研究者詳細 - J.R.H. Tame

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写真a

テイム　ジェレミー　ロビン

J.R.H. Tame

所属

生命医科学研究科生命医科学専攻教授
理学部理学科

ホームページ

http://www.tsurumi.yokohama-cu.ac.jp/pdl

プロフィール

私の研究はX線結晶学および他の生物物理学的技術によるたんぱく質構造の研究に関係する。私のグループは、金属のナノドットを作るなどのさまざまなバイオテクノロジー的用途のための人工タンパク質を設計しています。
タンパク質の熱力学とタンパク質-リガンドの親和性を制御する原因に長年関心を持もっている。

外部リンク

学位

Ph.D. （ Medical Research Council分子生物学研究所）

研究キーワード

人工タンパク質の設計
X線構造解析
タンパク質
MOLECULAR BIOLOGY
創薬
生物物理
BIOPHYSICS

研究分野

ライフサイエンス / 分子生物学
ライフサイエンス / 生物物理学

経歴

横浜市立大学国際総合科学部生命医科学コース生命医科学研究科生命医科学専攻教授

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所属学協会

BRITISH CRYSTALLOGRAPHIC ASSOCIATION

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委員歴

BRITISH CRYSTALLOGRAPHIC ASSOCIATION BCA

1991年

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団体区分：学協会

BRITISH CRYSTALLOGRAPHIC ASSOCIATION

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論文

Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens. 国際誌

Daisuke Adachi, Naito Ishimoto, Kenji Mizutani, Katsuya Takahashi, Reiji Kubota, Haruka Kawabata, Sam-Yong Park, Laurens Vandebroek, Arnout R D Voet, Masao Yamada, Yasuhiro Ozeki, Yuki Fujii, Hideaki Fujita, Jeremy R H Tame, Kenichi Kamata

Glycobiology 2025年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, investigations revealed the presence of various toxins, including a lectin (PPL) that apparently survives cooking and enters the bloodstream via the stomach. We have cloned PPL and solved its structure by X-ray crystallography and cryo-EM. We report the sugar binding properties of this β-trefoil lectin, which has a novel hexameric structure.

DOI： 10.1093/glycob/cwaf082

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Structural insights into Influenza A virus RNA polymerase PB1 binding to nuclear import host factor RanBP5

Tomomi Uchikubo-Kamo, Naito Ishimoto, Haruka Umezawa, Mikako Hirohama, Maasa Ono, Haruka Kawabata, Kenichi Kamata, Mio Ohki, Hisashi Yoshida, Jae-Hyun Park, Jeremy R.H. Tame, Atsushi Kawaguchi, Sam-Yong Park

Biochemical and Biophysical Research Communications 150952 - 150952 2024年11月

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掲載種別：研究論文（学術雑誌）出版者・発行元：Elsevier BV

DOI： 10.1016/j.bbrc.2024.150952

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Structural basis for hepatitis B virus restriction by a viral receptor homologue. 国際誌

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年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

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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The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM. 国際誌

Katsuya Takahashi, Yongchan Lee, Angela Fago, Naim M Bautista, Jay F Storz, Akihiro Kawamoto, Genji Kurisu, Tomohiro Nishizawa, Jeremy R H Tame

Nature communications 15 ( 1 ) 6505 - 6505 2024年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.

DOI： 10.1038/s41467-024-49947-x

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Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2. 国際誌

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年11月

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記述言語：英語掲載種別：研究論文（学術雑誌）

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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Structural basis of CXC chemokine receptor 1 ligand binding and activation. 国際誌

Naito Ishimoto, Jae-Hyun Park, Kouki Kawakami, Michiko Tajiri, Kenji Mizutani, Satoko Akashi, Jeremy R H Tame, Asuka Inoue, Sam-Yong Park

Nature communications 14 ( 1 ) 4107 - 4107 2023年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

Neutrophil granulocytes play key roles in innate immunity and shaping adaptive immune responses. They are attracted by chemokines to sites of infection and tissue damage, where they kill and phagocytose bacteria. The chemokine CXCL8 (also known as interleukin-8, abbreviated IL-8) and its G-protein-coupled receptors CXCR1 and CXCR2 are crucial elements in this process, and also the development of many cancers. These GPCRs have therefore been the target of many drug development campaigns and structural studies. Here, we solve the structure of CXCR1 complexed with CXCL8 and cognate G-proteins using cryo-EM, showing the detailed interactions between the receptor, the chemokine and Gαi protein. Unlike the closely related CXCR2, CXCR1 strongly prefers to bind CXCL8 in its monomeric form. The model shows that steric clashes would form between dimeric CXCL8 and extracellular loop 2 (ECL2) of CXCR1. Consistently, transplanting ECL2 of CXCR2 onto CXCR1 abolishes the selectivity for the monomeric chemokine. Our model and functional analysis of various CXCR1 mutants will assist efforts in structure-based drug design targeting specific CXC chemokine receptor subtypes.

DOI： 10.1038/s41467-023-39799-2

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Structure of the human galanin receptor 2 bound to galanin and Gq reveals the basis of ligand specificity and how binding affects the G-protein interface. 国際誌

Yunseok Heo, Naito Ishimoto, Ye-Eun Jeon, Ji-Hye Yun, Mio Ohki, Yuki Anraku, Mina Sasaki, Shunsuke Kita, Hideo Fukuhara, Tatsuya Ikuta, Kouki Kawakami, Asuka Inoue, Katsumi Maenaka, Jeremy R H Tame, Weontae Lee, Sam-Yong Park

PLoS biology 20 ( 8 ) e3001714 2022年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

Galanin is a neuropeptide expressed in the central and peripheral nervous systems, where it regulates various processes including neuroendocrine release, cognition, and nerve regeneration. Three G-protein coupled receptors (GPCRs) for galanin have been discovered, which is the focus of efforts to treat diseases including Alzheimer's disease, anxiety, and addiction. To understand the basis of the ligand preferences of the receptors and to assist structure-based drug design, we used cryo-electron microscopy (cryo-EM) to solve the molecular structure of GALR2 bound to galanin and a cognate heterotrimeric G-protein, providing a molecular view of the neuropeptide binding site. Mutant proteins were assayed to help reveal the basis of ligand specificity, and structural comparison between the activated GALR2 and inactive hβ2AR was used to relate galanin binding to the movements of transmembrane (TM) helices and the G-protein interface.

DOI： 10.1371/journal.pbio.3001714

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Structural insights into the HBV receptor and bile acid transporter NTCP. 国際誌

Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi Nomura, So Iwata, Koichi Watashi, Jeremy R H Tame, Tomohiro Nishizawa, Weontae Lee, Sam-Yong Park

Nature 2022年5月

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記述言語：英語掲載種別：研究論文（学術雑誌）

Roughly 250 million people are infected with hepatitis B virus (HBV) worldwide1, and perhaps 15 million also carry the satellite virus HDV, which confers even greater risk of severe liver disease2. Almost ten years ago the HBV receptor was identified as NTCP (sodium taurocholate co-transporting polypeptide), which interacts directly with the first 48 amino acid residues of the N-myristoylated N-terminal preS1 domain of the viral large (L) protein3. Despite the pressing need for therapeutic agents to counter HBV, the structure of NTCP remains unsolved. This 349-residue protein is closely related to human apical sodium-dependent bile acid transporter (ASBT), another member of the solute carrier family SLC10. Crystal structures have been reported of similar bile acid transporters from bacteria4, 5, and these models with ten transmembrane helices are believed to resemble strongly both NTCP and ASBT. Using cryo-electron microscopy we have solved the structure of NTCP bound to an antibody, clearly showing the transporter has no equivalent to the first transmembrane helix of other SLC10 models, leaving the N-terminus exposed on the extracellular face. Comparison of the different structures indicates a common mechanism of bile acid transport, but the NTCP structure also displays a pocket formed by residues known to interact with preS1, presenting new and enticing opportunities for structure-based drug design.

DOI： 10.1038/s41586-022-04857-0

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Reverse Engineering Analysis of the High-Temperature Reversible Oligomerization and Amyloidogenicity of PSD95-PDZ3. 査読国際誌

Sawaros Onchaiya, Tomonori Saotome, Kenji Mizutani, Jose C Martinez, Jeremy R H Tame, Shun-Ichi Kidokoro, Yutaka Kuroda

Molecules (Basel, Switzerland) 27 ( 9 ) 2022年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

PSD95-PDZ3, the third PDZ domain of the post-synaptic density-95 protein (MW 11 kDa), undergoes a peculiar three-state thermal denaturation (N ↔ In&nbsp;↔ D) and is amyloidogenic. PSD95-PDZ3 in the intermediate state (I) is reversibly oligomerized (RO: Reversible oligomerization). We previously reported a point mutation (F340A) that inhibits both ROs and amyloidogenesis and constructed the PDZ3-F340A variant. Here, we "reverse engineered" PDZ3-F340A for inducing high-temperature RO and amyloidogenesis. We produced three variants (R309L, E310L, and N326L), where we individually mutated hydrophilic residues exposed at the surface of the monomeric PDZ3-F340A but buried in the tetrameric crystal structure to a hydrophobic leucine. Differential scanning calorimetry indicated that two of the designed variants (PDZ3-F340A/R309L and E310L) denatured according to the two-state model. On the other hand, PDZ3-F340A/N326L denatured according to a three-state model and produced high-temperature ROs. The secondary structures of PDZ3-F340A/N326L and PDZ3-wt in the RO state were unfolded according to circular dichroism and differential scanning calorimetry. Furthermore, PDZ3-F340A/N326L was amyloidogenic as assessed by Thioflavin T fluorescence. Altogether, these results demonstrate that a single amino acid mutation can trigger the formation of high-temperature RO and concurrent amyloidogenesis.

