Yokohama City University   Graduate School of Medical Life Science   Associate Professor

    2025.4

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  • Yokohama City University   Graduate   Assistant Professor

    2018.4 - 2025.3

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  • Icahn School of Medicine at Mount Sinai   Department of Pharmacological Sciences   Postdoctoral Fellow

    2014.9 - 2018.3

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  • 日本学術振興会   海外特別研究員

    2014.9 - 2016.8

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  • SUNTORY FOUNDATION FOR LIFE SCIENCES

    2012.4 - 2014.8

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  • SUNTORY FOUNDATION FOR LIFE SCIENCES

    2011.4 - 2012.3

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  • 財団法人サントリー生物有機科学研究所   博士研究員

    2010.4 - 2011.3

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  • 日本学術振興会   特別研究員(DC2)

    2008.4 - 2010.3

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Professional Memberships

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Papers

  • Distinct Histone H3 Lysine 27 Modifications Dictate Different Outcomes of Gene Transcription Invited Reviewed

    Tsuyoshi Konuma, Ming-Ming Zhou

    Journal of Molecular Biology   436 ( 7 )   168376   2024.4

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

    DOI: 10.1016/j.jmb.2023.168376

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  • Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin. Reviewed International journal

    #Nan Liu, #Tsuyoshi Konuma, Rajal Sharma, Deyu Wang, Nan Zhao, Lingling Cao, Ying Ju, Di Liu, Shuai Wang, Almudena Bosch, Yifei Sun, Siwei Zhang, Donglei Ji, Satoru Nagatoishi, Noa Suzuki, Masaki Kikuchi, Masatoshi Wakamori, Chengcheng Zhao, Chunyan Ren, Thomas Jiachi Zhou, Yaoyao Xu, Jamel Meslamani, Shibo Fu, Takashi Umehara, Kouhei Tsumoto, Satoko Akashi, Lei Zeng, Robert G Roeder, Martin J Walsh, Qiang Zhang, Ming-Ming Zhou (#Co-first author)

    Molecular Cell (Selected as Featured Article)   83 ( 13 )   2206 - 2221   2023.6

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.

    DOI: 10.1016/j.molcel.2023.05.022

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  • Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger Reviewed

    Keiichi Hata, Naohiro Kobayashi, Keita Sugimura, Weihua Qin, Deis Haxholli, Yoshie Chiba, Sae Yoshimi, Gosuke Hayashi, Hiroki Onoda, Takahisa Ikegami, Christopher B Mulholland, Atsuya Nishiyama, Makoto Nakanishi, Heinrich Leonhardt, *Tsuyoshi Konuma, *Kyohei Arita (*Co-corresponding author)

    Nucleic Acids Research   50 ( 21 )   12527 - 12542   2022.11

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.

    DOI: 10.1093/nar/gkac1082

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  • Single-Cell Native Mass Spectrometry of Human Erythrocytes. Reviewed International journal

    Waka Sakamoto, Nanako Azegami, Tsuyoshi Konuma, Satoko Akashi

    Analytical Chemistry   93 ( 17 )   6583 - 6588   2021.5

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

    Native mass spectrometry (MS) enables the determination of the molecular mass of protein complexes. Generally, samples for native MS are isolated, purified, and prepared in volatile solutions. However, to understand the function of proteins in living cells, it is essential to characterize the protein complex as is, without isolation/purification of the protein, using the smallest possible amount of the sample. In the present study, we modified the "live single-cell MS" method, which has mainly been used in metabolomics, and applied it to observe hemoglobin directly sampled from human erythrocytes. By optimizing the experimental methods and conditions, we obtained native mass spectra of hemoglobin using only a single erythrocyte, which was directly sampled into a nanoelectrospray ionization emitter using a micromanipulator and microinjector system. That is, our method enables the analysis of ∼0.45 fmol of hemoglobin directly sampled from an erythrocyte. To our knowledge, this is the first report of native MS for endogenous proteins using a single intact human cell.

    DOI: 10.1021/acs.analchem.1c00588

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  • Analysis of the High-Order Conformational Changes in Glyceraldehyde-3-phosphate Dehydrogenase Induced by Nicotinamide Adenine Dinucleotide, Adenosine Triphosphate, and Oxidants Reviewed

    Himari Suzuki, Yuki Nicole Makiyama, Yuta Watanabe, Hideo Akutsu, Michiko Tajiri, Yoko Motoda, Ken-Ichi Akagi, Tsuyoshi Konuma, Satoko Akashi, Takahisa Ikegami

    Biochemistry   64 ( 9 )   1916 - 1932   2025.4

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

    DOI: 10.1021/acs.biochem.4c00794

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  • Revealing an origin of temperature-dependent structural change in intrinsically disordered proteins Reviewed

    Rintaro Inoue, Takashi Oda, Hiroshi Nakagawa, Taiki Tominaga, Takahisa Ikegami, Tsuyoshi Konuma, Hiroki Iwase, Yukinobu Kawakita, Mamoru Sato, Masaaki Sugiyama

    Biophysical Journal   124 ( 3 )   540 - 548   2025.2

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

    DOI: 10.1016/j.bpj.2024.12.022

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  • Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3 Reviewed

    Nao Shiraishi, Tsuyoshi Konuma, Yoshie Chiba, Sayaka Hokazono, Nao Nakamura, Md Hadiul Islam, Makoto Nakanishi, Atsuya Nishiyama, Kyohei Arita

    Communications Biology   7 ( 1 )   2024.6

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

    Abstract

    DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 <sup>85</sup>VRT<sup>87</sup> motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.

