2022/04/12 更新

写真a

タマ フロハンス 
TAMA Florence
TAMA Florence
所属
大学院理学研究科 理学専攻 物理学第一 教授
トランスフォーマティブ生命分子研究所 教授
大学院担当
大学院理学研究科
学部担当
理学部 物理学科
職名
教授

学位 2

  1. PhD, Computational Biophysics ( 2000年10月 ) 

  2. BS, Physics & Chemistry ( 1996年6月   University Paul Sabatier, France ) 

研究キーワード 3

  1. structure

  2. simulations

  3. biophysics

研究分野 1

  1. ライフサイエンス / 生物物理学

経歴 1

  1. 名古屋大学   トランスフォーマティブ生命分子研究所   研究員

    2016年4月 - 現在

 

論文 82

  1. NMMD: Efficient cryo-EM flexible fitting based on simultaneous Normal Mode and Molecular Dynamics atomic displacements. 査読有り 国際誌

    Rémi Vuillemot, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic

    Journal of molecular biology     頁: 167483 - 167483   2022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)  

    Atomic models of cryo electron microscopy (cryo-EM) maps of biomolecular conformations are often obtained by flexible fitting of the maps with available atomic structures of other conformations (e.g., obtained by X-ray crystallography). This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD). Given an atomic structure and a cryo-EM map to fit, NMMD simultaneously estimates global atomic displacements based on NMA and local displacements based on MD. NMMD was implemented by modifying EMfit, a flexible fitting method using MD only, in GENESIS 1.4. As EMfit, NMMD can be run with replica exchange umbrella sampling procedure. The new method was tested using a variety of EM maps (synthetic and experimental, with different noise levels and resolutions). The results of the tests show that adding normal modes to MD-based fitting makes the fitting faster (40% in average) and, in the majority of cases, more accurate.

    DOI: 10.1016/j.jmb.2022.167483

    PubMed

  2. Protocol for Retrieving Three-Dimensional Biological Shapes for a Few XFEL Single-Particle Diffraction Patterns 査読有り 国際誌

    Tiwari Sandhya P., Tama Florence, Miyashita Osamu

    JOURNAL OF CHEMICAL INFORMATION AND MODELING   61 巻 ( 8 ) 頁: 4108 - 4119   2021年8月

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    担当区分:責任著者   記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acs.jcim.1c00602

    Web of Science

    PubMed

  3. Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images 査読有り 国際誌

    Dasgupta Bhaskar, Miyashita Osamu, Uchihashi Takayuki, Tama Florence

    FRONTIERS IN MOLECULAR BIOSCIENCES   8 巻   頁: 704274 - 704274   2021年8月

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    担当区分:最終著者, 責任著者   記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.3389/fmolb.2021.704274

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    PubMed

  4. Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation 査読有り 国際誌

    Miller Simon, Srivastava Ashutosh, Nagai Yoshiko, Aikawa Yoshiki, Tama Florence, Hirota Tsuyoshi

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   118 巻 ( 26 )   2021年6月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1073/pnas.2026191118

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    PubMed

  5. Reversible modulation of circadian time with chronophotopharmacology 査読有り 国際誌

    Kolarski Dusan, Miro-Vinyals Carla, Sugiyama Akiko, Srivastava Ashutosh, Ono Daisuke, Nagai Yoshiko, Iida Mui, Itami Kenichiro, Tama Florence, Szymanski Wiktor, Hirota Tsuyoshi, Feringa Ben L.

    NATURE COMMUNICATIONS   12 巻 ( 1 ) 頁: 3164 - 3164   2021年5月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41467-021-23301-x

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    PubMed

  6. How CRY Regulates the Clock: Structural Studies of a Dynamic Mammalian Circadian Complex

    Sandate C., Fribourgh J., Michael A., Srivastava A., Hura G., Schneidman-Duhovny D., Tripathi S., Takahashi J., Lander G., Hirota T., Tama F., Partch C.

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   76 巻   頁: A122 - A122   2020年8月

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    記述言語:日本語  

    DOI: 10.1107/S0108767320098785

    Web of Science

  7. High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis. 査読有り 国際誌

    Kunio Nakata, Naoyuki Miyazaki, Hiroki Yamaguchi, Mika Hirose, Tatsuki Kashiwagi, Nidamarthi H V Kutumbarao, Osamu Miyashita, Florence Tama, Hiroshi Miyano, Toshimi Mizukoshi, Kenji Iwasaki

    Journal of structural biology     頁: 107842 - 107842   2022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)  

    In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called "bifid shunt." The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546-D547-H548-N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to "closed" and "open" states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

    DOI: 10.1016/j.jsb.2022.107842

    PubMed

  8. Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids 査読有り 国際誌

    Kuzuya Maki, Hirano Hidemi, Hayashida Kenichi, Watanabe Masakatsu, Kobayashi Kazumi, Terada Tohru, Mahmood Md Iqbal, Tama Florence, Tani Kazutoshi, Fujiyoshi Yoshinori, Oshima Atsunori

    SCIENCE SIGNALING   15 巻 ( 720 ) 頁: eabg6941   2022年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1126/scisignal.abg6941

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    PubMed

  9. Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock 査読有り 国際共著 国際誌

    Kolarski Dusan, Miller Simon, Oshima Tsuyoshi, Nagai Yoshiko, Aoki Yugo, Kobauri Piermichele, Srivastava Ashutosh, Sugiyama Akiko, Amaike Kazuma, Sato Ayato, Tama Florence, Szymanski Wiktor, Feringa Ben L., Itami Kenichiro, Hirota Tsuyoshi

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   143 巻 ( 4 ) 頁: 2078 - 2087   2021年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/jacs.0c12280