DOI： 10.3390/molecules27092813

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Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

Ji-Hye Yun, Xuanxuan Li, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia A. Zatsepin, Mio Ohki, Jeremy R.H. Tame, Sam-Yong Park, John C.H. Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu

Proceedings of the National Academy of Sciences of the United States of America 118 ( 13 ) 2021年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：National Academy of Sciences

DOI： 10.1073/pnas.2020486118

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The symmetric designer protein Pizza as a scaffold for metal coordination. 国際誌

Jeroen P M Vrancken, Hiroki Noguchi, Kam Y J Zhang, Jeremy R H Tame, Arnout R D Voet

Proteins 2021年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）

Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.

DOI： 10.1002/prot.26072

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Shape and Size Complementarity-Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters

Laurens Vandebroek, Hiroki Noguchi, Kenichi Kamata, Jeremy R. H. Tame, Luc Van Meervelt, Tatjana N. Parac-Vogt, Arnout R. D. Voet

Crystal Growth & Design 21 ( 2 ) 1307 - 1313 2021年2月

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掲載種別：研究論文（学術雑誌）出版者・発行元：American Chemical Society (ACS)

DOI： 10.1021/acs.cgd.0c01571

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Structural plasticity of a designer protein sheds light on β-propeller protein evolution. 国際誌

Bram Mylemans, Ina Laier, Kenichi Kamata, Satoko Akashi, Hiroki Noguchi, Jeremy R H Tame, Arnout R D Voet

The FEBS journal 288 ( 2 ) 530 - 545 2021年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）

β-propeller proteins are common in nature, where they are observed to adopt 4- to 10-fold internal rotational pseudo-symmetry. This size diversity can be explained by the evolutionary process of gene duplication and fusion. In this study, we investigated a distorted β-propeller protein, an apparent intermediate between two symmetries. From this template, we created a perfectly symmetric 9-bladed β-propeller named Cake, using computational design and ancestral sequence reconstruction. The designed repeat sequence was found to be capable of generating both 8-fold and 9-fold propellers which are highly stable. Cake variants with 2-10 identical copies of the repeat sequence were characterised by X-ray crystallography and in solution. They were found to be highly stable, and to self-assemble into 8- or 9-fold symmetrical propellers. These findings show that the β-propeller fold allows sufficient structural plasticity to permit a given blade to assemble different forms, a transition from even to odd changes in blade number, and provide a potential explanation for the wide diversity of repeat numbers observed in natural propeller proteins. DATABASE: Structural data are available in Protein Data Bank database under the accession numbers 6TJB, 6TJC, 6TJD, 6TJE, 6TJF, 6TJG, 6TJH and 6TJI.

DOI： 10.1111/febs.15347

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

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 ) 22102 - 22102 2020年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

SeviL is a recently isolated lectin found to bind to the linear saccharides of the ganglioside GM1b (Neu5Ac[Formula: see text](2-3)Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc) and its precursor, asialo-GM1 (Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc). The crystal structures of recombinant SeviL have been determined in the presence and absence of ligand. The protein belongs to the [Formula: see text]-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.

DOI： 10.1038/s41598-020-78926-7

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Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein

Bram Mylemans, Hiroki Noguchi, Els Deridder, Eveline Lescrinier, Jeremy R. H. Tame, Arnout R. D. Voet

Protein Science 29 ( 12 ) 2375 - 2386 2020年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Blackwell Publishing Ltd

DOI： 10.1002/pro.3961

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A GM1b/asialo-GM1 oligosaccharide-binding R-type lectin from purplish bifurcate mussels Mytilisepta virgata and its effect on MAP kinases. 国際誌

Yuki Fujii, Marco Gerdol, Sarkar M A Kawsar, Imtiaj Hasan, Francesca Spazzali, Tatsusada Yoshida, Yukiko Ogawa, Sultana Rajia, Kenichi Kamata, Yasuhiro Koide, Shigeki Sugawara, Masahiro Hosono, Jeremy R H Tame, Hideaki Fujita, Alberto Pallavicini, Yasuhiro Ozeki

The FEBS journal 287 ( 12 ) 2612 - 2630 2020年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

A 15-kDa lectin, termed SeviL, was isolated from Mytilisepta virgata (purplish bifurcate mussel). SeviL forms a noncovalent dimer that binds strongly to ganglio-series GM1b oligosaccharide (Neu5Acɑ2-3Galβ1-3GalNAcβ1-4Galβ1-4Glc) and its precursor, asialo-GM1 (Galβ1-3GalNAcβ1-4Galβ1-4Glc). SeviL also interacts weakly with the glycan moiety of SSEA-4 hexaose (Neu5Acα2-3Galβ1-3GalNAcβ1-3Galα1-4Galβ1-4Glc). A partial protein sequence of the lectin was determined by mass spectrometry, and the complete sequence was identified from transcriptomic analysis. SeviL, consisting of 129 amino acids, was classified as an R(icin B)-type lectin, based on the presence of the QxW motif characteristic of this fold. SeviL mRNA is highly expressed in gills and, in particular, mantle rim tissues. Orthologue sequences were identified in other species of the family Mytilidae, including Mytilus galloprovincialis, from which lectin MytiLec-1 was isolated and characterized in our previous studies. Thus, mytilid species contain lectins belonging to at least two distinct families (R-type lectins and mytilectins) that have a common β-trefoil fold structure but differing glycan-binding specificities. SeviL displayed notable cytotoxic (apoptotic) effects against various cultured cell lines (human breast, ovarian, and colonic cancer; dog kidney) that possess asialo-GM1 oligosaccharide at the cell surface. This cytotoxic effect was inhibited by the presence of anti-asialo-GM1 oligosaccharide antibodies. With HeLa ovarian cancer cells, SeviL showed dose- and time-dependent activation of kinase MKK3/6, p38 MAPK, and caspase-3/9. The transduction pathways activated by SeviL via the glycosphingolipid oligosaccharide were triggered apoptosis. DATABASE: Nucleotide sequence data have been deposited in the GenBank database under accession numbers MK434191, MK434192, MK434193, MK434194, MK434195, MK434196, MK434197, MK434198, MK434199, MK434200, and MK434201.

DOI： 10.1111/febs.15154

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Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family

Ji-Hye Yun, Mio Ohki, Jae-Hyun Park, Naito Ishimoto, Ayana Sato-Tomita, Wonbin Lee, Zeyu Jin, Jeremy R. H. Tame, Naoya Shibayama, Sam-Yong Park, Weontae Lee

Science Advances 6 ( 6 ) eaay2042 - eaay2042 2020年2月

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掲載種別：研究論文（学術雑誌）出版者・発行元：American Association for the Advancement of Science (AAAS)

A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium<italic>Nonlabens marinus</italic>, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys105, Ser60, Gln224, and Phe90—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.

DOI： 10.1126/sciadv.aay2042

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Molecular assemblies built with the artificial protein Pizza

Jeroen P.M. Vrancken, Jana Aupič, Christine Addy, Roman Jerala, Jeremy R.H. Tame, Arnout R.D. Voet

Journal of Structural Biology: X 4 2020年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Academic Press Inc.

DOI： 10.1016/j.yjsbx.2020.100027

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Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry

Laurens Vandebroek, Hiroki Noguchi, Kenichi Kamata, Jeremy R. H. Tame, Luc Van Meervelt, Tatjana N. Parac-Vogt, Arnout R. D. Voet

Chemical Communications 2020年

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掲載種別：研究論文（学術雑誌）

DOI： 10.1039/D0CC05071G

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Computational design of symmetrical eight-bladed β-propeller proteins. 国際誌

Hiroki Noguchi, Christine Addy, David Simoncini, Staf Wouters, Bram Mylemans, Luc Van Meervelt, Thomas Schiex, Kam Y J Zhang, Jeremy R H Tame, Arnout R D Voet

IUCrJ 6 ( Pt 1 ) 46 - 55 2019年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）

β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.

DOI： 10.1107/S205225251801480X

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The crystal structure and oligomeric form of Escherichia coli L,D-carboxypeptidase A 査読

Karen Meyer, Christine Addy, Satoko Akashi, David I. Roper, Jeremy R.H. Tame

Biochemical and Biophysical Research Communications 499 ( 3 ) 594 - 599 2018年5月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Elsevier B.V.