    DOI: 10.1038/s42003-024-06434-9

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    Other Link: https://www.nature.com/articles/s42003-024-06434-9

  • Analysis of the homodimeric structure of a D‐Ala‐D‐Ala metallopeptidase, VanX, from vancomycin‐resistant bacteria Reviewed

    Tsuyoshi Konuma, Tomoyo Takai, Chieko Tsuchiya, Masayuki Nishida, Miyu Hashiba, Yudai Yamada, Haruka Shirai, Yoko Motoda, Aritaka Nagadoi, Eriko Chikaishi, Ken‐ichi Akagi, Satoko Akashi, Toshio Yamazaki, Hideo Akutsu, Takahisa Ikegami

    Protein Science   33 ( 6 )   2024.5

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    Authorship:Lead author   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    Abstract

    Bacteria that have acquired resistance to most antibiotics, particularly those causing nosocomial infections, create serious problems. Among these, the emergence of vancomycin‐resistant enterococci was a tremendous shock, considering that vancomycin is the last resort for controlling methicillin‐resistant Staphylococcus aureus. Therefore, there is an urgent need to develop an inhibitor of VanX, a protein involved in vancomycin resistance. Although the crystal structure of VanX has been resolved, its asymmetric unit contains six molecules aligned in a row. We have developed a structural model of VanX as a stable dimer in solution, primarily utilizing nuclear magnetic resonance (NMR) residual dipolar coupling. Despite the 46 kDa molecular mass of the dimer, the analyses, which are typically not as straightforward as those of small proteins around 10 kDa, were successfully conducted. We assigned the main chain using an amino acid‐selective unlabeling method. Because we found that the zinc ion‐coordinating active sites in the dimer structure were situated in the opposite direction to the dimer interface, we generated an active monomer by replacing an amino acid at the dimer interface. The monomer consists of only 202 amino acids and is expected to be used in future studies to screen and improve inhibitors using NMR.

    DOI: 10.1002/pro.5002

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  • Biophysical insights into the dimer formation of human Sirtuin 2 Reviewed

    #Noa Suzuki, #,*Tsuyoshi Konuma, Takahisa Ikegami, *Satoko Akashi (#Co-first author, *Co-corresponding author)

    Protein Science   33 ( 5 )   2024.4

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    Abstract

    Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild‐type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52–357) forms a homodimer in a concentration‐dependent manner with a dimer–monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non‐dimerizing mutants exhibited deacetylation activity for the N‐terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292–306, which lacks a SIRT2‐specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X‐ray structure of the mutant Δ292–306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.

    DOI: 10.1002/pro.4994

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  • 1H, 13C and 15N backbone resonance assignments of hepatocyte nuclear factor-1-beta (HNF1β) POUS and POUHD Reviewed

    Sayaka Hokazono, Eri Imagawa, Daishi Hirano, Takahisa Ikegami, Kimihiko Oishi, Tsuyoshi Konuma

    Biomolecular NMR Assignments   18 ( 1 )   59 - 63   2024.3

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    Authorship:Last author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s12104-024-10168-4

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    Other Link: https://link.springer.com/article/10.1007/s12104-024-10168-4/fulltext.html

  • The Impact of FGFR3 Alterations on the Tumor Microenvironment and the Efficacy of Immune Checkpoint Inhibitors in Bladder Cancer Reviewed

    Kazumasa Komura, Kensuke Hirosuna, Satoshi Tokushige, Takuya Tsujino, Kazuki Nishimura, Mitsuaki Ishida, Takuo Hayashi, Ayako Ura, Takaya Ohno, Shogo Yamazaki, Keita Nakamori, Shoko Kinoshita, Ryoichi Maenosono, Masahiko Ajiro, Yuki Yoshikawa, Tomoaki Takai, Takeshi Tsutsumi, Kohei Taniguchi, Tomohito Tanaka, Kiyoshi Takahara, Tsuyoshi Konuma, Teruo Inamoto, Yoshinobu Hirose, Fumihito Ono, Yuichi Shiraishi, Akihide Yoshimi, Haruhito Azuma

    Molecular Cancer   22 ( 1 )   2023.11

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    Abstract

    Background

    Currently, only limited knowledge is available regarding the phenotypic association between fibroblast growth factor receptor 3 (FGFR3) alterations and the tumor microenvironment (TME) in bladder cancer (BLCA).

    Methods

    A multi-omics analysis on 389 BLCA and 35 adjacent normal tissues from a cohort of OMPU-NCC Consortium Japan was retrospectively performed by integrating the whole-exome and RNA-sequence dataset and clinicopathological record. A median follow-up duration of all BLCA cohort was 31 months.

    Results

    FGFR3 alterations (aFGFR3), including recurrent mutations and fusions, accounted for 44% of non-muscle invasive bladder cancer (NMIBC) and 15% of muscle-invasive bladder cancer (MIBC). Within MIBC, the consensus subtypes LumP was significantly more prevalent in aFGFR3, whereas the Ba/Sq subtype exhibited similarity between intact FGFR3 (iFGFR3) and aFGFR3 cases. We revealed that basal markers were significantly increased in MIBC/aFGFR3 compared to MIBC/iFGFR3. Transcriptome analysis highlighted TIM3 as the most upregulated immune-related gene in iFGFR3, with differential immune cell compositions observed between iFGFR3 and aFGFR3. Using EcoTyper, TME heterogeneity was discerned even within aFGFR cases, suggesting potential variations in the response to checkpoint inhibitors (CPIs). Among 72 patients treated with CPIs, the objective response rate (ORR) was comparable between iFGFR3 and aFGFR3 (20% vs 31%; p = 0.467). Strikingly, a significantly higher ORR was noted in LumP/aFGFR3 compared to LumP/iFGFR3 (50% vs 5%; p = 0.022). This trend was validated using data from the IMvigor210 trial. Additionally, several immune-related genes, including IDO1, CCL24, IL1RL1, LGALS4, and NCAM (CD56) were upregulated in LumP/iFGFR3 compared to LumP/aFGFR3 cases.

    Conclusions

    Differential pathways influenced by aFGFR3 were observed between NMIBC and MIBC, highlighting the upregulation of both luminal and basal markers in MIBC/aFGFR3. Heterogeneous TME was identified within MIBC/aFGFR3, leading to differential outcomes for CPIs. Specifically, a favorable ORR in LumP/aFGFR3 and a poor ORR in LumP/iFGFR3 were observed. We propose TIM3 as a potential target for iFGFR3 (ORR: 20%) and several immune checkpoint genes, including IDO1 and CCL24, for LumP/iFGFR3 (ORR: 5%), indicating promising avenues for precision immunotherapy for BLCA.