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    PubMed

  10. Isoform-selective regulation of mammalian cryptochromes 査読有り 国際誌

    Miller Simon, Son You Lee, Aikawa Yoshiki, Makino Eri, Nagai Yoshiko, Srivastava Ashutosh, Oshima Tsuyoshi, Sugiyama Akiko, Hara Aya, Abe Kazuhiro, Hirata Kunio, Oishi Shinya, Hagihara Shinya, Sato Ayato, Tama Florence, Itami Kenichiro, Kay Steve A., Hatori Megumi, Hirota Tsuyoshi

    NATURE CHEMICAL BIOLOGY   16 巻 ( 6 ) 頁: 676 - +   2020年6月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41589-020-0505-1

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  11. Computational Protocol for Assessing the Optimal Pixel Size to Improve the Accuracy of Single-particle Cryo-electron Microscopy Maps 査読有り 国際共著 国際誌

    Tiwari Sandhya P., Chhabra Sahil, Tama Florence, Miyashita Osamu

    JOURNAL OF CHEMICAL INFORMATION AND MODELING   60 巻 ( 5 ) 頁: 2570 - 2580   2020年5月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/acs.jcim.9b01107

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  12. Integrative/Hybrid Modeling Approaches for Studying Biomolecules 査読有り 国際誌

    Srivastava Ashutosh, Tiwari Sandhya Premnath, Miyashita Osamu, Tama Florence

    JOURNAL OF MOLECULAR BIOLOGY   432 巻 ( 9 ) 頁: 2846 - 2860   2020年4月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.jmb.2020.01.039

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    PubMed

  13. Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing 査読有り 国際誌

    Fribourgh Jennifer L., Srivastava Ashutosh, Sandate Colby R., Michael Alicia K., Hsu Peter L., Rakers Christin, Nguyen Leslee T., Torgrimson Megan R., Parico Gian Carlo G., Tripathi Sarvind, Zheng Ning, Lander Gabriel C., Hirota Tsuyoshi, Tama Florence, Partch Carrie L.

    ELIFE   9 巻   2020年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.7554/eLife.55275

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    PubMed

  14. Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations 査読有り 国際誌

    Srivastava Arpita, Bala Siqin, Motomura Hajime, Kohda Daisuke, Tama Florence, Miyashita Osamu

    BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS   1864 巻 ( 2 ) 頁: 129417 - 129417   2020年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.bbagen.2019.129417

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  15. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images 査読有り 国際誌

    Dasgupta Bhaskar, Miyashita Osamu, Tama Florence

    BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS   1864 巻 ( 2 ) 頁: 129420 - 129420   2020年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.bbagen.2019.129420

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    PubMed

  16. Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study 査読有り 国際誌

    Bala Siqin, Shinya Shoko, Srivastava Arpita, Ishikawa Marie, Shimada Atsushi, Kobayashi Naohiro, Kojima Chojiro, Tama Florence, Miyashita Osamu, Kohda Daisuke

    BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS   1864 巻 ( 2 ) 頁: 129418 - 129418   2020年2月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.bbagen.2019.129418

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    PubMed

  17. Controlling the Circadian Clock with High Temporal Resolution through Photodosing 査読有り 国際誌

    Kolarski Dusan, Sugiyama Akiko, Breton Ghislain, Rakers Christin, Ono Daisuke, Schulte Albert, Tama Florence, Itami Kenichiro, Szymanski Wiktor, Hirota Tsuyoshi, Feringa Ben L.

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   141 巻 ( 40 ) 頁: 15784 - 15791   2019年10月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1021/jacs.9b05445

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  18. Bipartite anchoring of SCREAM enforces stomatal initiation by coupling MAP kinases to SPEECHLESS 査読有り

    Putarjunan Aarthi, Ruble Jim, Srivastava Ashutosh, Zhao Chunzhao, Rychel Amanda L., Hofstetter Alex K., Tang Xiaobo, Zhu Jian-Kang, Tama Florence, Zheng Ning, Torii Keiko U.

    NATURE PLANTS   5 巻 ( 7 ) 頁: 742 - 754   2019年7月

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  19. Cryo-Cooling Effect on DHFR Crystal Studied by Replica-Exchange Molecular Dynamics Simulations 査読有り

    Nagai Tetsuro, Tama Florence, Miyashita Osamu

    BIOPHYSICAL JOURNAL   116 巻 ( 3 ) 頁: 395 - 405   2019年2月

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  20. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning 査読有り

    Mori Takaharu, Kulik Marta, Miyashita Osamu, Jung Jaewoon, Tama Florence, Sugita Yuji

    STRUCTURE   27 巻 ( 1 ) 頁: 161 - +   2019年1月

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    記述言語:日本語  

    DOI: 10.1016/j.str.2018.09.004

    Web of Science

  21. Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth 査読有り 国際誌

    Oshima Tsuyoshi, Niwa Yoshimi, Kuwata Keiko, Srivastava Ashutosh, Hyoda Tomoko, Tsuchiya Yoshiki, Kumagai Megumi, Tsuyuguchi Masato, Tamaru Teruya, Sugiyama Akiko, Ono Natsuko, Zolboot Norjin, Aikawa Yoshiki, Oishi Shunsuke, Nonami Atsushi, Arai Fumio, Hagihara Shinya, Yamaguchi Junichiro, Tama Florence, Kunisaki Yuya, Yagita Kazuhiro, Ikeda Masaaki, Kinoshita Takayoshi, Kay Steve A., Itami Kenichiro, Hirota Tsuyoshi

    SCIENCE ADVANCES   5 巻 ( 1 ) 頁: eaau9060   2019年1月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1126/sciadv.aau9060