DOI： 10.1016/j.bbrc.2018.03.195

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Molecular basis of hemoglobin adaptation in the high-flying bar-headed goose 査読

Chandrasekhar Natarajan, Agnieszka Jendroszek, Amit Kumar, Roy E. Weber, Jeremy R. H. Tame, Angela Fago, Jay F. Storz

PLoS Genetics 14 ( 4 ) 2018年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Public Library of Science

DOI： 10.1371/journal.pgen.1007331

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Direct observation of conformational population shifts in crystalline human hemoglobin 査読

Naoya Shibayama, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park

JOURNAL OF BIOLOGICAL CHEMISTRY 292 ( 44 ) 18258 - 18269 2017年11月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M117.781146

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Molecular mechanism of photoactivation of a light-regulated adenylate cyclase 査読

Mio Ohki, Ayana Sato-Tomita, Shigeru Matsunaga, Mineo Iseki, Jeremy R. H. Tame, Naoya Shibayama, Sam-Yong Park

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 ( 32 ) 8562 - 8567 2017年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.1704391114

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Computational design of a symmetrical β-trefoil lectin with cancer cell binding activity 査読

Terada D, Voet ARD, Noguchi H, Kamata K, Ohki M, Addy C, Fujii Y, Yamamoto D, Ozeki Y, Tame JRH, Zhang KYJ

Sci Rep 7 5943 2017年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1038/s41598-017-06332-7

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Evolution-Inspired Computational Design of Symmetric Proteins. 国際誌

Arnout R D Voet, David Simoncini, Jeremy R H Tame, Kam Y J Zhang

Methods in molecular biology (Clifton, N.J.) 1529 309 - 322 2017年

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記述言語：英語掲載種別：研究論文（学術雑誌）

Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.

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Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types 査読

Daiki Terada, Fumihiro Kawai, Hiroki Noguchi, Satoru Unzai, Imtiaj Hasan, Yuki Fujii, Sam-Yong Park, Yasuhiro Ozeki, Jeremy R. H. Tame

SCIENTIFIC REPORTS 6 28344 2016年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1038/srep28344

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Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium 査読

Mio Ohki, Kanako Sugiyama, Fumihiro Kawai, Hitomi Tanaka, Yuuki Nihei, Satoru Unzai, Masumi Takebe, Shigeru Matsunaga, Shin-ichi Adachi, Naoya Shibayama, Zhiwen Zhou, Ryuta Koyama, Yuji Ikegaya, Tetsuo Takahashi, Jeremy R. H. Tame, Mineo Iseki, Sam-Yong Park

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113 ( 24 ) 6659 - 6664 2016年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.1517520113

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Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein 査読

Arnout R. D. Voet, Hiroki Noguchi, Christine Addy, Kam Y. J. Zhang, Jeremy R. H. Tame

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 54 ( 34 ) 9857 - 9860 2015年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1002/anie.201503575

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The crystal and solution structure of YdiE from Escherichia coli 査読

Kaoru Nishimura, Christine Addy, Rojan Shrestha, Arnout R. D. Voet, Kam Y. J. Zhang, Yutaka Ito, Jeremy R. H. Tame

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 71 ( Pt 7 ) 919 - 924 2015年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S2053230X15009140

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The structure and conformational switching of Rap1B 査読

Hiroki Noguchi, Takahisa Ikegami, Aritaka Nagadoi, Yuji O. Kamatari, Sam-Yong Park, Jeremy R. H. Tame, Satoru Unzai

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 462 ( 1 ) 46 - 51 2015年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.bbrc.2015.04.103

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Computational design of a self-assembling symmetrical β-propeller protein. 査読

Voet AR, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KY, Tame JRH

Proc Natl Acad Sci U S A. 111 ( 42 ) 15102 - 15107 2014年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.1412768111

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The Crystal Structure of the Active Domain of Anopheles Anti-platelet Protein, a Powerful Anti-coagulant, in Complex with an Antibody 査読

Kanako Sugiyama, Mitsuhiro Iyori, Asuka Sawaguchi, Satoko Akashi, Jeremy R. H. Tame, Sam-Yong Park, Shigeto Yoshida

JOURNAL OF BIOLOGICAL CHEMISTRY 289 ( 23 ) 16303 - 16312 2014年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M114.564526

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Capturing the Hemoglobin Allosteric Transition in a Single Crystal Form 査読

Naoya Shibayama, Kanako Sugiyama, Jeremy R. H. Tame, Sam-Yong Park

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136 ( 13 ) 5097 - 5105 2014年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/ja500380e

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The structure of the deacetylase domain of Escherichia coli PgaB, an enzyme required for biofilm formation: a circularly permuted member of the carbohydrate esterase 4 family 査読

Takashi Nishiyama, Hiroki Noguchi, Hisashi Yoshida, Sam-Yong Park, Jeremy R. H. Tame

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 69 ( Pt1 ) 44 - 51 2013年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S0907444912042059

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Influence of Structural Symmetry on Protein Dynamics 査読

Yasuhiro Matsunaga, Ryotaro Koike, Motonori Ota, Jeremy R. H. Tame, Akinori Kidera

PLOS ONE 7 ( 11 ) 2012年11月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1371/journal.pone.0050011

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Structures of haemoglobin from woolly mammoth in liganded and unliganded states 査読

Hiroki Noguchi, Kevin L. Campbell, Chien Ho, Satoru Unzai, Sam-Yong Park, Jeremy R. H. Tame

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 68 ( Pt11 ) 1441 - 1449 2012年11月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S0907444912029459

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Crystal Structures of Penicillin-Binding Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo and Cefotaxime-Bound Forms 査読

Hisashi Yoshida, Fumihiro Kawai, Eiji Obayashi, Satoko Akashi, David I. Roper, Jeremy R. H. Tame, Sam-Yong Park

JOURNAL OF MOLECULAR BIOLOGY 423 ( 3 ) 351 - 364 2012年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2012.07.012

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Structural Basis for Broad Detection of Genogroup II Noroviruses by a Monoclonal Antibody That Binds to a Site Occluded in the Viral Particle 査読

Grant S. Hansman, David W. Taylor, Jason S. McLellan, Thomas J. Smith, Ivelin Georgiev, Jeremy R. H. Tame, Sam-Yong Park, Makoto Yamazaki, Fumio Gondaira, Motohiro Miki, Kazuhiko Katayama, Kazuyoshi Murata, Peter D. Kwong

JOURNAL OF VIROLOGY 86 ( 7 ) 3635 - 3646 2012年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1128/JVI.06868-11

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Autotransporter protein secretion 査読

Jeremy R.H. Tame

Biomolecular Concepts 2 ( 6 ) 525 - 536 2011年12月

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記述言語：英語出版者・発行元：De Gruyter Mouton

DOI： 10.1515/BMC.2011.045

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4000 Holes 査読

Jeremy R. H. Tame

JOURNAL OF MOLECULAR BIOLOGY 412 ( 4 ) 551 - 552 2011年9月

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記述言語：英語

DOI： 10.1016/j.jmb.2011.07.065

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Crystal structure of unliganded TRAP: implications for dynamic allostery 査読

Ali D. Malay, Masahiro Watanabe, Jonathan G. Heddle, Jeremy R. H. Tame

BIOCHEMICAL JOURNAL 434 ( 3 ) 427 - 434 2011年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1042/BJ20101813

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Role of domains within the autotransporter Hbp/Tsh 査読

Kaoru Nishimura, Young-Ho Yoon, Atsushi Kurihara, Satoru Unzai, Joen Luirink, Sam-Yong Park, Jeremy R. H. Tame

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 66 ( Pt 12 ) 1295 - 1300 2010年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S0907444910036966

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A Conserved Aromatic Residue in the Autochaperone Domain of the Autotransporter Hbp Is Critical for Initiation of Outer Membrane Translocation 査読

Zora Soprova, Ana Sauri, Peter van Ulsen, Jeremy R. H. Tame, Tanneke den Blaauwen, Wouter S. P. Jong, Joen Luirink

JOURNAL OF BIOLOGICAL CHEMISTRY 285 ( 49 ) 38224 - 38233 2010年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M110.180505

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A Novel Intein-Like Autoproteolytic Mechanism in Autotransporter Proteins 査読

Nami Tajima, Fumihiro Kawai, Sam-Yong Park, Jeremy R. H. Tame

JOURNAL OF MOLECULAR BIOLOGY 402 ( 4 ) 645 - 656 2010年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2010.06.068

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Order and Disorder in the Domain Organization of the Plasmid Partition Protein KorB 査読

Karthik Rajasekar, Sidra Tul Muntaha, Jeremy R. H. Tame, Sireesha Kommareddy, Gordon Morris, Christopher W. Wharton, Christopher M. Thomas, Scott A. White, Eva I. Hyde, David J. Scott

JOURNAL OF BIOLOGICAL CHEMISTRY 285 ( 20 ) 15440 - 15449 2010年5月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M109.096099

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Crystal Structures of Penicillin-Binding Proteins 4 and 5 from Haemophilus influenzae 査読

Fumihiro Kawai, Thomas B. Clarke, David I. Roper, Gab-Jo Han, Kwang Yeon Hwang, Satoru Unzai, Eiji Obayashi, Sam-Yong Park, Jeremy R. H. Tame

JOURNAL OF MOLECULAR BIOLOGY 396 ( 3 ) 634 - 645 2010年2月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2009.11.055

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A self-assembled artificial protein nanotube 査読

Mir, a, F.F., Iwasaki, K., Akashi, S., Sumitomo, K., Kobayashi, M., Yamashita, I., Tame, J.R.H., Heddle, J.G.