    DOI: 10.1186/s12943-023-01897-6

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    Other Link: https://link.springer.com/article/10.1186/s12943-023-01897-6/fulltext.html

  • GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain Reviewed

    Masaki Kikuchi, Shohei Takase, Tsuyoshi Konuma, Kota Noritsugu, Saaya Sekine, Takahisa Ikegami, Akihiro Ito, Takashi Umehara

    Proceedings of the National Academy of Sciences   120 ( 43 )   2023.10

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    Glioma amplified sequence 41 (GAS41), which has the Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain that recognizes lysine acetylation (Kac), regulates gene expression as a subunit of the SRCAP (SNF2-related CREBBP activator protein) complex that deposits histone H2A.Z at promoters in eukaryotes. The YEATS domains of the proteins AF9 and ENL recognize Kac by hydrogen bonding the aromatic cage to arginine situated just before K9ac or K27ac in the N-terminal tail of histone H3. Curiously, the YEATS domain of GAS41 binds most preferentially to the sequence that contains K14ac of H3 (H3K14ac) but lacks the corresponding arginine. Here, we biochemically and structurally elucidated the molecular mechanism by which GAS41 recognizes H3K14ac. First, stable binding of the GAS41 YEATS domain to H3K14ac required the N terminus of H3 (H3NT). Second, we revealed a pocket in the GAS41 YEATS domain responsible for the H3NT binding by crystallographic and NMR analyses. This pocket is away from the aromatic cage that recognizes Kac and is unique to GAS41 among the YEATS family. Finally, we showed that E109 of GAS41, a residue essential for the formation of the H3NT-binding pocket, was crucial for chromatin occupancy of H2A.Z and GAS41 at H2A.Z-enriched promoter regions. These data suggest that binding of GAS41 to H3NT via its YEATS domain is essential for its intracellular function.

    DOI: 10.1073/pnas.2304103120

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  • Evaluation of Drug Responses to Human β<sub>2</sub>AR Using Native Mass Spectrometry Reviewed

    Michiko Tajiri, Shunsuke Imai, Tsuyoshi Konuma, Keiko Shimamoto, Ichio Shimada, Satoko Akashi

    ACS Omega   8 ( 27 )   24544 - 24551   2023.6

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

    DOI: 10.1021/acsomega.3c02737

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  • Functional insight into a neurodevelopmental disorder caused by missense variants in an RNA-binding protein, RBM10 Reviewed

    Eri Imagawa, Latisha Moreta, Vinod K. Misra, Claire Newman, Tsuyoshi Konuma, Kimihiko Oishi

    Journal of Human Genetics   68 ( 9 )   643 - 648   2023.6

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

    DOI: 10.1038/s10038-023-01162-0

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    Other Link: https://www.nature.com/articles/s10038-023-01162-0

  • CPMG pulse sequence for relaxation dispersion that cancels artifacts independently of spin states. Reviewed International journal

    Tsuyoshi Konuma, Jun-Ichi Kurita, Takahisa Ikegami

    Journal of magnetic resonance   352   107489   2023.5

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    The relaxation dispersion (rd) of nuclear magnetic resonance provides thermodynamic and kinetic information regarding molecules for which the conformations are exchanging in equilibrium. Experiments have often been implemented with Carr-Purcell-Meiboom-Gill (CPMG) pulse sequences for heteronuclear S-spin in SI and SI3 spin systems. One of the most common CPMG sequences contains a sequence called a P-element in the middle to average the different relaxation rates of anti-phase and in-phase coherences; however, its drawback is that the artifacts that can be compensated for are only those in one of the two S-spin doublet magnetization components, for example, SIα or SIβ in an SI spin system. Thus, when the CPMG sequence is followed by a normal heteronuclear single-quantum correlation (HSQC) sequence, the detected signal will also include the other component with accumulated artifacts. To overcome this issue, we developed a new pulse sequence (AFTAC) that can suppress artifacts in both the magnetization components. Its effectiveness was demonstrated by simulations and actual measurements targeting the methyl groups of dimethylsulfoxide and N, N-dimethyltrichloroacetamide. The results demonstrated that the AFTAC sequence sufficiently suppressed the artifacts, despite being followed by an HSQC sequence that detects both components. AFTAC is particularly suitable for the rd measurements of small molecules, which are usually not deuterated and are not subject to transverse relaxation optimized spectroscopy (TROSY) sequences. AFTAC does not require 1H continuous wave irradiation for I-spin decoupling, which is necessary for certain CPMG methods that maintain S-spin in-phase coherence during the CPMG period (Tcpmg). Therefore, AFTAC places less burden on the probe, even with a long Tcpmg. Furthermore, the AFTAC method achieves a similar artifact suppression quality not only in SI but also in SI2 and SI3 spin systems.

    DOI: 10.1016/j.jmr.2023.107489

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  • Native Mass Spectrometry of BRD4 Bromodomains Linked to a Long Disordered Region Reviewed

    Nanako Azegami, Rina Taguchi, Noa Suzuki, Yusuke Sakata, *Tsuyoshi Konuma, *Satoko Akashi (*Co-corresponding author)

    Mass Spectrometry   11 ( 1 )   A0110   2022.12

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:The Mass Spectrometry Society of Japan  

    DOI: 10.5702/massspectrometry.a0110

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  • Aberrant <i>EVI1</i> splicing contributes to <i>EVI1</i>-rearranged leukemia Reviewed

    Atsushi Tanaka, Taizo A. Nakano, Masaki Nomura, Hiromi Yamazaki, Jan P. Bewersdorf, Roger Mulet-Lazaro, Simon Hogg, Bo Liu, Alex Penson, Akihiko Yokoyama, Weijia Zang, Marije Havermans, Miho Koizumi, Yasutaka Hayashi, Hana Cho, Akinori Kanai, Stanley C. Lee, Muran Xiao, Yui Koike, Yifan Zhang, Miki Fukumoto, Yumi Aoyama, Tsuyoshi Konuma, Hiroyoshi Kunimoto, Toshiya Inaba, Hideaki Nakajima, Hiroaki Honda, Hiroshi Kawamoto, Ruud Delwel, Omar Abdel-Wahab, Daichi Inoue