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  22. Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes 査読有り

    Srivastava Arpita, Tama Florence, Kohda Daisuke, Miyashita Osamu

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   87 巻 ( 1 ) 頁: 81 - 90   2019年1月

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    記述言語:日本語  

    DOI: 10.1002/prot.25625

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  23. Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching 査読有り

    Nakano Miki, Miyashita Osamu, Tama Florence

    BIOPHYSICS AND PHYSICOBIOLOGY   16 巻   頁: 367 - 376   2019年

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.2142/biophysico.16.0_367

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  24. Poisson image denoising by piecewise principal component analysis and its application in single-particle X-ray diffraction imaging 査読有り

    Jin Qiyu, Miyashita Osamu, Tama Florence, Yang Jie, Jonic Slavica

    IET IMAGE PROCESSING   12 巻 ( 12 ) 頁: 2264 - 2274   2018年12月

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    記述言語:日本語  

    DOI: 10.1049/iet-ipr.2018.5145

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  25. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics 査読有り

    Srivastava Ashutosh, Nagai Tetsuro, Srivastava Arpita, Miyashita Osamu, Tama Florence

    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES   19 巻 ( 11 )   2018年11月

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    記述言語:日本語  

    DOI: 10.3390/ijms19113401

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  26. Gaussian mixture model for coarse-grained modeling from XFEL 査読有り

    Nagai Tetsuro, Mochizuki Yuki, Joti Yasumasa, Tama Florence, Miyashita Osamu

    OPTICS EXPRESS   26 巻 ( 20 ) 頁: 26734 - 26749   2018年10月

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    記述言語:日本語  

    DOI: 10.1364/OE.26.026734

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  27. Searching for 3D structural models from a library of biological shapes using a few 2D experimental images 査読有り

    Tiwari Sandhya P., Tama Florence, Miyashita Osamu

    BMC BIOINFORMATICS   19 巻   2018年9月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1186/s12859-018-2358-0

    Web of Science

  28. Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution 査読有り

    Nakano Miki, Miyashita Osamu, Jonic Slavica, Tokuhisa Atsushi, Tama Florence

    JOURNAL OF SYNCHROTRON RADIATION   25 巻   頁: 1010 - 1021   2018年7月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1107/S1600577518005568

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  29. Conformational dynamics of human protein kinase CK2 alpha and its effect on function and inhibition 査読有り

    Srivastava Ashutosh, Hirota Tsuyoshi, Irle Stephan, Tama Florence

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   86 巻 ( 3 ) 頁: 344 - 353   2018年3月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1002/prot.25444

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    Scopus

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  30. Hybrid Methods for Macromolecular Modeling by Molecular Mechanics Simulations with Experimental Data 査読有り

    Miyashita Osamu, Tama Florence

    INTEGRATIVE STRUCTURAL BIOLOGY WITH HYBRID METHODS   1105 巻   頁: 199 - 217   2018年

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  31. Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL. 査読有り

    Nakano M, Miyashita O, Jonic S, Song C, Nam D, Joti Y, Tama F

    Journal of synchrotron radiation   24 巻 ( Pt 4 ) 頁: 727 - 737   2017年7月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)   出版者・発行元:International Union of Crystallography ({IUCr})  

    DOI: 10.1107/S1600577517007767

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  32. Computational investigation of binding and dynamics in Tom20-mitochondrial targeting signal complex

    Srivastava A., Miyashita O., Tama F.

    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS   46 巻   頁: S232 - S232   2017年7月

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  33. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations 査読有り

    Miyashita Osamu, Kobayashi Chigusa, Mori Takaharu, Sugita Yuji, Tama Florence

    JOURNAL OF COMPUTATIONAL CHEMISTRY   38 巻 ( 16 ) 頁: 1447 - 1461   2017年6月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1002/jcc.24785

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  34. Editorial overview: Macromolecular assemblies 査読有り

    Shimizu Toshiyuki, Tama Florence

    CURRENT OPINION IN STRUCTURAL BIOLOGY   43 巻   頁: VII - ix   2017年4月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.sbi.2017.04.009

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  35. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory 査読有り

    Nakano Miki, Tateishi-Karimata Hisae, Tanaka Shigenori, Tama Florence, Miyashita Osamu, Nakano Shu-ichi, Sugimoto Naoki

    CHEMICAL PHYSICS LETTERS   660 巻   頁: 250 - 255   2016年9月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.cplett.2016.08.032

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  36. Hybrid approach for structural modeling of biological systems from X-ray free electron laser diffraction patterns 査読有り

    Tokuhisa Atsushi, Jonic Slavica, Tama Florence, Miyashita Osamu

    JOURNAL OF STRUCTURAL BIOLOGY   194 巻 ( 3 ) 頁: 325 - 336   2016年6月

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.jsb.2016.03.009

    Web of Science

  37. Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory 査読有り

    Nakano Miki, Tateishi-Karimata Hisae, Tanaka Shigenori, Tama Florence, Miyashita Osamu, Nakano Shu-ichi, Sugimoto Naoki

    NUCLEIC ACIDS RESEARCH   43 巻 ( 21 ) 頁: 10114-10125   2015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/nar/gkv1133

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  38. Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol 査読有り

    Carlos Oscar S. Sorzano, Jose Miguel de la Rosa-Trevin, Florence Tama, Slavica Jonic

    JOURNAL OF STRUCTURAL BIOLOGY   188 巻 ( 2 ) 頁: 134 - 141   2014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)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction. (C) 2014 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2014.09.005

    Web of Science

  39. Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins 査読有り

    Sunita Patel, Elizabeth Vierling, Florence Tama

    BIOPHYSICAL JOURNAL   106 巻 ( 12 ) 頁: 2644 - 2655   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)   出版者・発行元:CELL PRESS  