European Cells and Materials 20 ( SUPPL.3 ) 107 - 107 2010年1月

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掲載種別：研究論文（学術雑誌）

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Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase 査読

Sugiyama K, Obayashi E, Kawaguchi A, Suzuki Y, Tame JRH, Nagata K, Park SY

EMBO Journal 28 ( 12 ) 1803 - 1811 2009年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：NATURE PUBLISHING GROUP

DOI： 10.1038/emboj.2009.138

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Structural insight into a novel subunit contact within influenza virus RNA polymerase 査読

Kanako, Sugiyama, Eiji, Obayashi, Atsushi, Kawaguchi, Jeremy, R. H. Tame, Kyosuke, Nagata, Sam-Yong, Park

EMBO J 28 1803-1811 2009年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

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Mutational Analysis of the Substrate Specificity of Escherichia coli Penicillin Binding Protein 4 査読

Thomas B. Clarke, Fumihiro Kawai, Sam-Yong Park, Jeremy R. H. Tame, Christopher G. Dowson, David I. Roper

BIOCHEMISTRY 48 ( 12 ) 2675 - 2683 2009年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/bi801993x

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The nature of the TRAP-Anti-TRAP complex 査読

Watanabe, M, Heddle, J.G, Kikuchi, K, Unzai, S, Akashi, S, Park, S.Y, Tame, J.R.H

Proc Nat Acad Sci USA 106 2176 - 2181 2009年

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.0801032106

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A Self-Assembled Protein Nanotube with High Aspect Ratio. 査読

Miranda, F.F, Iwasaki, K, Akashi, S, Sumitomo, K, Kobayashi, M, Yamashita, I, Tame, J.R, Heddle, J.G

Small 5 2077 - 2084 2009年

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1002/smll.200900667

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RNA and protein complexes of TRAP characterized by mass spectrometry. 査読

Akashi, S, Watanabe, M, Heddle, J.G, Unzai, S, Park, S.Y, Tame, J.R.H

Analytical Chemistry 81 2218 - 2226 2009年

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/ac802354j

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The structural basis for an essential subunit interaction in influenza virus RNA polymerase 査読

Obayashi E, Yoshida H, Kawai F, Shibayama N, Kawaguchi A, Nagata K, Tame JRH, Park SY

Nature 454 ( 7208 ) 1127 - 0 2008年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：NATURE PUBLISHING GROUP

DOI： 10.1038/nature07225

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Intersubunit linker length as a modifier of protein stability: Crystal structures and thermostability of mutant TRAP 査読

Masahiro Watanabe, Yumiko Mishima, Ichiro Yamashita, Sam-Yong Park, Jeremy R. H. Tame, Jonathan G. Heddle

PROTEIN SCIENCE 17 ( 3 ) 518 - 526 2008年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1110/ps.073059308

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Effect of N-terminal residues on the structural stability of recombinant horse L-chain apoferritin in an acidic environment 査読

Keiko Yoshizawa, Yumiko Mishima, Sam-Yong Park, Jonathan G. Heddle, Jeremy R. H. Tame, Kenji Iwahori, Mime Kobayashi, Ichiro Yamashita

JOURNAL OF BIOCHEMISTRY 142 ( 6 ) 707 - 713 2007年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1093/jb/mvm187

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Using the ring-shaped protein TRAP to capture and confine gold nanodots on a surface

Jonathan G. Heddle, Isamu Fujiwara, Hirokazu Yamadaki, Shigeo Yoshii, Kazuaki Nishio, Christine Addy, Ichiro Yamashita, Jeremy R.H. Tame

Small 3 ( 11 ) 1950 - 1956 2007年11月

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掲載種別：研究論文（学術雑誌）

DOI： 10.1002/smll.200700400

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Crystallization and preliminary crystallographic studies of the metalloglycoprotein esterase A4 using a baculovirus expression system 査読

Toshiki Hiraki, Naoya Shibayama, Young-Ho Yoon, Kyung-Mook Yun, Toshiro Hamamoto, Jeremy R. H. Tame, Sam-Yong Park

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS 63 734 - 736 2007年9月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S1744309107033854

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Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli 査読

Atsushi Izumi, Dean Rea, Tomoko Adachi, Satoru Unzai, Sam-Yong Park, David I. Roper, Jeremy R. H. Tame

JOURNAL OF MOLECULAR BIOLOGY 370 ( 5 ) 899 - 911 2007年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2007.05.006

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Backbone 1H, 13C and 15N assignments of a 59 kDa Salmonella typhimurium periplasmic oligopeptide binding protein, OppA 査読

Kaori Kurashima-Ito, Kayano Moromisato, Ckaoru Nishimura, Markus Wälchli, Jeremy R. H. Tame, Yutaka Ito

Biomolecular NMR Assignments 1 ( 1 ) 37 - 39 2007年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1007/s12104-007-9008-1

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

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年2月

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記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：WILEY-BLACKWELL

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.

DOI： 10.1107/S0907444906048712

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

Addy, C, Ohara, M, Kawai, F, Kidera, A, Ikeguchi, M, Fuchigami, S, Osawa, M, Shimada, I, Park, S. Y, Tame, J. R, Heddle, J. G

Acta Crystallogr D Biol Crystallogr 63 ( Pt 2 ) 221 - 9 2007年2月

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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 character

DOI： 10.1107/S0907444906048712

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Dynamic Allostery in the Ring Protein TRAP. 査読

Heddle, J.G, Okajima, T, Scott, D.J, Akashi, S, Park, S.Y, Tame, J.R.H

J Mol Biol. 371 ( 1 ) 154 - 167 2007年

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2007.05.013

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Expression, purification and crystallization of 2-oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C

Dean Rea, Tomoko Adachi, Atsushi Izumi, Sam-Yong Park, Jeremy R. H. Tame, David I. Roper

Acta Crystallographica Section F: Structural Biology and Crystallization Communications 62 ( 10 ) 1010 - 1012 2006年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S1744309106035901

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1.25 angstrom resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms 査読

Sam-Yong Park, Takeshi Yokoyama, Naoya Shibayama, Yoshitsugu Shiro, Jeremy R. H. Tame

JOURNAL OF MOLECULAR BIOLOGY 360 ( 3 ) 690 - 701 2006年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.jmb.2006.05.036

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Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP 査読

JG Heddle, T Yokoyama, Yamashita, I, SY Park, JRH Tame

STRUCTURE 14 ( 5 ) 925 - 933 2006年5月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1016/j.str.2006.03.013

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Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics 査読

H Kishida, S Unzai, DI Roper, A Lloyd, SY Park, JRH Tame

BIOCHEMISTRY 45 ( 3 ) 783 - 792 2006年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/bi051533t

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Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli 査読

BR Otto, R Sijbrandi, J Luirink, B Oudega, JG Heddle, K Mizutani, SY Park, JRH Tame

JOURNAL OF BIOLOGICAL CHEMISTRY 280 ( 17 ) 17339 - 17345 2005年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M412885200

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Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8 査読

N Handa, T Terada, Y Doi-Katayama, H Hirota, JRH Tame, SY Park, S Kuramitsu, M Shirouzu, S Yokoyama

PROTEIN SCIENCE 14 ( 4 ) 1004 - 1010 2005年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1110/ps.041183305

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Backbone H-1, C-13, and N-15 assignments of a 56 kDa E-coli nickel binding protein NikA 査読

Rajesh S, Heddle JG, Kurashima-Ito K, Nietlispach D, Shirakawa M, Tame JRH, Ito Y

Journal of Biomolecular Nmr 32 ( 2 ) 177 2005年

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DOI： 10.1007/s10858-005-6072-7

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Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8 査読

S Kishishita, A Tatsuguchi, R Ushikoshi-Nakayama, T Terada, S Kuramitsu, SY Park, JRH Tame, M Shirouzu, S Yokoyama

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 57 ( 4 ) 883 - 887 2004年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1002/prot.20282

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Novel mechanisms of pH sensitivity in tuna hemoglobin - A structural explanation of the root effect 査読

T Yokoyama, KT Chong, G Miyazaki, H Morimoto, DTB Shih, S Unzai, JRH Tame, SY Park

JOURNAL OF BIOLOGICAL CHEMISTRY 279 ( 27 ) 28632 - 28640 2004年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M401740200

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Crystal structure of elongation factor P from Thermus thermophilus HB8 査読

K Hanawa-Suetsugu, S Sekine, H Sakai, C Hori-Takemoto, T Terada, S Unzai, JRH Tame, S Kuramitsu, M Shirouzu, S Yokoyama