    Blood   140 ( 8 )   875 - 888   2022.8

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    Publishing type:Research paper (scientific journal)   Publisher:American Society of Hematology  

    Abstract

    Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 drives inv(3)/t(3;3) myeloid leukemias via structural rearrangement of an enhancer that upregulates transcription of EVI1. Here, we identify a novel, previously unannotated oncogenic RNA-splicing derived isoform of EVI1 that is frequently present in inv(3)/t(3;3) acute myeloid leukemia (AML) and directly contributes to leukemic transformation. This EVI1 isoform is generated by oncogenic mutations in the core RNA splicing factor SF3B1, which is mutated in &amp;gt;30% of inv(3)/t(3;3) myeloid neoplasm patients and thereby represents the single most commonly cooccurring genomic alteration in inv(3)/t(3;3) patients. SF3B1 mutations are statistically uniquely enriched in inv(3)/t(3;3) myeloid neoplasm patients and patient-derived cell lines compared with other forms of AML and promote mis-splicing of EVI1 generating an in-frame insertion of 6 amino acids at the 3′ end of the second zinc finger domain of EVI1. Expression of this EVI1 splice variant enhanced the self-renewal of hematopoietic stem cells, and introduction of mutant SF3B1 in mice bearing the humanized inv(3)(q21q26) allele resulted in generation of this novel EVI1 isoform in mice and hastened leukemogenesis in vivo. The mutant SF3B1 spliceosome depends upon an exonic splicing enhancer within EVI1 exon 13 to promote usage of a cryptic branch point and aberrant 3′ splice site within intron 12 resulting in the generation of this isoform. These data provide a mechanistic basis for the frequent cooccurrence of SF3B1 mutations as well as new insights into the pathogenesis of myeloid leukemias harboring inv(3)/t(3;3).

    DOI: 10.1182/blood.2021015325

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  • Increased BUB1B/BUBR1 expression contributes to aberrant DNA repair activity leading to resistance to DNA-damaging agents. Reviewed International journal

    Kazumasa Komura, Teruo Inamoto, Takuya Tsujino, Yusuke Matsui, Tsuyoshi Konuma, Kazuki Nishimura, Taizo Uchimoto, Takeshi Tsutsumi, Tomohisa Matsunaga, Ryoichi Maenosono, Yuki Yoshikawa, Kohei Taniguchi, Tomohito Tanaka, Hirofumi Uehara, Koichi Hirata, Hajime Hirano, Hayahito Nomi, Yoshinobu Hirose, Fumihito Ono, Haruhito Azuma

    Oncogene   40 ( 43 )   6210 - 6222   2021.10

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    There has been accumulating evidence for the clinical benefit of chemoradiation therapy (CRT), whereas mechanisms in CRT-recurrent clones derived from the primary tumor are still elusive. Herein, we identified an aberrant BUB1B/BUBR1 expression in CRT-recurrent clones in bladder cancer (BC) by comprehensive proteomic analysis. CRT-recurrent BC cells exhibited a cell-cycle-independent upregulation of BUB1B/BUBR1 expression rendering an enhanced DNA repair activity in response to DNA double-strand breaks (DSBs). With DNA repair analyses employing the CRISPR/cas9 system, we revealed that cells with aberrant BUB1B/BUBR1 expression dominantly exploit mutagenic nonhomologous end joining (NHEJ). We further found that phosphorylated ATM interacts with BUB1B/BUBR1 after ionizing radiation (IR) treatment, and the resistance to DSBs by increased BUB1B/BUBR1 depends on the functional ATM. In vivo, tumor growth of CRT-resistant T24R cells was abrogated by ATM inhibition using AZD0156. A dataset analysis identified FOXM1 as a putative BUB1B/BUBR1-targeting transcription factor causing its increased expression. These data collectively suggest a redundant role of BUB1B/BUBR1 underlying mutagenic NHEJ in an ATM-dependent manner, aside from the canonical activity of BUB1B/BUBR1 on the G2/M checkpoint, and offer novel clues to overcome CRT resistance.

    DOI: 10.1038/s41388-021-02021-y

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  • Crystal structure of higher plant heme oxygenase-1 and its mechanism of interaction with ferredoxin Reviewed

    Rei Tohda, Hideaki Tanaka, Risa Mutoh, Xuhong Zhang, Young-Ho Lee, Tsuyoshi Konuma, Takahisa Ikegami, Catharina T. Migita, Genji Kurisu

    Journal of Biological Chemistry   296   100217   2021.1

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

    DOI: 10.1074/jbc.ra120.016271

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  • The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata Reviewed

    Kenichi Kamata, Kenji Mizutani, Katsuya Takahashi, Roberta Marchetti, Alba Silipo, Christine Addy, Sam-Yong Park, Yuki Fujii, Hideaki Fujita, Tsuyoshi Konuma, Takahisa Ikegami, Yasuhiro Ozeki, Jeremy R. H. Tame

    Scientific Reports   10 ( 1 )   2020.12

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

    Abstract

    SeviL is a recently isolated lectin found to bind to the linear saccharides of the ganglioside GM1b (Neu5Ac$$\alpha$$(2-3)Gal$$\beta$$(1-3)GalNAc$$\beta$$(1-4)Gal$$\beta$$(1-4)Glc) and its precursor, asialo-GM1 (Gal$$\beta$$(1-3)GalNAc$$\beta$$(1-4)Gal$$\beta$$(1-4)Glc). The crystal structures of recombinant SeviL have been determined in the presence and absence of ligand. The protein belongs to the$$\beta$$-trefoil family, but shows only weak sequence similarity to known structures. SeviL forms a dimer in solution, with one binding site per subunit, close to the subunit interface. Molecular details of glycan recognition by SeviL in solution were analysed by ligand- and protein-based NMR techniques as well as ligand binding assays. SeviL shows no interaction with GM1 due to steric hindrance with the sialic acid branch that is absent from GM1b. This unusual specificity makes SeviL of great interest for the detection and control of certain cancer cells, and cells of the immune system, that display asialo-GM1.