    The small heat shock proteins (sHSPs) are a virtually ubiquitous and diverse group of molecular chaperones that can bind and protect unfolding proteins from irreversible aggregation. It has been suggested that intrinsic disorder of the N-terminal arm (NTA) of sHSPs is important for substrate recognition. To investigate conformations of the NTA that could recognize substrates we performed replica exchange molecular dynamics simulations. Behavior at normal and stress temperatures of the dimeric building blocks of dodecameric HSPs from wheat (Ta16.9) and pea (Ps18.1) were compared because they display high sequence similarity, but Ps18.1 is more efficient in binding specific substrates. In our simulations, the NTAs of the dimer are flexible and dynamic; however, rather than exhibiting highly extended conformations they retain considerable alpha-helical character and contacts with the conserved alpha-crystallin domain (ACD). Network analysis and clustering methods reveal that there are two major conformational forms designated either "open" or "closed" based on the relative position of the two NTAs and their hydrophobic solvent accessible surface area. The equilibrium constant for the closed to open transition is significantly different for Ta16.9 and Ps18.1, with the latter showing more open conformations at elevated temperature correlated with its more effective chaperone activity. In addition, the Ps18.1 NTAs have more hydrophobic solvent accessible surface than those of Ta16.9. NTA hydrophobic patches are comparable in size to the area buried in many protein-protein interactions, which would enable sHSPs to bind early unfolding intermediates. Reduced interactions of the Ps18.1 NTAs with each other and with the ACD contribute to the differences in dynamics and hydrophobic surface area of the two sHSPs. These data support a major role for the conformational equilibrium of the NTA in substrate binding and indicate features of the NTA that contribute to sHSP chaperone efficiency.

    DOI: 10.1016/j.bpj.2014.04.048

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  40. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging 査読有り

    Marcus Gallagher-Jones, Yoshitaka Bessho, Sunam Kim, Jaehyun Park, Sangsoo Kim, Daewoong Nam, Chan Kim, Yoonhee Kim, Do Young Noh, Osamu Miyashita, Florence Tama, Yasumasa Joti, Takashi Kameshima, Takaki Hatsui, Kensuke Tono, Yoshiki Kohmura, Makina Yabashi, S. Samar Hasnain, Tetsuya Ishikawa, Changyong Song

    NATURE COMMUNICATIONS   5 巻   2014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:NATURE PUBLISHING GROUP  

    Nanostructures formed from biological macromolecular complexes utilizing the self-assembly properties of smaller building blocks such as DNA and RNA hold promise for many applications, including sensing and drug delivery. New tools are required for their structural characterization. Intense, femtosecond X-ray pulses from X-ray free-electron lasers enable single-shot imaging allowing for instantaneous views of nanostructures at ambient temperatures. When combined judiciously with synchrotron X-rays of a complimentary nature, suitable for observing steady-state features, it is possible to perform ab initio structural investigation. Here we demonstrate a successful combination of femtosecond X-ray single-shot diffraction with an X-ray free-electron laser and coherent diffraction imaging with synchrotron X-rays to provide an insight into the nanostructure formation of a biological macromolecular complex: RNA interference microsponges. This newly introduced multimodal analysis with coherent X-rays can be applied to unveil nano-scale structural motifs from functional nanomaterials or biological nanocomplexes, without requiring a priori knowledge.

    DOI: 10.1038/ncomms4798

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  41. Iterative Elastic 3D-to-2D Alignment Method Using Normal Modes for Studying Structural Dynamics of Large Macromolecular Complexes 査読有り

    Qiyu Jin, Carlos Oscar S. Sorzano, Jose Miguel de la Rosa-Trevin, Jose Roman Bilbao-Castro, Rafael Nunez-Ramirez, Oscar Llorca, Florence Tama, Slavica Jonic

    STRUCTURE   22 巻 ( 3 ) 頁: 496 - 506   2014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:CELL PRESS  

    This article presents a method to study large-scale conformational changes by combining electron microscopy (EM) single-particle image analysis and normal mode analysis (NMA). It is referred to as HEMNMA, which stands for hybrid electron microscopy normal mode analysis. NMA of a reference structure (atomic-resolution structure or EM volume) is used to predict possible motions that are then confronted with EM images within an automatic iterative elastic 3D-to-2D alignment procedure to identify actual motions in the imaged samples. HEMNMA can be used to extensively analyze the conformational changes and may be used in combination with classic discrete procedures. The identified conformations allow modeling of deformation pathways compatible with the experimental data. HEMNMA was tested with synthetic and experimental data sets of E. coli 70S ribosome, DNA polymerase Pol alpha and B subunit complex of the eukaryotic primosome, and tomato bushy stunt virus.

    DOI: 10.1016/j.str.2014.01.004

    Web of Science

  42. ELASTIC IMAGE REGISTRATION TO FULLY EXPLORE MACROMOLECULAR DYNAMICS BY ELECTRON MICROSCOPY 査読有り

    Jin Qiyu, Sanchez Sorzano Carlos Oscar, Callebaut Isabelle, Tama Florence, Jonic Slavica

    2014 IEEE INTERNATIONAL CONFERENCE ON IMAGE PROCESSING (ICIP)     頁: 2075-2079   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Web of Science

  43. ELASTIC IMAGE REGISTRATION TO FULLY EXPLORE MACROMOLECULAR DYNAMICS BY ELECTRON MICROSCOPY 査読有り

    Qiyu Jin, Carlos Oscar Sanchez Sorzano, Isabelle Callebaut, Florence Tama, Slavica Jonic

