Updated on 2026/04/04

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写真a

 
J.R.H. Tame
 
Organization
Graduate School of Medical Life Science Department of Medical Life Science Professor
School of Science Department of Science
Title
Professor
Homepage
http://www.tsurumi.yokohama-cu.ac.jp/pdl
Profile
My work involves the study of protein structures by X-ray crystallography and other biophysical techniques.
My group is designing artificial proteins for different biotechnological uses, such as detecting and killing cancer cells or making metallic nanodots.
I have a long-standing interest in protein thermodynamics, the factors controlling ligand binding, and drug design. In particular I am interested in new targets for antibacterial compounds.
External link

Degree

  • BIOCHEMISTRY ( BA/CAMBRIDGE UNIVERSITY )

Research Interests

  • 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

Research Areas

  • Life Science / Molecular biology

  • Life Science / Biophysics

Research History

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

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Professional Memberships

  • BRITISH CRYSTALLOGRAPHIC ASSOCIATION

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Committee Memberships

  • BRITISH CRYSTALLOGRAPHIC ASSOCIATION   BCA  

    1991   

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    Committee type：Academic society

    BRITISH CRYSTALLOGRAPHIC ASSOCIATION

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Papers

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

    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   2025.12

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

    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   2024.11

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    Publishing type：Research paper (scientific journal)   Publisher：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. International journal

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

    Nature communications   15 ( 1 )   9241 - 9241   2024.10

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    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. International journal

    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   2024.8

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    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. International journal

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

    Nature communications   14 ( 1 )   7150 - 7150   2023.11

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

    DOI： 10.1038/s41467-023-42764-8

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  • Structural basis of CXC chemokine receptor 1 ligand binding and activation. International journal

    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   2023.7

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    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. International journal

    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   2022.8

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    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. International journal

    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   2022.5

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    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. Reviewed International journal

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

    Molecules (Basel, Switzerland)   27 ( 9 )   2022.4

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    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 ↔ 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 )   2021.3

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：National Academy of Sciences  

    DOI： 10.1073/pnas.2020486118

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  • The symmetric designer protein Pizza as a scaffold for metal coordination. International journal

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

    Proteins   2021.3

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    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   2021.2

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    Publishing type：Research paper (scientific journal)   Publisher：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. International journal

    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   2021.1

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    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. International journal

    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   2020.12

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    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   2020.12

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：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. International journal

    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   2020.6

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    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   2020.2

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    Publishing type：Research paper (scientific journal)   Publisher：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—Cys<sup>105</sup>, Ser<sup>60</sup>, Gln<sup>224</sup>, and Phe<sup>90</sup>—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   2020.1

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

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    Publishing type：Research paper (scientific journal)  

    DOI： 10.1039/D0CC05071G

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  • Computational design of symmetrical eight-bladed β-propeller proteins. International journal

    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   2019.1

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    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 Reviewed

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

    Biochemical and Biophysical Research Communications   499 ( 3 )   594 - 599   2018.5

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

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

    PLoS Genetics   14 ( 4 )   2018.4

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Public Library of Science  

    DOI： 10.1371/journal.pgen.1007331

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  • Direct observation of conformational population shifts in crystalline human hemoglobin Reviewed

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   292 ( 44 )   18258 - 18269   2017.11

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    DOI： 10.1074/jbc.M117.781146

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  • Molecular mechanism of photoactivation of a light-regulated adenylate cyclase Reviewed

    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   2017.8

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    DOI： 10.1073/pnas.1704391114

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

    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   2017.7

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    DOI： 10.1038/s41598-017-06332-7

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  • Evolution-Inspired Computational Design of Symmetric Proteins. International journal

    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

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    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 Reviewed

    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   2016.6

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    DOI： 10.1038/srep28344

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

    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   2016.6

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    DOI： 10.1073/pnas.1517520113

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  • Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein Reviewed

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

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   54 ( 34 )   9857 - 9860   2015.8

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    DOI： 10.1002/anie.201503575

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  • The crystal and solution structure of YdiE from Escherichia coli Reviewed

    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   2015.7

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    DOI： 10.1107/S2053230X15009140

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  • The structure and conformational switching of Rap1B Reviewed

    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   2015.6

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    DOI： 10.1016/j.bbrc.2015.04.103

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  • Computational design of a self-assembling symmetrical beta-propeller protein Reviewed