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  • A novel missense variant in RBM10 can cause a mild form of TARP syndrome with developmental delay and dysmorphic features. Reviewed International journal

    #Eri Imagawa, #Tsuyoshi Konuma, #Emalyn E Cork, George A Diaz, Kimihiko Oishi (#Co-first author)

    Clinical Genetics   98 ( 6 )   606 - 612   2020.8

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    RBM10, is an RNA binding protein that is important for development by regulating the expression of multiple genes. RBM10 is on the X chromosome, and nonsense and frameshift RBM10 variants cause TARP syndrome in males. In a 4-year-old male, we identified a novel maternally inherited missense RBM10 variant in the RRM2 RNA binding domain, c.965C>T, p.Pro322Leu. His clinical features included intellectual disability, developmental delay, growth restriction, hypotonia, and craniofacial malformations. These features were much milder than those described in previously reported cases of TARP syndrome. By in vitro assays, we found that the mutant p.Pro322Leu RBM10 protein retained its specific RNA binding capacity, while gaining a low-affinity nonspecific RNA binding. It was normally localized to the nucleus, but its expression level was significantly reduced with a significantly short half-life. These results indicated that the p.Pro322Leu missense variant causes a developmental disorder in humans through a unique loss-of-function mechanism.

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  • Screening of protein-ligand interactions under crude conditions by native mass spectrometry Reviewed

    Kotaro Takano, Shunsuke Arai, Seiji Sakamoto, Hiroshi Ushijima, Takahisa Ikegami, Kazumi Saikusa, Tsuyoshi Konuma, Itaru Hamachi, Satoko Akashi

    Analytical and Bioanalytical Chemistry   412 ( 17 )   4037 - 4043   2020.7

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    DOI: 10.1007/s00216-020-02649-x

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  • Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer Reviewed

    Schuller JM, Birrell JA, Tanaka H, Konuma T, Wulfhorst H, Cox N, Schuller SK, Thiemann J, Lubitz W, Sétif P, Ikegami T, Engel BD, Kurisu G, Nowaczyk MM

    Science   363 ( 6424 )   257 - 260   2019

  • Analysis of artifacts caused by pulse imperfections in CPMG pulse trains in NMR relaxation dispersion experiments Reviewed

    Konuma T, Nagadoi A, Kurita J, Ikegami T

    Magnetochemistry   4 ( 3 )   33 - 50   2018

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  • A new quinolone BRD4 inhibitor targets a distinct latent HIV-1 reservoir for re-activation from other ‘shock’ drugs Reviewed

    Abner E, Stoszko M, Zeng L, Chen HC, Izquierdo-Bouldstridge A, Konuma T, Zorita E, Fanunza E, Zhang Q, Mahmoundi T, Zhou MM, Filion G. J, Jordan A

    J. Virology   92 ( 10 )   e02056   2018

  • Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4 Reviewed

    Tsuyoshi Konuma, Di Yu, Chengcheng Zhao, Ying Ju, Rajal Sharma, Chunyan Ren, Qiang Zhang, Ming-Ming Zhou, Lei Zeng

    Scientific Reports   7 ( 1 )   2017.11

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    Abstract

    Jumonji domain-containing protein 6 (JMJD6) is a member of the Jumonji C family of Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. It possesses unique bi-functional oxygenase activities, acting as both an arginine demethylase and a lysyl-hydroxylase. JMJD6 has been reported to be over-expressed in oral, breast, lung, and colon cancers and plays important roles in regulation of transcription through interactions with transcription regulator BRD4, histones, U2AF65, Luc7L3, and SRSF11. Here, we report a structural mechanism revealed by NMR of JMJD6 recognition by the extraterminal (ET) domain of BRD4 in that a JMJD6 peptide (Lys84-Asn96) adapts an α-helix when bound to the ET domain. This intermolecular recognition is established through JMJD6 interactions with the conserved hydrophobic core of the ET domain, and reinforced by electrostatic interactions of JMJD6 with residues in the inter-helical α1-α2 loop of the ET domain. Notably, this mode of ligand recognition is different from that of ET domain recognition of NSD3, LANA of herpesvirus, and integrase of MLV, which involves formation of an intermolecular amphipathic two- or three- strand antiparallel β sheet. Furthermore, we demonstrate that the association between the BRD4 ET domain and JMJD6 likely requires a protein conformational change induced by single-stranded RNA binding.

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  • Non-Native alpha-Helices in the Initial Folding Intermediate Facilitate the Ordered Assembly of the beta-Barrel in beta-Lactoglobulin Reviewed

    Kazumasa Sakurai, Masanori Yagi, Tsuyoshi Konuma, Satoshi Takahashi, Chiaki Nishimura, Yuji Goto

    BIOCHEMISTRY   56 ( 36 )   4799 - 4807   2017.9

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    The roles of non-native alpha-helices frequently observed in the initial folding stage of beta-sheet proteins have been examined for many years. We herein investigated the residue-level structures of several mutants of bovine beta-lactoglobulin (beta LG) in quenched-flow pH-pulse labeling experiments. beta LG assumes a collapsed intermediate with a non-native alpha-helical structure (I-s) in the early stage of folding, although its native form is predominantly composed of beta structures. The protection profile in I-0 of pseudo-wild type (WT*) beta LG was found to deviate from the pattern of the "average area buried upon folding" (AABUF). In particular, the level of protection at "the region of strand A, at which non-native alpha-helices form in the I-0 state, was significantly low compared to AABUF. G17E, the mutant with an increased helical propensity, showed a similar protection pattern. In contrast, the protection pattern for I-0 of E44L, the mutant with an increased beta-sheet propensity, was distinct from that of WT'* and resembled the AABUF pattern. Transverse relaxation measurements demonstrated that the positions of the residual structures in the unfolded states of these mutants were consistent with those of the protected residues in the respective I-0 states. On the basis of the slower conversion of I-0 to the native state for E44L to that for WT*, non-native alpha-helices facilitate the ordered assembly of the beta-barrel by preventing interactions that trap folding.