    2014 IEEE INTERNATIONAL CONFERENCE ON IMAGE PROCESSING (ICIP)     頁: 2075 - 2079   2014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)   出版者・発行元:IEEE  

    Structural changes are critical for biological functions of proteins and describing conformational changes in large macromolecular complexes is a major challenge. We have recently developed a hybrid method (HEMNMA) combining transmission electron microscopy (EM), normal mode analysis (NMA), and image analysis to study macromolecular dynamics. NMA is traditionally used to study macromolecular motions while HEMNMA provides insight into actual conformational changes seen by EM. HEMNMA uses normal modes to elastically align EM images with a reference structure in order to determine the conformations present in images and evaluate their pertinence. In this paper, we show how HEMNMA can be used with an atomic-resolution reference structure, using as an example the study of the conformational dynamics of Tomato Bushy Stunt Virus.

    Web of Science

  44. Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization 査読有り

    Dmitry Lyumkis, Heather Talley, Andrew Stewart, Santosh Shah, Chad K. Park, Florence Tama, Clinton S. Potter, Bridget Carragher, Nancy C. Horton

    STRUCTURE   21 巻 ( 10 ) 頁: 1848 - 1858   2013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)   出版者・発行元:CELL PRESS  

    SgrAl is a sequence specific DNA endonuclease that functions through an unusual enzymatic mechanism that is allosterically activated 200- to 500-fold by effector DNA, with a concomitant expansion of its DNA sequence specificity. Using single-particle transmission electron microscopy to reconstruct distinct populations of SgrAl oligomers, we show that in the presence of allosteric, activating DNA, the enzyme forms regular, repeating helical structures characterized by the addition of DNA-binding dimeric SgrAl subunits in a run-on manner. We also present the structure of oligomeric SgrAl at 8.6 angstrom resolution, demonstrating the conformational state of SgrAl in its activated form. Activated and oligomeric SgrAl displays key protein-protein interactions near the helix axis between its N termini, as well as allosteric protein-DNA interactions that are required for enzymatic activation. The hybrid approach reveals an unusual mechanism of enzyme activation that explains SgrAl's oligomerization and allosteric behavior.

    DOI: 10.1016/j.str.2013.08.012

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  45. 3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy 査読有り

    R. Nogales-Cadenas, S. Jonic, F. Tama, A. A. Arteni, D. Tabas-Madrid, M. Vazquez, A. Pascual-Montano, C. O. S. Sorzano

    NUCLEIC ACIDS RESEARCH   41 巻 ( W1 ) 頁: W363 - W367   2013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)   出版者・発行元:OXFORD UNIV PRESS  

    Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 angstrom resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.

    DOI: 10.1093/nar/gkt385

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  46. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data 査読有り

    Aqeel Ahmed, Florence Tama

    JOURNAL OF STRUCTURAL BIOLOGY   182 巻 ( 2 ) 頁: 67 - 77   2013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:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    Cryo-electron microscopy (cryo-EM) can provide low-resolution density maps of large macromolecular assemblies. As the number of structures deposited in the Protein Data Bank by fitting a high-resolution structure into a low-resolution cryo-EM map is increasing, there is a need to revise the protocols and improve the measures for fitting. A recent study suggested using a combination of multiple automated flexible fitting approaches to improve the interpretation of cryo-EM data. The current work further explores the use of multiple approaches by validating this "consensus" fitting approach and deriving a local reliability measure. Here four different flexible fitting approaches are applied for fitting an initial structure into a simulated density map of known target structure from a dataset of proteins. It is found that the models produced from different approaches often have a consensus in conformation and are also near to the target structure, whereas cases not showing consensus are away from the target. A high correlation is also observed between the RMSF profiles calculated with respect to the average and the target structures, which indicates that the relation between consensus and accuracy can also be extended to a per-residue level. Therefore, the RMSF among the fitted models is proposed as a local reliability measure, which can be used to assess the reliability of the fit at specific regions. Hence, we encourage the community to use consensus flexible fitting with different methods to report on local reliability of the resulting models and improve the interpretation of cryo-EM data. (c) 2013 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2013.02.002

    Web of Science

  47. Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition 査読有り

    Joseph L. Baker, Nicolas Biais, Florence Tama

    PLOS COMPUTATIONAL BIOLOGY   9 巻 ( 4 )   2013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 SCIENCE  

    Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin alpha 1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin alpha 1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching.

    DOI: 10.1371/journal.pcbi.1003032

    Web of Science

  48. Molecular Model of a Soluble Guanylyl Cyclase Fragment Determined by Small-Angle X-ray Scattering and Chemical Cross-Linking 査読有り

    Bradley G. Fritz, Sue A. Roberts, Aqeel Ahmed, Linda Breci, Wenzhou Li, Andrzej Weichsel, Jacqueline L. Brailey, Vicki H. Wysocki, Florence Tama, William R. Montfort

    BIOCHEMISTRY   52 巻 ( 9 ) 頁: 1568 - 1582   2013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:AMER CHEMICAL SOC  