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 ( 26 ) 9595 - 9600 2004年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1073/pnas.0308667101

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Crystal Structure of the Conserved Hypothetical Protein TT1380 from Thermus thermophilus HB8 査読

Takashi Wada, Mikako Shirouzu, Takaho Terada, Yuki Kamewari, Sam-Yong Park, Jeremy R.H. Tame, Seiki Kuramitsu, Shigeyuki Yokoyama

Proteins: Structure, Function and Genetics 55 ( 3 ) 778 - 780 2004年5月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1002/prot.20122

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Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli 査読

K Mizutani, Y Machida, S Unzai, SY Park, JRH Tame

BIOCHEMISTRY 43 ( 15 ) 4454 - 4463 2004年4月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/bi036079c

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Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli 査読

J Heddle, DJ Scott, S Unzai, SY Park, JRH Tame

JOURNAL OF BIOLOGICAL CHEMISTRY 278 ( 50 ) 50322 - 50329 2003年12月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M307941200

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Crystal structure of 4-(cytidine 5 '-diphospho)-2-C-methyl-D-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis 査読

T Wada, T Kuzuyama, S Satoh, S Kuramitsu, S Yokoyama, S Unzai, JRH Tame, SY Park

JOURNAL OF BIOLOGICAL CHEMISTRY 278 ( 32 ) 30022 - 30027 2003年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M304339200

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Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 査読

N Handa, T Terada, Y Kamewari, H Hamana, JRH Tame, SY Park, K Kinoshita, M Ota, H Nakamura, S Kuramitsu, M Shirouzu, S Yokoyama

PROTEIN SCIENCE 12 ( 8 ) 1621 - 1632 2003年8月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1110/gad.03104003

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Structure of a conserved CoA-binding protein synthesized by a cell-free system 査読

T Wada, M Shirouzu, T Terada, Y Ishizuka, T Matsuda, T Kigawa, S Kuramitsu, SY Park, JRH Tame, S Yokoyama

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 59 1213 - 1218 2003年7月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S0907444903011028

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Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis 査読

H Kishida, T Wada, S Unzai, T Kuzuyama, M Takagi, T Terada, M Shirouzu, S Yokoyama, JRH Tame, SY Park

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 59 ( Pt 1 ) 23 - 31 2003年1月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1107/S0907444902017705

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Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-angstrom resolution - A novel allosteric binding site in R-state hemoglobin 査読

N Shibayama, S Miura, JRH Tame, T Yonetani, SY Park

JOURNAL OF BIOLOGICAL CHEMISTRY 277 ( 41 ) 38791 - 38796 2002年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M205461200

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Crystal structures of deoxy- and carbonmonoxyhemoglobin F1 from the hagfish Eptatretus burgeri 査読

M Mito, KT Chong, G Miyazaki, S Adachi, SY Park, JRH Tame, H Morimoto

JOURNAL OF BIOLOGICAL CHEMISTRY 277 ( 24 ) 21898 - 21905 2002年6月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1074/jbc.M111492200

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The crystal structure of HpcE, a bifunctional decarboxylase/isomerase with a multifunctional fold 査読

JRH Tame, K Namba, EJ Dodson, DI Roper

BIOCHEMISTRY 41 ( 9 ) 2982 - 2989 2002年3月

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記述言語：英語掲載種別：研究論文（学術雑誌）

DOI： 10.1021/bi015717t

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Proteolytic analysis of the FliH/Flil complex, the ATPase component of the type III flagellar export apparatus of Salmonella 査読

T Minamino, JRH Tame, K Namba, RM Macnab

JOURNAL OF MOLECULAR BIOLOGY 312 ( 5 ) 1027 - 1036 2001年10月

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記述言語：英語掲載種別：研究論文（学術雑誌）

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Isothermal titration calorimetry of biomolecules 査読

JRH Tame, R O'Brien, JE Ladbury

BIOCALORIMETRY 27 - 38 1998年

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記述言語：英語掲載種別：研究論文（国際会議プロシーディングス）

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PROTEIN ENGINEERING STUDIES OF HEMOGLOBIN ALLOSTERISM 査読

DT SHIH, K IMAI, J TAME, G MIYAZAKI, K NAGAI

PROTEIN STRUCTURE-FUNCTION 199 - 208 1990年

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記述言語：英語掲載種別：研究論文（国際会議プロシーディングス）

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SITE-DIRECTED MUTAGENIC STUDIES ON THE MOLECULAR MECHANISM OF OXYGEN BINDING COOPERATIVITY IN HEMOGLOBIN 査読

K IMAI, K ISHIMORI, K FUSHITANI, G MIYAZAKI, T KITAGAWA, Y WADA, H MORIMOTO, MORISHIMA, I, D SHIH, J TAME, K NAGAI

PROTEIN ENGINEERING // 213 - 218 1990年

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記述言語：英語掲載種別：研究論文（国際会議プロシーディングス）

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Structural and functional consequences of amino acid substitutions in hemoglobin as manifested in natural and artificial mutants.

K. Imai, D. T. Shih, J. Tame, K. Nagai, G. Miyazaki

Protein sequences & data analysis 2 ( 2 ) 81 - 86 1989年

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記述言語：英語掲載種別：研究論文（学術雑誌）

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▼全件表示

書籍等出版物

Approaches To Entropy

J・R・H Tame（担当：単著）

Springer 2019年8月

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MISC

Development and applications of artificial symmetrical proteins

Jeroen P.M. Vrancken, Jeremy R.H. Tame, Arnout R.D. Voet

Computational and Structural Biotechnology Journal 18 3959 - 3968 2020年1月

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記述言語：英語掲載種別：書評論文，書評，文献紹介等出版者・発行元：Elsevier B.V.

DOI： 10.1016/j.csbj.2020.10.040

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Seeing the light with BLUF proteins

Sam-Yong Park, Jeremy R. H. Tame

Biophysical Reviews 9 ( 2 ) 169 - 176 2017年4月

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記述言語：英語掲載種別：書評論文，書評，文献紹介等出版者・発行元：Springer Verlag

DOI： 10.1007/s12551-017-0258-6

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The structural basis for the essential PA-PB1 subunit interaction in influenza RNA polymerase

Hisashi Yoshida, Eiji Obayashi, Atsushi Kawaguchi, Kyosuke Nagata, Jeremy R. H. Tame, Sam-Yong Park

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 67 C413 - C413 2011年

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記述言語：英語掲載種別：研究発表ペーパー・要旨（国際会議）

DOI： 10.1107/S0108767311089641

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Structure of PB1-PB2 subunit interface of inflenza A virus RNA polymerase

Kanako Sugiyama, Eiji Obayashi, Atsushi Kawaguchi, Yukari Suzuki, Jeremy R. H. Tame, Kyosuke Nagata, Sam-Yong Park

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 67 C411 - C412 2011年

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記述言語：英語掲載種別：研究発表ペーパー・要旨（国際会議）

DOI： 10.1107/S0108767311089677

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Autotransporter passenger proteins: virulence factors with common structural themes

Kaoru Nishimura, Nami Tajima, Young-Ho Yoon, Sam-Yong Park, Jeremy R. H. Tame

JOURNAL OF MOLECULAR MEDICINE-JMM 88 ( 5 ) 451 - 458 2010年5月

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記述言語：英語掲載種別：書評論文，書評，文献紹介等

DOI： 10.1007/s00109-010-0600-y

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R-state haemoglobin with low oxygen affinity: Crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35

T Yokoyama, S Neya, A Tsuneshige, T Yonetani, SY Park, JRH Tame

JOURNAL OF MOLECULAR BIOLOGY 356 ( 3 ) 790 - 801 2006年2月

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記述言語：英語

DOI： 10.1016/j.jmb.2005.12.018

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Crystal structures of unliganded and half-liganded human hemoglobin derivatives cross-linked between Lys 82 beta(1) and Lys 82 beta(2)

SY Park, N Shibayama, T Hiraki, JRH Tame

BIOCHEMISTRY 43 ( 27 ) 8711 - 8717 2004年7月

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記述言語：英語

DOI： 10.1021/bi049932w

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Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8

M Kukimoto-Niino, K Murayama, M Inoue, T Terada, JRH Tame, S Kuramitsu, M Shirouzu, S Yokoyama

JOURNAL OF MOLECULAR BIOLOGY 337 ( 3 ) 761 - 770 2004年3月

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記述言語：英語

DOI： 10.1016/j.jmb.2004.01.047

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Direct observation of photolysis-induced tertiary structural changes in hemoglobin

S Adachi, SY Park, JRH Tame, Y Shiro, N Shibayama

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100 ( 12 ) 7039 - 7044 2003年6月

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記述言語：英語

DOI： 10.1073/pnas.1230629100

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The dimerization interface of the metastasis-associated protein S100A4 (Mts1) - In vivo and in vitro studies

S Tarabykina, DJ Scott, P Herzyk, TJ Hill, JRH Tame, M Kriajevska, D Lafitte, PJ Derrick, GG Dodson, NJ Maitland, EM Lukanidin, IB Bronstein