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  • Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation Reviewed

    Ka Lung Cheung, Fan Zhang, Anbalagan Jaganathan, Rajal Sharma, Qiang Zhang, Tsuyoshi Konuma, Tong Shen, June-Yong Lee, Chunyan Ren, Chih-Hung Chen, Geming Lu, Matthew R. Olson, Weijia Zhang, Mark H. Kaplan, Dan R. Littman, Martin J. Walsh, Huabao Xiong, Lei Zeng, Ming-Ming Zhou

    Molecular Cell   65 ( 6 )   1068 - 1080.e5   2017.3

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    DOI: 10.1016/j.molcel.2016.12.022

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  • Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain Reviewed

    Qiang Zhang, Lei Zeng, Chengcheng Zhao, Ying Ju, Tsuyoshi Konuma, Ming-Ming Zhou

    STRUCTURE   24 ( 9 )   1606 - 1612   2016.9

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    Histone lysine acylations play an important role in the regulation of gene transcription in chromatin. Unlike histone acetyl-lysine, molecular recognition of a recently identified crotonyl-lysine mark is much less understood. Here, we report that the YEATS domain of AF9 preferentially binds crotonyl-lysine over acetyl-lysine in histone H3. Nuclear magnetic resonance structural analysis reveals that crotonyl-lysine of histone H3 lysine 18 is engulfed deep in an aromatic cage of the YEATS domain where the carbonyl oxygen of crotonyl-lysine forms a hydrogen bond with the backbone amide of protein residue Tyr78. The crotonyl-lysine, through its unique electron-rich double-bond side chain, engages pi-pi aromatic stacking and extended hydrophobic/aromatic interactions with the YEATS domain compared with acetyl-lysine. Our mutational analysis confirmed key protein residues Phe59 and Tyr78 for crotonyllysine recognition. Importantly, our findings present a new structural mechanism of protein-protein interactions mediated by histone lysine crotonylation, and show how the cells interpret acyl-lysine marks in different biological contexts.

    DOI: 10.1016/j.str.2016.05.023

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  • Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH Reviewed

    Masahiko Okuda, Junichi Higo, Tadashi Komatsu, Tsuyoshi Konuma, Kenji Sugase, Yoshifumi Nishimura

    Biophysical Journal   111 ( 5 )   950 - 962   2016.9

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    DOI: 10.1016/j.bpj.2016.07.042

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  • Quantitative analysis of protein–ligand interactions by NMR Reviewed

    Ayako Furukawa, Tsuyoshi Konuma, Saeko Yanaka, Kenji Sugase

    Progress in Nuclear Magnetic Resonance Spectroscopy   96   47 - 57   2016.8

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    DOI: 10.1016/j.pnmrs.2016.02.002

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  • Structural Mechanism of Transcriptional Regulator NSD3 Recognition by the ET Domain of BRD4 Reviewed

    Qiang Zhang, Lei Zeng, Chen Shen, Ying Ju, Tsuyoshi Konuma, Chengcheng Zhao, Christopher R. Vakoc, Ming-Ming Zhou

    Structure   24 ( 7 )   1201 - 1208   2016.7

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    DOI: 10.1016/j.str.2016.04.019

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  • Use of glass capillaries to suppress thermal convection in NMR tubes in diffusion measurements Reviewed

    Takashi Iwashita, Tsuyoshi Konuma, Erisa Harada, Shoko Mori, Kenji Sugase

    Magnetic Resonance in Chemistry   54 ( 9 )   729 - 733   2016.4

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    DOI: 10.1002/mrc.4437

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  • Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy Reviewed

    Tsuyoshi Konuma, Erisa Harada, Kenji Sugase

    Journal of Biomolecular NMR   63 ( 4 )   367 - 373   2015.10

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    DOI: 10.1007/s10858-015-9995-7

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  • Highly Collapsed Conformation of the Initial Folding Intermediates of β-Lactoglobulin with Non-Native α-Helix Reviewed

    Tsuyoshi Konuma, Kazumasa Sakurai, Masanori Yagi, Yuji Goto, Tetsuro Fujisawa, Satoshi Takahashi

    Journal of Molecular Biology   427 ( 19 )   3158 - 3165   2015.9

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    DOI: 10.1016/j.jmb.2015.07.018

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  • Solution Structure of the Ubiquitin-associated (UBA) Domain of Human Autophagy Receptor NBR1 and Its Interaction with Ubiquitin and Polyubiquitin Reviewed

    Erik Walinda, Daichi Morimoto, Kenji Sugase, Tsuyoshi Konuma, Hidehito Tochio, Masahiro Shirakawa

    Journal of Biological Chemistry   289 ( 20 )   13890 - 13902   2014.5

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    DOI: 10.1074/jbc.m114.555441

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  • Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE Reviewed

    Kenji Sugase, Tsuyoshi Konuma, Jonathan C. Lansing, Peter E. Wright

    Journal of Biomolecular NMR   56 ( 3 )   275 - 283   2013.6

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    DOI: 10.1007/s10858-013-9747-5

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  • Principal component analysis of chemical shift perturbation data of a multiple-ligand-binding system for elucidation of respective binding mechanism Reviewed

    Tsuyoshi Konuma, Young-Ho Lee, Yuji Goto, Kazumasa Sakurai

    Proteins: Structure, Function, and Bioinformatics   81 ( 1 )   107 - 118   2012.9

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    DOI: 10.1002/prot.24166

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  • The Monomer–Seed Interaction Mechanism in the Formation of the β2-Microglobulin Amyloid Fibril Clarified by Solution NMR Techniques Reviewed

    Kotaro Yanagi, Kazumasa Sakurai, Yuichi Yoshimura, Tsuyoshi Konuma, Young-Ho Lee, Kenji Sugase, Takahisa Ikegami, Hironobu Naiki, Yuji Goto

    Journal of Molecular Biology   422 ( 3 )   390 - 402   2012.9

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    DOI: 10.1016/j.jmb.2012.05.034

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  • Boosting Protein Dynamics Studies Using Quantitative Nonuniform Sampling NMR Spectroscopy Reviewed

    Yoh Matsuki, Tsuyoshi Konuma, Toshimichi Fujiwara, Kenji Sugase

    The Journal of Physical Chemistry B   115 ( 46 )   13740 - 13745   2011.11

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    DOI: 10.1021/jp2081116

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  • Structure and stability of Gyuba, a β-lactoglobulin chimera Reviewed