    Soluble guanylyl/guanylate cyclase (sGC) converts GTP to cGMP after binding nitric oxide, leading to smooth muscle relaxation and vasodilation. Impaired sGC activity is common in cardiovascular disease, and sGC stimulatory compounds are vigorously sought. sGC is a 150 kDa heterodimeric protein with two H-NOX domains (one with heme, one without), two PAS domains, a coiled-coil domain, and two cyclase domains. Binding of NO to the sGC heme leads to proximal histidine release and stimulation of catalytic activity. To begin to understand how binding leads to activation, we examined truncated sGC proteins from Manduca sexta (tobacco hornworm) that bind NO, CO, and stimulatory compound YC-1 but lack the cyclase domains. We determined the overall shape of truncated M. sexta sGC using analytical ultracentrifugation and small-angle X-ray scattering (SAXS), revealing an elongated molecule with dimensions of 115 angstrom x 90 angstrom x 75 angstrom. Binding of NO, CO, or YC-1 had little effect on shape. Using chemical cross-linking and tandem mass spectrometry, we identified 20 intermolecular contacts, allowing us to fit homology models of the individual domains into the SAXS-derived molecular envelope. The resulting model displays a central parallel coiled-coil platform upon which the H-NOX and PAS domains are assembled. The beta(1) H-NOX and alpha(1) PAS domains are in contact and form the core signaling complex, while the alpha(1) H-NOX domain can be removed without a significant effect on ligand binding or overall shape. Removal of 21 residues from the C-terminus yields a protein with dramatically increased proximal histidine release rates upon NO binding.

    DOI: 10.1021/bi301570m

    Web of Science

  49. Network visualization of conformational sampling during molecular dynamics simulation 査読有り

    Logan S. Ahlstrom, Joseph Lee Baker, Kent Ehrlich, Zachary T. Campbell, Sunita Patel, Ivan I. Vorontsov, Florence Tama, Osamu Miyashita

    Journal of Molecular Graphics and Modelling   46 巻   頁: 140 - 149   2013年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Effective data reduction methods are necessary for uncovering the inherent conformational relationships present in large molecular dynamics (MD) trajectories. Clustering algorithms provide a means to interpret the conformational sampling of molecules during simulation by grouping trajectory snapshots into a few subgroups, or clusters, but the relationships between the individual clusters may not be readily understood. Here we show that network analysis can be used to visualize the dominant conformational states explored during simulation as well as the connectivity between them, providing a more coherent description of conformational space than traditional clustering techniques alone. We compare the results of network visualization against 11 clustering algorithms and principal component conformer plots. Several MD simulations of proteins undergoing different conformational changes demonstrate the effectiveness of networks in reaching functional conclusions. © 2013 Elsevier Inc.

    DOI: 10.1016/j.jmgm.2013.10.003

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    Scopus

    PubMed

  50. Twelve Transmembrane Helices Form the Functional Core of Mammalian MATE1 (Multidrug and Toxin Extruder 1) Protein 査読有り

    Xiaohong Zhang, Xiao He, Joseph Baker, Florence Tama, Geoffrey Chang, Stephen H. Wright

    JOURNAL OF BIOLOGICAL CHEMISTRY   287 巻 ( 33 ) 頁: 27971 - 27982   2012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:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

    The x-ray structure of the prototypic MATE family member, NorM from Vibrio cholerae, reveals a protein fold composed of 12 transmembrane helices (TMHs), confirming hydropathy analyses of the majority of (prokaryotic and plant) MATE transporters. However, the mammalian MATEs are generally predicted to have a 13th TMH and an extracellular C terminus. Here we affirm this prediction, showing that the C termini of epitope-tagged, full-length human, rabbit, and mouse MATE1 were accessible to antibodies from the extracellular face of the membrane. Truncation of these proteins at or near the predicted junction between the 13th TMH and the long cytoplasmic loop that precedes it resulted in proteins that (i) trafficked to the membrane and (ii) interacted with antibodies only after permeabilization of the plasma membrane. CHO cells expressing rbMate1 truncated at residue Gly-545 supported levels of pH-sensitive transport similar to that of cells expressing the full-length protein. Although the high transport rate of the Gly-545 truncation mutant was associated with higher levels of membrane expression (than full-length MATE1), suggesting the 13th TMH may influence substrate translocation, the selectivity profile of the mutant indicated that TMH13 has little impact on ligand binding. We conclude that the functional core of MATE1 consists of 12 (not 13) TMHs. Therefore, we used the x-ray structure of NorM to develop a homology model of the first 12 TMHs of MATE1. The model proved to be stable in molecular dynamic simulations and agreed with topology evident from preliminary cysteine scanning of intracellular versus extracellular loops.

    DOI: 10.1074/jbc.M112.386979

    Web of Science

  51. Simulations of substrate transport in the multidrug transporter EmrD 査読有り

    Joseph Baker, Stephen H. Wright, Florence Tama

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   80 巻 ( 6 ) 頁: 1620 - 1632   2012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:WILEY  

    EmrD is a multidrug resistance (MDR) transporter from Escherichia coli, which is involved in the efflux of amphipathic compounds from the cytoplasm, and the first MDR member of the major facilitator superfamily to be crystallized. Molecular dynamics simulation of EmrD in a phospholipid bilayer was used to characterize the conformational dynamics of the protein. Motions that support a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the EmrD central cavity were observed. In addition, the translocation pathway of meta-chloro carbonylcyanide phenylhydrazone (CCCP) was probed using both standard and steered molecular dynamics simulation. In particular, interactions of a few specific residues with CCCP have been identified. Finally, a large motion of two residues, Val 45 and Leu 233, was observed with the passage of CCCP into the periplasmic space, placing a lower bound on the extent of opening required at this end of the protein for substrate transport. Overall, our simulations probe details of the transport pathway, motions of EmrD at an atomic level of detail, and offer new insights into the functioning of MDR transporters. Proteins 2012; (c) 2012 Wiley Periodicals, Inc.