JOURNAL OF BIOLOGICAL CHEMISTRY 276 ( 26 ) 24212 - 24222 2001年6月

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記述言語：英語出版者・発行元：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

The S100 calcium-binding proteins are implicated in signal transduction, motility, and cytoskeletal dynamics. The three-dimensional structure of several 5100 proteins revealed that the proteins form non-covalent dimers. However, the mechanism of the S100 dimerization is still obscure. In this study we characterized the dimerization of S100A4 (also named Mts1) in vitro and in vivo. Analytical ultracentrifugation revealed that apoS100A4 was present in solution as a mixture of monomers and dimers in a rapidly reversible equilibrium (K-d = 4 +/- 2 muM) The binding of calcium promoted dimerization. Replacement of Tyr-75 by Phe resulted in the stabilization of the dimer. Helix IV is known to form the major part of the dimerization interface in homologous S100 proteins. By using the yeast two-hybrid system we showed that only a few residues of helix TV, namely Phe-72, Tyr-75, Phe-78, and Leu-79, are essential for dimerization in vivo. A homology model demonstrated that these residues form a hydrophobic cluster on helix TV. Their role is to stabilize the structure of individual subunits rather than provide specific interactions across the dimerization surface. Our mutation data showed that the specificity at the dimerization surface is not particularly stringent, which is consistent with recent: data indicating that S100 proteins can form heterodimers.

DOI： 10.1074/jbc.M009477200

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The dimerization interface of the metastasis-associated protein S100A4 (Mts1) - In vivo and in vitro studies

S Tarabykina, DJ Scott, P Herzyk, TJ Hill, JRH Tame, M Kriajevska, D Lafitte, PJ Derrick, GG Dodson, NJ Maitland, EM Lukanidin, IB Bronstein

JOURNAL OF BIOLOGICAL CHEMISTRY 276 ( 26 ) 24212 - 24222 2001年6月

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記述言語：英語出版者・発行元：AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC

The S100 calcium-binding proteins are implicated in signal transduction, motility, and cytoskeletal dynamics. The three-dimensional structure of several 5100 proteins revealed that the proteins form non-covalent dimers. However, the mechanism of the S100 dimerization is still obscure. In this study we characterized the dimerization of S100A4 (also named Mts1) in vitro and in vivo. Analytical ultracentrifugation revealed that apoS100A4 was present in solution as a mixture of monomers and dimers in a rapidly reversible equilibrium (K-d = 4 +/- 2 muM) The binding of calcium promoted dimerization. Replacement of Tyr-75 by Phe resulted in the stabilization of the dimer. Helix IV is known to form the major part of the dimerization interface in homologous S100 proteins. By using the yeast two-hybrid system we showed that only a few residues of helix TV, namely Phe-72, Tyr-75, Phe-78, and Leu-79, are essential for dimerization in vivo. A homology model demonstrated that these residues form a hydrophobic cluster on helix TV. Their role is to stabilize the structure of individual subunits rather than provide specific interactions across the dimerization surface. Our mutation data showed that the specificity at the dimerization surface is not particularly stringent, which is consistent with recent: data indicating that S100 proteins can form heterodimers.

DOI： 10.1074/jbc.M009477200

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The functional similarity and structural diversity of human and cartilaginous fish hemoglobins

Y Naoi, KT Chong, K Yoshimatsu, G Miyazaki, JRH Tame, SY Park, S Adachi, H Morimoto

JOURNAL OF MOLECULAR BIOLOGY 307 ( 1 ) 259 - 270 2001年3月

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記述言語：英語

DOI： 10.1006/jmbi.2000.4446

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Ab initio phasing of a 4189-atom protein structure at 1.2 angstrom resolution

JRH Tame

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 56 1554 - 1559 2000年12月

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記述言語：英語出版者・発行元：WILEY-BLACKWELL

The phase problem remains a key rate-limiting step in the determination of macromolecular X-ray structures. Direct methods, applying probability theory to the native data set, can routinely solve structures of up to about 200 non-H atoms, although much larger structures have been solved given sufficiently high resolution data and the presence of heavy atoms. Here it is shown that maximum-likelihood refinement of free-atom models with ARP/wARP can solve ab initio a much larger metalloprotein structure than the largest so far solved by conventional direct methods. The protein, OppA, is not naturally associated with metal ions but was cocrystallized with uranium.

DOI： 10.1107/S0907444900011987

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The structures of deoxy human haemoglobin and the mutant Hb Tyr alpha 42His at 120 K

JRH Tame, B Vallone

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 56 ( 7 ) 805 - 811 2000年7月

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記述言語：英語出版者・発行元：MUNKSGAARD INT PUBL LTD

The structures of deoxy human haemoglobin and an artificial mutant (Tyr alpha 42-->His) have been solved at 120 K. While overall agreement between these structures and others in the PDB is very good, certain side chains are found to be shifted, absent from the electron-density map or in different rotamers. Non-crystallographic symmetry (NCS) is very well obeyed in the native protein, but not around the site of the changed residue in the mutant. NCS is also not obeyed by the water molecule invariably found in the alpha-chain haem pocket in room-temperature crystal structures of haemoglobin. At 120 K, this water molecule disappears from one alpha chain in the asymmetric unit but not the other.

DOI： 10.1107/S0907444900006387

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The structures of deoxy human haemoglobin and the mutant Hb Tyr alpha 42His at 120 K

JRH Tame, B Vallone

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 56 805 - 811 2000年7月

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記述言語：英語出版者・発行元：MUNKSGAARD INT PUBL LTD

The structures of deoxy human haemoglobin and an artificial mutant (Tyr alpha 42-->His) have been solved at 120 K. While overall agreement between these structures and others in the PDB is very good, certain side chains are found to be shifted, absent from the electron-density map or in different rotamers. Non-crystallographic symmetry (NCS) is very well obeyed in the native protein, but not around the site of the changed residue in the mutant. NCS is also not obeyed by the water molecule invariably found in the alpha-chain haem pocket in room-temperature crystal structures of haemoglobin. At 120 K, this water molecule disappears from one alpha chain in the asymmetric unit but not the other.

DOI： 10.1107/S0907444900006387

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Specificity and interactions of the protein OppA: Partitioning solvent binding effects using mass spectrometry

AA Rostom, JRH Tame, JE Ladbury, CV Robinson

JOURNAL OF MOLECULAR BIOLOGY 296 ( 1 ) 269 - 279 2000年2月

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記述言語：英語

DOI： 10.1006/jmbi.1999.3431

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Ab initio phasing of a 4189 atom protein structurl at 1・2(]E88FD[) resolution

Acta Crystallographica Section D 56 ( 12 ) 1554 2000年

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DOI： 10.1107/S0907444900011987

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What is the true structure of liganded haemoglobin?

JRH Tame

TRENDS IN BIOCHEMICAL SCIENCES 24 ( 10 ) 372 - 377 1999年10月

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記述言語：英語出版者・発行元：ELSEVIER SCIENCE LONDON

Does the crystal structure of a protein accurately represent its structure in solution? Or does the crystallization process perturb the structure significantly? Although aware of the problem, most crystallographers would argue that the highly solvated and weakly held lattice in protein crystals is, in general, unlikely to shift ordered parts of the molecule. In the case of conformationally flexible proteins, however, there is the possibility that one form might be favoured over another. Several lines of evidence suggest that. this might be the case for the crystal structure of liganded Hb, although conflicting data exist.

DOI： 10.1016/S0968-0004(99)01444-9

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Crystallographic and calorimetric analysis of peptide binding to OppA protein

SH Sleigh, PR Seavers, AJ Wilkinson, JE Ladbury, JRH Tame

JOURNAL OF MOLECULAR BIOLOGY 291 ( 2 ) 393 - 415 1999年8月

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記述言語：英語出版者・発行元：ACADEMIC PRESS LTD

Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system. (C) 1999 Academic Press.

DOI： 10.1006/jmbi.1999.2929

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Crystallographic and calorimetric analysis of peptide binding to OppA protein

SH Sleigh, PR Seavers, AJ Wilkinson, JE Ladbury, JRH Tame

JOURNAL OF MOLECULAR BIOLOGY 291 ( 2 ) 393 - 415 1999年8月

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記述言語：英語出版者・発行元：ACADEMIC PRESS LTD

Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system. (C) 1999 Academic Press.

DOI： 10.1006/jmbi.1999.2929

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Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes

TG Davies, RE Hubbard, JRH Tame

PROTEIN SCIENCE 8 ( 7 ) 1432 - 1444 1999年7月

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記述言語：英語

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Scoring functions: A view from the bench

JRH Tame

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 13 ( 2 ) 99 - 108 1999年3月

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記述言語：英語

DOI： 10.1023/A:1008068903544

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What is the true structure of liganded hemoglobin?