    Hideaki Ohtomo, Tsuyoshi Konuma, Hiroko Utsunoiya, Hideaki Tsuge, Masamichi Ikeguchi

    Protein Science   20 ( 11 )   1867 - 1875   2011.9

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    DOI: 10.1002/pro.720

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  • A Circumventing Role for the Non-Native Intermediate in the Folding of beta-Lactoglobulin Reviewed

    Kazumasa Sakurai, Shunsuke Fujioka, Tsuyoshi Konuma, Masanori Yagi, Yuji Goto

    BIOCHEMISTRY   50 ( 29 )   6498 - 6507   2011.7

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    Folding experiments have suggested that some proteins have kinetic intermediates with a non-native structure. A simple G (o) over bar model does not explain such non-native intermediates. Therefore, the folding energy landscape of proteins with non-native intermediates should have characteristic properties. To identify such properties, we investigated the folding of bovine beta-lactoglobulin (beta LG). This protein has an intermediate with a non-native alpha-helical structure, although its native form is predominantly composed of beta-structure. In this study, we prepared mutants whose a-helical and beta-sheet propensities are modified and observed their folding using a stopped-flow circular dichroism apparatus. One interesting finding was that E44L, whose beta-sheet propensity was increased, showed a folding intermediate with an amount of beta-structure similar to that of the wild type, though its folding took longer. Thus, the intermediate seems to be a trapped intermediate. The high a-helical propensity of the wild-type sequence likely causes the folding pathway to circumvent such time-consuming intermediates. We propose that the role of the non-native intermediate is to control the pathway at the beginning of the folding reaction.

    DOI: 10.1021/bi200241a

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  • Time-Resolved Small-Angle X-ray Scattering Study of the Folding Dynamics of Barnase Reviewed

    Tsuyoshi Konuma, Tetsunari Kimura, Shuzo Matsumoto, Yuji Goto, Tetsuro Fujisawa, Alan R. Fersht, Satoshi Takahashi

    Journal of Molecular Biology   405 ( 5 )   1284 - 1294   2011.2

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    DOI: 10.1016/j.jmb.2010.11.052

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  • Kinetic Intermediates of β2-Microglobulin Fibril Elongation Probed by Pulse-Labeling H/D Exchange Combined with NMR Analysis Reviewed

    Tsuyoshi Konuma, Eri Chatani, Masanori Yagi, Kazumasa Sakurai, Takahisa Ikegami, Hironobu Naiki, Yuji Goto

    Journal of Molecular Biology   405 ( 3 )   851 - 862   2011.1

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    DOI: 10.1016/j.jmb.2010.11.029

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  • Pre-Steady-State Kinetic Analysis of the Elongation of Amyloid Fibrils of β2-Microglobulin with Tryptophan Mutagenesis Reviewed

    Eri Chatani, Reina Ohnishi, Tsuyoshi Konuma, Kazumasa Sakurai, Hironobu Naiki, Yuji Goto

    Journal of Molecular Biology   400 ( 5 )   1057 - 1066   2010.7

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    DOI: 10.1016/j.jmb.2010.05.071

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  • Structural dynamics and folding of β-lactoglobulin probed by heteronuclear NMR Reviewed

    Kazumasa Sakurai, Tsuyoshi Konuma, Masanori Yagi, Yuji Goto

    Biochimica et Biophysica Acta (BBA) - General Subjects   1790 ( 6 )   527 - 537   2009.6

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    DOI: 10.1016/j.bbagen.2009.04.003

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  • Promiscuous Binding of Ligands by β-Lactoglobulin Involves Hydrophobic Interactions and Plasticity Reviewed

    Tsuyoshi Konuma, Kazumasa Sakurai, Yuji Goto

    Journal of Molecular Biology   368 ( 1 )   209 - 218   2007.4

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    DOI: 10.1016/j.jmb.2007.01.077

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MISC

  • ヒストンH3リジン27クロトニル化はクロマチンにおける遺伝子転写抑制を媒介する

    小沼 剛

    生物物理   64 ( 2 )   94 - 96   2024.4

  • The compactification of intrinsically disordered proteins from hyperthermophilic archaeon under high temperatures.

    小田隆, 井上倫太郎, 富永大輝, 中川洋, 守島健, 岩瀬裕希, 小沼剛, 池上貴久, 石野園子, 石野良純, 奥隆之, 佐藤衛, 佐藤衛, 杉山正明

    KURNS-EKR (Web)   ( 19 )   2024

  • FGFR muts/fusion-CD274/PD-L1のマルチオミクス解析 最適化医療応用の可能性(The Association of FGFR Genetic Alternation with CD274/PD-L1 Profiling in Bladder Cancer)

    小村 和正, 吉見 昭秀, 谷口 高平, 小沼 剛, 稲元 輝生, 廣瀬 善信, 東 治人

    日本癌学会総会記事   81回   MS5 - 3   2022.9

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  • 光合成型複合体Ⅰがフェレドキシン依存的に循環型電子伝達を行う構造基盤

    栗栖 源嗣, 田中 秀明, 小沼 剛, 池上 貴久, Schuller Jan M., Nowaczyk Marc M.

    光合成研究 = News letter   29 ( 3 )   242 - 246   2019.12

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  • Structural Basis for the Ferredoxin-dependency of Photosynthetic Complex I

    KURISU Genji, TANAKA Hideaki, SCHULLER Jan M., KONUMA Tsuyoshi, IKEGAMI Takahisa, NOWACZYK Marc M.