    DOI: 10.1002/prot.24056

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  52. Twelve transmembrane helices form the functional core of mammalian MATE1 査読有り

    Zhang Xiaohong, He Xiao, Baker Joseph, Tama Florence, Chang Geoffrey, Wright Stephen

    FASEB JOURNAL   26 巻   頁: .   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)  

    Web of Science

  53. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data 査読有り

    Aqeel Ahmed, Paul C. Whitford, Karissa Y. Sanbonmatsu, Florence Tama

    JOURNAL OF STRUCTURAL BIOLOGY   177 巻 ( 2 ) 頁: 561 - 570   2012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:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    Cryo-elecron microscopy (cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map. A commonly used protocol for accommodating the conformational changes between the X-ray structure and the cryo-EM map is rigid body fitting of individual domains. With the emergence of different flexible fitting approaches, there is a need to compare and revise these different protocols for the fitting. We have applied three diverse automated flexible fitting approaches on a protein dataset for which rigid domain fitting (RDF) models have been deposited in the PDB. In general, a consensus is observed in the conformations, which indicates a convergence from these theoretically different approaches to the most probable solution corresponding to the cryo-EM map. However, the result shows that the convergence might not be observed for proteins with complex conformational changes or with missing densities in cryo-EM map. In contrast, RDF structures deposited in the PDB can represent conformations that not only differ from the consensus obtained by flexible fitting but also from X-ray crystallography. Thus, this study emphasizes that a "consensus" achieved by the use of several automated flexible fitting approaches can provide a higher level of confidence in the modeled configurations. Following this protocol not only increases the confidence level of fitting, but also highlights protein regions with uncertain fitting. Hence, this protocol can lead to better interpretation of cryo-EM data. (C) 2011 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2011.10.002

    Web of Science

  54. Phosphorylated Smooth Muscle Heavy Meromyosin Shows an Open Conformation: Implications for the Structure of Myosin with One Head Phosphorylated 査読有り

    Taylor Kenneth A., Baumann Bruce A. J., Taylor Dianne W., Huang Zhong, Tama Florence, Fagnant Patricia M., Trybus Kathleen M.

    BIOPHYSICAL JOURNAL   102 巻 ( 3 ) 頁: 159A-159A   2012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)  

    Web of Science

  55. Phosphorylated Smooth Muscle Heavy Meromyosin Shows an Open Conformation Linked to Activation 査読有り

    Bruce A. J. Baumann, Dianne W. Taylor, Zhong Huang, Florence Tama, Patricia M. Fagnant, Kathleen M. Trybus, Kenneth A. Taylor

    JOURNAL OF MOLECULAR BIOLOGY   415 巻 ( 2 ) 頁: 274 - 287   2012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 LTD- ELSEVIER SCIENCE LTD  

    Smooth muscle myosin and smooth muscle heavy meromyosin (smHMM) are activated by regulatory light chain phosphorylation, but the mechanism remains unclear. Dephosphorylated, inactive smHMM assumes a closed conformation with asymmetric intramolecular head head interactions between motor domains. The "free head" can bind to actin, but the actin binding interface of the "blocked head" is involved in interactions with the free head. We report here a three-dimensional structure for phosphorylated, active smHMM obtained using electron crystallography of two-dimensional arrays. Head head interactions of phosphorylated smHMM resemble those found in the dephosphorylated state but occur between different molecules, not within the same molecule. The light chain binding domain structure of phosphorylated smHMM differs markedly from that of the "blocked" head of dephosphorylated smHMM. We hypothesize that regulatory light chain phosphorylation opens the inhibited conformation primarily by its effect on the blocked head. Singly phosphorylated smHMM is not compatible with the closed conformation if the blocked head is phosphorylated. This concept has implications for the extent of myosin activation at low levels of phosphorylation in smooth muscle. (C) 2011 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.jmb.2011.10.047

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  56. Excited states of ribosome translocation revealed through integrative molecular modeling 査読有り

    Paul C. Whitford, Aqeel Ahmed, Yanan Yu, Scott P. Hennelly, Florence Tama, Christian M. T. Spahn, Jose N. Onuchic, Karissa Y. Sanbonmatsu

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   108 巻 ( 47 ) 頁: 18943 - 18948   2011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)   出版者・発行元:NATL ACAD SCIENCES  

    The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles). Here, we present a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements. To demonstrate the approach, we present a sequence of configurations that are suggested to be associated with transfer RNA (tRNA) movement through the ribosome (translocation). The models were constructed by combining information from X-ray crystallography, cryo-electron microscopy, and biochemical data. These models provide a structural framework for translocation that may be further investigated experimentally and theoretically to determine the precise energetic character of each configuration and the transition dynamics between them.

    DOI: 10.1073/pnas.1108363108

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  57. Structure modeling from small angle X-ray scattering data with elastic network normal mode analysis 査読有り

    Osamu Miyashita, Christian Gorba, Florence Tama

    JOURNAL OF STRUCTURAL BIOLOGY   173 巻 ( 3 ) 頁: 451 - 460   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)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    Computational algorithms to construct structural models from SAXS experimental data are reviewed. SAXS data provides a wealth of information to study the structure and dynamics of biological molecules, however it does not provide atomic details of structures. Thus combining the low-resolution data with already known X-ray structure is a common approach to study conformational transitions of biological molecules. This review provides a survey of SAXS modeling approaches. In addition, we will discuss theoretical backgrounds and performance of our approach, in which elastic network normal mode analysis is used to predict reasonable conformational transitions from known X-ray structures, and find alternative conformations that are consistent with SAXS data. (C) 2010 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2010.09.008

    Web of Science

  58. Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles 査読有り

    H. Katayama, J. Wang, F. Tama, L. Chollet, E. P. Gogol, R. J. Collier, M. T. Fisher

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   107 巻 ( 8 ) 頁: 3453 - 3457   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)   出版者・発行元:NATL ACAD SCIENCES  