Trends in Biochemical Science 24 ( 10 ) 372 1999年

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DOI： 10.1016/S0968-0004(99)01444-9

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Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine

SH Sleigh, JRH Tame, EJ Dodson, AJ Wilkinson

BIOCHEMISTRY 36 ( 32 ) 9747 - 9758 1997年8月

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記述言語：英語

DOI： 10.1021/bi970457u

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The role of water in sequence-independent ligand binding by an oligopeptide transporter protein

JRH Tame, SH Sleigh, AJ Wilkinson, JE Ladbury

NATURE STRUCTURAL BIOLOGY 3 ( 12 ) 998 - 1001 1996年12月

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記述言語：英語掲載種別：速報，短報，研究ノート等（学術雑誌）

DOI： 10.1038/nsb1296-998

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A hemoglobin-based blood substitute: Transplanting a novel allosteric effect of crocodile Hb

N Komiyama, J Tame, K Nagai

BIOLOGICAL CHEMISTRY 377 ( 9 ) 543 - 548 1996年9月

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記述言語：英語掲載種別：書評論文，書評，文献紹介等

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The crystal structures of trout Hb I in the deoxy and carbonmonoxy forms

JRH Tame, JC Wilson, RE Weber

JOURNAL OF MOLECULAR BIOLOGY 259 ( 4 ) 749 - 760 1996年6月

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記述言語：英語

DOI： 10.1006/jmbi.1996.0355

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Crystal structure of T state haemoglobin with oxygen bound at all four haems

M Paoli, R Liddington, J Tame, A Wilkinson, G Dodson

JOURNAL OF MOLECULAR BIOLOGY 256 ( 4 ) 775 - 792 1996年3月

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記述言語：英語

DOI： 10.1006/jmbi.1996.0124

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The crystal structure of a high oxygen affinity species of haemoglobin (bar-headed goose haemoglobin in the oxy form)

J Zhang, ZQ Hua, JRH Tame, GY Lu, RJ Zhang, XC Gu

JOURNAL OF MOLECULAR BIOLOGY 255 ( 3 ) 484 - 493 1996年1月

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記述言語：英語

DOI： 10.1006/jmbi.1996.0040

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The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands

JRH Tame, EJ Dodson, G Murshudov, CF Higgins, AJ Wilkinson

STRUCTURE 3 ( 12 ) 1395 - 1406 1995年12月

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記述言語：英語

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STRUCTURE DETERMINATION OF OPPA AT 2.3-ANGSTROM RESOLUTION USING MULTIPLE-WAVELENGTH ANOMALOUS-DISPERSION METHODS

ID GLOVER, RC DENNY, ND NGUTI, SM MCSWEENEY, SH KINDER, AW THOMPSON, EJ DODSON, AJ WILKINSON, JRH TAME

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 51 39 - 47 1995年1月

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記述言語：英語

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TRANSPLANTING A UNIQUE ALLOSTERIC EFFECT FROM CROCODILE INTO HUMAN HEMOGLOBIN

NH KOMIYAMA, G MIYAZAKI, J TAME, K NAGAI

NATURE 373 ( 6511 ) 244 - 246 1995年1月

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記述言語：英語

DOI： 10.1038/373244a0

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THE STRUCTURAL BASIS OF SEQUENCE-INDEPENDENT PEPTIDE BINDING BY OPPA PROTEIN

JRH TAME, GN MURSHUDOV, EJ DODSON, TK NEIL, GG DODSON, CF HIGGINS, AJ WILKINSON

SCIENCE 264 ( 5165 ) 1578 - 1581 1994年6月

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記述言語：英語

DOI： 10.1126/science.8202710

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PRODUCTION OF HUMAN HEMOGLOBIN IN ESCHERICHIA-COLI USING CLEAVABLE FUSION PROTEIN EXPRESSION VECTOR

TH JESSEN, NH KOMIYAMA, J TAME, J PAGNIER, D SHIH, B LUISI, G FERMI, K NAGAI

HEMOGLOBINS, PT B 231 347 - 364 1994年

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記述言語：英語掲載種別：書評論文，書評，文献紹介等

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MUTANT HEMOGLOBINS (ALPHA(119)-ALA AND BETA(55)-SER) - FUNCTIONS RELATED TO HIGH-ALTITUDE RESPIRATION IN GEESE

RE WEBER, TH JESSEN, H MALTE, J TAME

JOURNAL OF APPLIED PHYSIOLOGY 75 ( 6 ) 2646 - 2655 1993年12月

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記述言語：英語

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PROTEIN ENGINEERING IN HEMOGLOBIN - REPLY

K NAGAI, N KOMIYAMA, J TAME

NATURE 355 ( 6363 ) 777 - 778 1992年2月

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記述言語：英語掲載種別：速報，短報，研究ノート等（学術雑誌）

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Protein engineering in hemoglobin-reply.(共著)

Nature 355 777 - 778 1992年

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THE ASSIGNMENT OF CARBON-MONOXIDE ASSOCIATION RATE CONSTANTS TO THE ALPHA-SUBUNIT AND BETA-SUBUNIT IN NATIVE AND MUTANT HUMAN DEOXYHEMOGLOBIN TETRAMERS

AJ MATHEWS, JS OLSON, JP RENAUD, J TAME, K NAGAI

JOURNAL OF BIOLOGICAL CHEMISTRY 266 ( 32 ) 21631 - 21639 1991年11月

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記述言語：英語

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ADAPTATION OF BIRD HEMOGLOBINS TO HIGH-ALTITUDES - DEMONSTRATION OF MOLECULAR MECHANISM BY PROTEIN ENGINEERING

TH JESSEN, RE WEBER, G FERMI, J TAME, G BRAUNITZER

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 88 ( 15 ) 6519 - 6522 1991年8月

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記述言語：英語

DOI： 10.1073/pnas.88.15.6519

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WAS THE LOSS OF THE D-HELIX IN ALPHA-GLOBIN A FUNCTIONALLY NEUTRAL MUTATION

NH KOMIYAMA, DTB SHIH, D LOOKER, J TAME, K NAGAI

NATURE 352 ( 6333 ) 349 - 351 1991年7月

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記述言語：英語

DOI： 10.1038/352349a0

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FUNCTIONAL-ROLE OF THE DISTAL VALINE (E11) RESIDUE OF ALPHA-SUBUNITS IN HUMAN HEMOGLOBIN

J TAME, DTB SHIH, J PAGNIER, G FERMI, K NAGAI

JOURNAL OF MOLECULAR BIOLOGY 218 ( 4 ) 761 - 767 1991年4月

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記述言語：英語

DOI： 10.1016/0022-2836(91)90264-7

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SITE-DIRECTED MUTAGENESIS IN HEMOGLOBIN - FUNCTIONAL-ROLE OF TYROSINE-42(C7)ALPHA AT THE ALPHA-1-BETA-2 INTERFACE

K IMAI, K FUSHITANI, G MIYAZAKI, K ISHIMORI, T KITAGAWA, Y WADA, H MORIMOTO, MORISHIMA, I, DT SHIH, J TAME

JOURNAL OF MOLECULAR BIOLOGY 218 ( 4 ) 769 - 778 1991年4月

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記述言語：英語

DOI： 10.1016/0022-2836(91)90265-8

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EFFECT OF THE DISTAL RESIDUES ON THE VIBRATIONAL-MODES OF THE FE-CO BOND IN HEMOGLOBIN STUDIED BY PROTEIN ENGINEERING

SH LIN, NT YU, J TAME, D SHIH, JP RENAUD, J PAGNIER, K NAGAI

BIOCHEMISTRY 29 ( 23 ) 5562 - 5566 1990年6月

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記述言語：英語

DOI： 10.1021/bi00475a021

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THE EFFECTS OF E7 AND E11 MUTATIONS ON THE KINETICS OF LIGAND-BINDING TO R-STATE HUMAN-HEMOGLOBIN

AJ MATHEWS, RJ ROHLFS, JS OLSON, J TAME, JP RENAUD, K NAGAI

JOURNAL OF BIOLOGICAL CHEMISTRY 264 ( 28 ) 16573 - 16583 1989年10月

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記述言語：英語

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NMR-STUDY OF HUMAN MUTANT HEMOGLOBINS SYNTHESIZED IN ESCHERICHIA-COLI - CONSEQUENCES OF TYROSINE-ALPHA-42 SUBSTITUTIONS

K ISHIMORI, MORISHIMA, I, K IMAI, K FUSHITANI, G MIYAZAKI, D SHIH, J TAME, J PEGNIER, K NIGAI

JOURNAL OF BIOLOGICAL CHEMISTRY 264 ( 25 ) 14624 - 14626 1989年9月

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記述言語：英語掲載種別：記事・総説・解説・論説等（学術雑誌）

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THE ROLE OF THE DISTAL HISTIDINE IN MYOGLOBIN AND HEMOGLOBIN

JS OLSON, AJ MATHEWS, RJ ROHLFS, BA SPRINGER, KD EGEBERG, SG SLIGAR, J TAME, JP RENAUD, K NAGAI

NATURE 336 ( 6196 ) 265 - 266 1988年11月

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記述言語：英語

DOI： 10.1038/336265a0

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▼全件表示

講演・口頭発表等

Protein allostery 国際会議

J・R・H Tame

Bari 2010年

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記述言語：英語会議種別：口頭発表（一般）

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Influenza RNA Polymerase 国際会議