    Arnout R. D. Voet, Hiroki Noguchi, Christine Addy, David Simoncini, Daiki Terada, Satoru Unzai, Sam-Yong Park, Kam Y. J. Zhang, Jeremy R. H. Tame

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   111 ( 42 )   15102 - 15107   2014.10

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    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 Reviewed

    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   2014.6

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    DOI： 10.1074/jbc.M114.564526

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  • Capturing the Hemoglobin Allosteric Transition in a Single Crystal Form Reviewed

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

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   136 ( 13 )   5097 - 5105   2014.4

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    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 Reviewed

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

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   69 ( Pt1 )   44 - 51   2013.1

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    DOI： 10.1107/S0907444912042059

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  • Influence of Structural Symmetry on Protein Dynamics Reviewed

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

    PLOS ONE   7 ( 11 )   2012.11

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    DOI： 10.1371/journal.pone.0050011

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  • Structures of haemoglobin from woolly mammoth in liganded and unliganded states Reviewed

    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   2012.11

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    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 Reviewed

    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   2012.10

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    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 Reviewed

    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   2012.4

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    DOI： 10.1128/JVI.06868-11

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  • Autotransporter protein secretion Reviewed

    Jeremy R.H. Tame

    Biomolecular Concepts   2 ( 6 )   525 - 536   2011.12

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    DOI： 10.1515/BMC.2011.045

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  • 4000 Holes Reviewed

    Jeremy R. H. Tame

    JOURNAL OF MOLECULAR BIOLOGY   412 ( 4 )   551 - 552   2011.9

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  • Crystal structure of unliganded TRAP: implications for dynamic allostery Reviewed

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

    BIOCHEMICAL JOURNAL   434 ( 3 )   427 - 434   2011.3

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    DOI： 10.1042/BJ20101813

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  • Role of domains within the autotransporter Hbp/Tsh Reviewed

    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   2010.12

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    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 Reviewed

    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   2010.12

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    DOI： 10.1074/jbc.M110.180505

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  • A Novel Intein-Like Autoproteolytic Mechanism in Autotransporter Proteins Reviewed

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

    JOURNAL OF MOLECULAR BIOLOGY   402 ( 4 )   645 - 656   2010.10

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    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 Reviewed

    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   2010.5

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    DOI： 10.1074/jbc.M109.096099

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

    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   2010.2

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    DOI： 10.1016/j.jmb.2009.11.055

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  • A self-assembled artificial protein nanotube Reviewed

    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   2010.1

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

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

    EMBO Journal   28 ( 12 )   1803 - 1811   2009.6

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    DOI： 10.1038/emboj.2009.138

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

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

    EMBO J   28   1803-1811   2009.6

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

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

    BIOCHEMISTRY   48 ( 12 )   2675 - 2683   2009.3

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    DOI： 10.1021/bi801993x

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  • The nature of the TRAP-Anti-TRAP complex Reviewed

    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

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    DOI： 10.1073/pnas.0801032106

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  • A Self-Assembled Protein Nanotube with High Aspect Ratio. Reviewed

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

    Small   5   2077 - 2084   2009

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    DOI： 10.1002/smll.200900667

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  • RNA and protein complexes of TRAP characterized by mass spectrometry. Reviewed

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

    Anal. chem.   81   2218 - 2226   2009

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    DOI： 10.1021/ac802354j

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

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

    Nature   454 ( 7208 )   1127 - 0   2008.8

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    DOI： 10.1038/nature07225

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

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

    PROTEIN SCIENCE   17 ( 3 )   518 - 526   2008.3

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    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 Reviewed

    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   2007.12

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    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   2007.11

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    DOI： 10.1002/smll.200700400

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

    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   2007.9

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    DOI： 10.1107/S1744309107033854

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

    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   2007.7

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    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 Reviewed

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

    Biomolecular NMR Assignments   1 ( 1 )   37 - 39   2007.7

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    DOI： 10.1007/s12104-007-9008-1

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

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

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

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

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

    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   2007.2

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

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  • Dynamic Allostery in the Ring Protein TRAP. Reviewed

    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

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    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   2006.10

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    DOI： 10.1107/S1744309106035901

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

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

    JOURNAL OF MOLECULAR BIOLOGY   360 ( 3 )   690 - 701   2006.7

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    DOI： 10.1016/j.jmb.2006.05.036