    生物物理(Web)   59 ( Supplement 1-2 )   2019

  • アミロイド線維伸長における中間体構造の捕捉と構造解析

    CHATANI Eri, 小沼 剛, 後藤 祐児

    生物物理   52 ( 3 )   148 - 149   2012.5

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    DOI: 10.2142/biophys.52.148

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Awards

  • Poster award, FASEB Science Research Conference, Biology of Acetylation in Health and Disease

    2024.8   FASEB Science Research Conference, Biology of Acetylation in Health and Disease  

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  • JMSA Scholarship (Nippon Life)

    2016.5   Japanese Medical Society of America  

    小沼 剛

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  • 第51回NMR討論会 若手ポスター賞II

    2012.11   日本核磁気共鳴学会  

    小沼 剛

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  • 若手研究者渡航費助成金

    2012.8   日本核磁気共鳴学会  

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  • International Workshop of Biofunctional Chemistry for Young Scientists Presentation Award

    2009.7   大阪大学  

    Tsuyoshi Konuma

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Research Projects

  • 遺伝子型に立脚した膵がん個別化医療開発基盤の創出

    Grant number:23K27450  2023.4 - 2027.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    園下 将大, 五十嵐 学, 小沼 剛, 市川 聡, 合田 圭介

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  • Drug development for COVID-19 targeting BRD4

    Grant number:23K05720  2023.4 - 2026.3

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

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  • Developing a novel therapy for pancreatic cancer targeting the riboflavin pathway

    Grant number:20K07558  2020.4 - 2023.3

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

    Ooshio Takako

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    To develop a novel therapy for pancreatic ductal adenocarcinoma (PDAC), we established the first animal model, a 4-hit fly, that mimics the four-gene mutations observed in PDAC. Most of these flies died before reaching adulthood due to the abnormal proliferation of transformed cells. To clarify the signaling pathways involved in their decreased viability, we performed genetic screening with the 4-hit fly. As a result, we revealed that riboflavin (RF) kinase and MEK promote their malignant traits. RF kinase is a rate-limiting enzyme in RF pathway and unclear their roles in PDAC. Therefore, we conducted chemical testing and elucidated that a combination of RF pathway and MEK inhibitors markedly increased the viability of the 4-hit fly. Furthermore, the combination significantly suppressed tumor expansion in mice orthotopically implanted with human PDAC cells. These results indicate that the combination is a novel therapeutic candidate for PDAC.

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  • 膵臓がんの頑健性の分子基盤の解明とその破壊による新規治療法の確立

    Grant number:20H03524  2020.4 - 2023.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    園下 将大, 藤井 清永, 小沼 剛, 市川 聡, 大塩 貴子

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

    がんは日本人の死因の第一位で、対策が急務となっている。種々のがんの中でも特に治療の選択肢が少なく、患者の予後が最も悪いものが膵がんである。哺乳類実験系で膵がんの本態の解明や治療標的候補の同定が進められてきたものの、それらの知識はいまだ断片的で、詳細な発生機序や、他のがん種に比べて治療に対する頑健性が極めて高い理由は解明されていない。
    そこで本研究では、治療に対する膵がんの頑健性の成立機序を解明し、その知見に基づいて新規膵がん治療戦略を創出する。特に本研究は、脆弱性を人為的に誘導する新しい方法論の提唱を目指す。本研究の遂行により、膵がんの治療応答性の詳細な分子機序を明らかにして新規膵がん治療法を確立し、膵がんの本態解明と福祉向上の両面に貢献することを目指す。
    我々はこれまでに、膵がん患者の中で最も予後不良の患者群が有する4遺伝子変異(がん遺伝子KRASの活性化、がん抑制遺伝子群TP53やCDKN2A、SMAD4の不活性化)を模倣したハエを作出することに成功している。そして、このハエを使用してキナーゼの網羅的解析を実施し、膵がんの新規治療標的となるキナーゼ群を同定した。我々はこれらを阻害する化合物も見出したが、臨床と同様、効果は限定的だった。
    そこで我々は本年度、この頑健性に関わるシグナル経路の同定に取り組んだ。すなわち、この化合物を上記ハエに投与した状態で網羅的遺伝学スクリーニングを実施した。その結果、阻害によりこの化合物の抗腫瘍効果を向上させるキナーゼが存在することを突き止めた。この結果は、このキナーゼが当該化合物に対する膵がんの頑健性の成立に重要な役割を果たしていることを示唆している。

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  • タンデムドメイン蛋白質によるヒストン認識機構の構造基盤

    2014.9 - 2016.8

    日本学術振興会  海外特別研究員 

    小沼 剛

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    Authorship:Principal investigator  Grant type:Competitive

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  • 動的構造解析によるOct3/4の多様なDNA配列認識機構の解明

    2013.4 - 2014.7

    日本学術振興会  若手研究(B) 

    小沼 剛

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    Authorship:Principal investigator  Grant type:Competitive

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  • 溶液NMRによるアミロイド線維形成機構の解明

    Grant number:08J06417  2008.4 - 2010.3

    日本学術振興会  特別研究員  特別研究員奨励費

    小沼 剛

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    Authorship:Principal investigator  Grant type:Competitive

    アミロイド線維は蛋白質が会合して形成する超分子複合体である。このアミロイド線維は様々なアミロイド病に関与している。しかしながらアミロイド線維の構造、形成機構そして毒性など未だ情報が少ない。アミロイド線維の研究はアミロイド病の予防・治療法の確立のために重要である。
    本研究では、透析アミロイドーシスの原因蛋白質であるβ2ミクログロブリン(β2m)アミロイド線維形成に着目した。そしてβ2mのアミロイド線維形成についてアミノ酸残基レベルで解明、具体的には線維末端に結合したβ2mの中間体構造の情報を得ることを目的とした。そこで本研究では、原子レベルの情報が得られるNMRを用いる。しかし、アミロイド線維は高分子量の超分子複合体であるため、NMRで直接観測することは困難である。そこでアミロイド線維をジメチルスルホキシドに溶解し、モノマーに解離することでNMR測定が可能となる。ここでアミロイド線維形成途中に水素/重水素(H/D)交換反応を行い、HSQCスペクトルを測定した。そして、得られたスペクトルのピーク強度から、残基ごとのH/D交換度合いを調べ、比較した。その結果、アミロイド線維形成の初期段階で完全に変性した中間体を形成することが明らかとなった。以上の結果からβ2mのアミロイド線維形成モデルを提案した。
    これはアミロイド線維形成中間体についての情報を初めての与えた結果である。また本研究の実験手法は、アミロイド線維を形成する他の蛋白質の研究にも応用されることが期待できる。

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