J・R・H Tame

Nottingham 2010年

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記述言語：英語会議種別：口頭発表（一般）

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Some thoughts on scoring functions 国際会議

J・R・H Tame

Newcastle University 2012年

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記述言語：英語会議種別：口頭発表（招待・特別）

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Some thoughts on scoring functions

J・R・H Tame

J-CUP II 2011年

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記述言語：英語会議種別：口頭発表（基調）

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Seminar

J・R・H Tame

Riken Wako Institute 2011年

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記述言語：英語会議種別：公開講演，セミナー，チュートリアル，講習，講義等

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Autotransporter proteins 国際会議

J・R・H Tame

Nottingham University 2010年

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記述言語：英語会議種別：公開講演，セミナー，チュートリアル，講習，講義等

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アデェニルシクラゼの光活性化招待国際会議

J・R・H Tame

Astbury Conversation 2018年4月

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記述言語：英語会議種別：口頭発表（一般）

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The Power of the Intangible 国際会議

J・R・H Tame

the OpenEye CUP meeting in Santa Fe, the British Biophysical Society biennial meeting (Warwick), and the Oxygen Binding Proteins meeting (Sheffield) 2014年

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記述言語：英語会議種別：公開講演，セミナー，チュートリアル，講習，講義等

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▼全件表示

Works（作品等）

ERATO PROTONIC NANOMACHINE PROJECT

1999年 - 2001年

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共同研究・競争的資金等の研究課題

改変レクチンの創製による自己免疫性神経疾患の糖鎖に着目した回復技術の開発

研究課題/領域番号：24K08716 2024年4月 - 2027年3月

日本学術振興会科学研究費助成事業基盤研究(C)

大関泰裕, 山田雅雄, 小川由起子, 鎌田健一, 宮西伸光, 藤井佑樹, J・R・H Tame

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配分額：4680000円（直接経費：3600000円、間接経費：1080000円）

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実験と計算科学の融合による任意の標的ガングリオシドに選択的な人工レクチンの開発

研究課題/領域番号：23K06190 2023年4月 - 2027年3月

日本学術振興会科学研究費助成事業基盤研究(C)

藤井佑樹, 小関準, 大関泰裕, 鎌田健一, J・R・H Tame, 川嵜達也

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配分額：4680000円（直接経費：3600000円、間接経費：1080000円）

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人工タンパク質デザインによる新機能の創出

研究課題/領域番号：16H04779 2016年4月 - 2019年3月

日本学術振興会科学研究費助成事業基盤研究(B)

J・R・H Tame, 池上貴久

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配分額：17680000円（直接経費：13600000円、間接経費：4080000円）

いくつかの新規タンパク質が作製され、そしてそれらが別々のサブユニットから自己集合する能力について試験された。様々なポリオキソメタレート（POM）クラスターおよび対称性が一致する対称人工タンパク質を組み合わせて、我々が以前に設計および記載したピザと呼ばれるタンパク質との大規模ハイブリッドアセンブリを構築した。様々な生物物理学的技法を使用してPOM-ピザ相互作用を測定し、複合体の結晶構造を解明した。

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BAM 複合体による細胞膜タンパク質輸送機構の解明

研究課題/領域番号：22370044 2010年 - 2012年

日本学術振興会科学研究費助成事業基盤研究(B)

ジェレミーテイム, 朴三用, 雲財悟

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配分額：18980000円（直接経費：14600000円、間接経費：4380000円）

多剤耐性菌の出現により、抗生剤が効かない病原菌で社会的に大きな問題となっている。特にグラム陰性の病原菌が世界に広かっており、大きな問題になっている。そこで本研究では多剤耐性グラム陰性菌に有効な新規薬剤標的分子として BAM(β-barrel assembly machinery) 複合体の構造生物学的な基盤構築を行い、新規薬剤の開発を研究目的である。BAM 複合体はグラム陰性菌の外膜生合成で中心的な役割を担う装置であり、菌の生存に必須な機能を有する。しかし、新規薬剤開発のための構造基盤の情報は少なく、我々は、BamA-D をターゲットとし、発現系構築に成功し結晶化を試みたが、良好な結晶を得る事は出来なかった。そこで、我々は BamC と BamD の複合体での機能解析や、結晶化に成功した。BamC と BamD の X線小角散乱(small angle X-ray scattering)法や分析超遠心(AUC)により、溶液中での相互作用を確認する事が出来た。また、複合体での微結晶ながら X 線による反射点も確認する事が出来たが、構造決定までには結晶化の最適化が必要である。引き続き、結晶化条件の最適化と、Bam 機構解析を行う。

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病原性細菌由来オートトランスポーターの分泌機構と高次構造相関

研究課題/領域番号：19370045 2007年 - 2008年

日本学術振興会科学研究費助成事業基盤研究(B)

JEREMY R.H.Tame, 朴三用, 雲財悟

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配分額：18460000円（直接経費：14200000円、間接経費：4260000円）

オートトランスポータータンパク質Heme Binding Protein (HBP)のパッセンジャードメイン立体構造解析に成功した。HBPの外膜貫通領域βバレルドメインとオートシャペロン部分の発現系構築に成功し、タンパク質の結晶化および立体構造解析に成功した。

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ヘム結合プロテイン

研究課題/領域番号：04F04725 2004年 - 2006年

日本学術振興会科学研究費助成事業特別研究員奨励費

JEREMY R.H. Tame, TAME Jeremy・R・H, KINGSTON Isabel Jane

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配分額：2400000円（直接経費：2400000円）

オートトランスポーターは病原性細菌が分泌するタンパク質である。オートトランスポーターには色々な役割がある。SPATEというオートトランスポーターは、宿主のタンパク質を消化するためにセリンプロテアーゼドメインを持っている。腹膜炎の原因菌として、病原性大腸菌が知られている。この大腸菌は、HbpというSPATEを分泌する。Hbp(ヘモグロビンプロテアーゼ)の病態生理学的特徴を明らかにするため、我々の研究室ではHbpを結晶化した。X線構造解析を行うことによって、Hbpには三つのドメインがあることがわかった。N末端ドメインはセリンプロテアーゼドメインである。C末端ドメインはオートシャペロンである。この二つのドメインの間には、長いbetaヘリックス構造がある。Kingston博士は、オートトランスポーター分泌メカニズムを解明するために色々な変異体を作っている。オートシャペロン部分の表面に、結晶構造解析の電子密度が見えないalanine残基に富むループ構造がある。保存されたlysine残基もある。このlysineを変えるとオートトランスポーター分泌が停止される。現在、このlysineの役割を調べている。

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鉄イオン標的タンパク質(Fur)の機能と構造解析

研究課題/領域番号：14780514 2002年 - 2003年

日本学術振興会科学研究費助成事業若手研究(B)

TAME J.R.H.

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配分額：3500000円（直接経費：3500000円）

鉄元素は生物にとって欠くことのできない成分であるが、鉄(III)イオンは生理的pH条件ではほとんど水に溶けない。そこでバクテリアは、周囲の環境から鉄を吸収するための精巧なシステムを細胞内に発達させている。多くの病原性バクテリアは、鉄イオンの有無を毒素生産の制御スイッチとして使っている。また、大腸菌の内部では、鉄イオン取り込み調節タンパク質(ferric Iron Uptake Regulator, Fur)が、30以上もの遺伝子発現を制御している。鉄イオン存在条件下で、このタンパク質は特定のDNA配列に結合し、その下流の遺伝子発現を抑制することが知られている。Fur相同タンパク質は、結核菌や淋菌をはじめとした多くのグラム陽性菌、陰性菌も持っていることがわかっている。Fur相同タンパク質の立体構造に関する報告はほとんど無い。Furタンパクは、病原菌の毒素発現システムと、鉄イオン吸収システムの両方で、中心的な役割を果たしているが、哺乳類には類似タンパク質は存在しない。だから、Furタンパクは、薬剤設計の標的として適していると言える。
今回、Furに類似したNikAと呼ばれる蛋白質の結晶構造解析に成功した。NikAはABCトランスポーターファミリーでニッケルイオン結合蛋白質として働いている。バクテリアのペリプラズム層で、ニッケルイオンの初期結合蛋白質および受け渡し役を担っていて、バクテリアの金属イオン濃度による走化性反応を引き起こしている。NikAの高分解能立体構造を、ニッケルイオンのあり、なしの両方の条件で決定したところ、他のペリプラズム層蛋白質と同様の蛋白質全体の構造変化が確認された。しかし、ニッケルイオンと蛋白質の直接の結合が存在しないなど、今までに見つかっている蛋白質には見られない特徴があった。NikAは、ニッケルイオンにのみ結合能力を持っている。

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PROTEIN DESIGN

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資金種別：競争的資金

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BACTERIAL FLAGELLAR MOTOR

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資金種別：競争的資金

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HEME UPTAKE BY BACTERIA

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資金種別：競争的資金

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HEMOGLOBIN EVOLUTION

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資金種別：競争的資金

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