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

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

    STRUCTURE   14 ( 5 )   925 - 933   2006.5

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    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 Reviewed

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

    BIOCHEMISTRY   45 ( 3 )   783 - 792   2006.1

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    DOI： 10.1021/bi051533t

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

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   280 ( 17 )   17339 - 17345   2005.4

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    DOI： 10.1074/jbc.M412885200

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

    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   2005.4

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

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

    Journal of Biomolecular Nmr   32 ( 2 )   177   2005

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

    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   2004.12

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    DOI： 10.1002/prot.20282

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

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   279 ( 27 )   28632 - 28640   2004.7

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    DOI： 10.1074/jbc.M401740200

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  • Crystal structure of elongation factor P from Thermus thermophilus HB8 Reviewed

    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   2004.6

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    DOI： 10.1073/pnas.0308667101

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

    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   2004.5

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    DOI： 10.1002/prot.20122

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

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

    BIOCHEMISTRY   43 ( 15 )   4454 - 4463   2004.4

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    DOI： 10.1021/bi036079c

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

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   278 ( 50 )   50322 - 50329   2003.12

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    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 Reviewed

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   278 ( 32 )   30022 - 30027   2003.8

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    DOI： 10.1074/jbc.M304339200

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  • Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 Reviewed

    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   2003.8

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    DOI： 10.1110/gad.03104003

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

    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   2003.7

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    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 Reviewed

    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   2003.1

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    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 Reviewed

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   277 ( 41 )   38791 - 38796   2002.10

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    DOI： 10.1074/jbc.M205461200

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

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

    JOURNAL OF BIOLOGICAL CHEMISTRY   277 ( 24 )   21898 - 21905   2002.6

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    DOI： 10.1074/jbc.M111492200

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

    JRH Tame, K Namba, EJ Dodson, DI Roper

    BIOCHEMISTRY   41 ( 9 )   2982 - 2989   2002.3

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    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 Reviewed

    T Minamino, JRH Tame, K Namba, RM Macnab

    JOURNAL OF MOLECULAR BIOLOGY   312 ( 5 )   1027 - 1036   2001.10

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  • Isothermal titration calorimetry of biomolecules Reviewed

    JRH Tame, R O'Brien, JE Ladbury

    BIOCALORIMETRY   27 - 38   1998

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  • PROTEIN ENGINEERING STUDIES OF HEMOGLOBIN ALLOSTERISM Reviewed

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

    PROTEIN STRUCTURE-FUNCTION   199 - 208   1990

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

    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

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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 &amp; data analysis   2 ( 2 )   81 - 86   1989

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▼display all

Books

  • Approaches To Entropy

    J.R.H. Tame（ Role： Sole author）

    Springer  2019.8 

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  • 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   2020.1

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    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   2017.4

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    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

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    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

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    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   2010.5

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    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   2006.2

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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   2004.7

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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   2004.3

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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   2003.6

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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   2001.6

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    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.

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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   2001.6

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    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.

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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   2001.3

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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   2000.12

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    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.

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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   2000.7

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    The structures of deoxy human haemoglobin and an artificial mutant (Tyr alpha 42--&gt;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.

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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   2000.7

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    The structures of deoxy human haemoglobin and an artificial mutant (Tyr alpha 42--&gt;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.

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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   2000.2

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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

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  • What is the true structure of liganded haemoglobin?

    JRH Tame

    TRENDS IN BIOCHEMICAL SCIENCES   24 ( 10 )   372 - 377   1999.10

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    Language：English   Publisher：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.

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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   1999.8

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    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   1999.8

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    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.

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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   1999.7

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  • Scoring functions: A view from the bench

    JRH Tame

    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN   13 ( 2 )   99 - 108   1999.3

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  • What is the true structure of liganded hemoglobin?

    Trends in Biochemical Science   24 ( 10 )   372   1999

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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   1997.8

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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   1996.12

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    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   1996.9

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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   1996.6

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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   1996.3

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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   1996.1

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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   1995.12

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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   1995.1

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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   1995.1

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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   1994.6

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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

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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   1993.12

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  • PROTEIN ENGINEERING IN HEMOGLOBIN - REPLY

    K NAGAI, N KOMIYAMA, J TAME

    NATURE   355 ( 6363 )   777 - 778   1992.2

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  • Protein engineering in hemoglobin-reply.(共著)

    Nature   355   777 - 778   1992

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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   1991.11

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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   1991.8

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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   1991.7

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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   1991.4

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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   1991.4

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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   1990.6

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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   1989.10

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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   1989.9

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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   1988.11

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Presentations

  • Protein allostery International conference

    J.R.H. Tame

    Bari  2010 

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    Language：English   Presentation type：Oral presentation (general)  

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  • Influenza RNA Polymerase International conference

    J.R.H. Tame

    Nottingham  2010 

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    Language：English   Presentation type：Oral presentation (general)  

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  • Some thoughts on scoring functions International conference

    J.R.H. Tame

    Newcastle University  2012 

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    Language：English   Presentation type：Oral presentation (invited, special)  

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  • Some thoughts on scoring functions

    J.R.H. Tame

    J-CUP II  2011 

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    Language：English   Presentation type：Oral presentation (keynote)  

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  • Seminar

    J.R.H. Tame

    Riken Wako Institute  2011 

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  • Autotransporter proteins International conference

    J.R.H. Tame

    Nottingham University  2010 

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  • Photoactivation of a light-regulated adenylate cyclase Invited International conference

    J.R.H. Tame

    Astbury Conversation  2018.4 

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  • The Power of the Intangible International conference

    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 

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Works

  • ERATO PROTONIC NANOMACHINE PROJECT

    1999 - 2001

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Research Projects

  • Establishment of recovery procedures on glycans for autoimmune neurological diseases by creation of artificail lectins

    Grant number：24K08716  2024.4 - 2027.3

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

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

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  • Development of artificial lectin recognizing the optional target ganglioside by combining experimental and computational science

    Grant number：23K06190  2023.4 - 2027.3

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

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

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  • Development of novel materials by design of artificial proteins

    Grant number：16H04779  2016.4 - 2019.3

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

    Tame Jeremy

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    Grant amount：\17680000 （ Direct Cost: \13600000 、 Indirect Cost：\4080000 ）

    Several novel proteins have been created, and tested for their ability to self-assemble from separate subunits. Various polyoxometalate (POM) clusters and symmetrical artificial proteins of matching symmetry have been combined to build large-scale hybrid assemblies with a protein called Pizza, that we designed and described previously. The POM-Pizza interaction was measured using various biophysical techniques, and crystal structures of the complexes were solved. In a separate project, a novel lectin from a species of mussel was found to bind to the glycan of asialo-GM1. The crystal structure of this protein has been solved, and further work to develop a useful biomedical tool from this protein, by building larger networks with it, is underway.

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  • Analysis of the outer membrane BAM complex

    Grant number：22370044  2010 - 2012

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

    J・R・H Tame, PARK Sam-yong, UNZAI Satoru

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    Grant amount：\18980000 （ Direct Cost: \14600000 、 Indirect Cost：\4380000 ）

    Gram negative bacteria require the BAM complex for the insertion of membrane proteins into the outer membrane. This essential complex consists of five proteins, the large transmembrane barrel being BamA. BamA carries five POTRA domains at its N terminus which interact with other proteins in the complex. Only BamA and BamD are essential, but the roles of these proteins is unknown. We have solved the crystal structure of an outer membrane protein, Hbp, and studied the interaction between BamC and BamD. The Hbp beta-barrel is a substrate of BAM, but the interactions between the two are unclear. We have shown that BamC and BamD interact to give a flexible complex.

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  • Structure and function of autotransporter proteins from pathogenic bacteria

    Grant number：19370045  2007 - 2008

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

    TAME Jeremy R.H., PARK Sam-yong, UNZAI Satoru

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    Grant amount：\18460000 （ Direct Cost: \14200000 、 Indirect Cost：\4260000 ）

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  • ヘム結合プロテイン

    Grant number：04F04725  2004 - 2006

    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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    Grant amount：\2400000 （ Direct Cost: \2400000 ）

    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

    Grant number：14780514  2002 - 2003

    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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    Grant amount：\3500000 （ Direct Cost: \3500000 ）

    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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    Grant type：Competitive

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  • BACTERIAL FLAGELLAR MOTOR

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    Grant type：Competitive

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  • HEME UPTAKE BY BACTERIA

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    Grant type：Competitive

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  • HEMOGLOBIN EVOLUTION

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    Grant type：Competitive

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