    A major goal in understanding the pathogenesis of the anthrax bacillus is to determine how the protective antigen (PA) pore mediates translocation of the enzymatic components of anthrax toxin across membranes. To obtain structural insights into this mechanism, we constructed PA-pore membrane complexes and visualized them by using negative-stain electron microscopy. Two populations of PA pores were visualized in membranes, vesicle-inserted and nanodisc-inserted, allowing us to reconstruct two virtually identical PA-pore structures at 22-angstrom resolution. Reconstruction of a domain 4-truncated PA pore inserted into nanodiscs showed that this domain does not significantly influence pore structure. Normal mode flexible fitting of the x-ray crystallographic coordinates of the PA prepore indicated that a prominent flange observed within the pore lumen is formed by the convergence of mobile loops carrying Phe427, a residue known to catalyze protein translocation. Our results have identified the location of a crucial functional element of the PA pore and documented the value of combining nanodisc technology with electron microscopy to examine the structures of membrane-interactive proteins.

    DOI: 10.1073/pnas.1000100107

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  59. Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps 査読有り

    Ivan Grubisic, Maxim N. Shokhirev, Marek Orzechowski, Osamu Miyashita, Florence Tama

    JOURNAL OF STRUCTURAL BIOLOGY   169 巻 ( 1 ) 頁: 95 - 105   2010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 ELSEVIER SCIENCE  

    Several approaches have been introduced to interpret, in terms of high-resolution structure, low-resolution structural data as obtained from cryo-EM. As conformational changes are often observed in biological molecules, these techniques need to take into account the flexibility of proteins. Flexibility has been described in terms of movement between rigid domains and between rigid secondary structure elements, which present some limitations for studying dynamical properties. Normal mode analysis has also been used, but is limited to medium resolution data. All-atom molecular dynamics fitting techniques are more appropriate to fit structures into higher-resol uti on data as full protein flexibility is considered, but are cumbersome in terms of computational time. Here, we introduce a coarse-grained approach; a Go-model was used to represent biological molecules, combined with biased molecular dynamics to reproduce accurately conformational transitions. Illustrative examples on simulated data are shown. Accurate fittings can be obtained for resolution ranging from 5 to 20 angstrom. The approach was also tested on experimental data of Elongation Factor G and Escherichia coli RNA polymerase, where its validity is compared to previous models obtained from different techniques. This comparison demonstrates that quantitative flexible techniques, as opposed to manual docking, need to be considered to interpret low-resolution data. (C) 2009 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2009.09.010

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  60. Flexible Fitting of High-Resolution X-Ray Structures into Cryoelectron Microscopy Maps Using Biased Molecular Dynamics Simulations 査読有り

    Marek Orzechowski, Florence Tama

    BIOPHYSICAL JOURNAL   95 巻 ( 12 ) 頁: 5692 - 5705   2008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:CELL PRESS  

    A methodology for flexible fitting of all-atom high-resolution structures into low-resolution cryoelectron microscopy (cryo-EM) maps is presented. Flexibility of the modeled structure is simulated by classical molecular dynamics and an additional effective potential is introduced to enhance the fitting process. The additional potential is proportional to the correlation coefficient between the experimental cryo-EM map and a synthetic map generated for an all-atom structure being fitted to the map. The additional forces are calculated as a gradient of the correlation coefficient. During the molecular dynamics simulations under the additional forces, the molecule undergoes a conformational transition that maximizes the correlation coefficient, which results in a high-accuracy fit of all-atom structure into a cryo-EM map. Using five test proteins that exhibit structural rearrangement during their biological activity, we demonstrate performance of our method. We also test our method on the experimental cryo-EM of elongation factor G and show that the model obtained is comparable to previous studies. In addition, we show that over fitting can be avoided by assessing the quality of the fitted model in terms of correlation coefficient and secondary structure preservation.

    DOI: 10.1529/biophysj.108.139451

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  61. Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data 査読有り

    Christian Gorba, Osamu Miyashita, Florence Tama

    BIOPHYSICAL JOURNAL   94 巻 ( 5 ) 頁: 1589 - 1599   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)   出版者・発行元:BIOPHYSICAL SOC  

    We present a method for reconstructing a 3D structure from a pair distribution function by flexibly fitting known x-ray structures toward a conformation that agrees with the low-resolution data. This method uses a linear combination of low-frequency normal modes from elastic-network description of the molecule in an iterative manner to deform the structure optimally to conform to the target pair distribution function. A simple function, pair distance distribution function between atoms, is chosen as a test model to establish computational algorithms-optimization algorithm and scoring function-that can utilize low-resolution 1 D data. To select a correct structural model based on less information, we developed a scoring function that takes into account a characteristic of pair distribution functions. In addition, we employ a new optimization algorithm, the trusted region method, that relies on both first and second derivatives of the scoring function. Illustrative results of our studies on simulated 1D data from five different proteins, for which large conformational changes are known to occur, are presented.

    DOI: 10.1529/biophysj.107.122218

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  62. Normal Mode Analysis Techniques in Structural Biology. 招待有り 査読有り

    eLS     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: 10.1002/9780470015902.a0020204

  63. Removal of divalent cations induces structural transitions in Red clover necrotic mosaic virus, revealing a potential mechanism for RNA release 査読有り

    Michael B. Sherman, Richard H. Guenther, Florence Tama, Tim L. Sit, Charles L. Brooks, Albert M. Mikhailov, Elena V. Orlova, Timothy S. Baker, Steven A. Lommel

    JOURNAL OF VIROLOGY   80 巻 ( 21 ) 頁: 10395 - 10406   2006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)   出版者・発行元:AMER SOC MICROBIOLOGY  

    The structure of Red clover necrotic mosaic virus (RCNW), an icosahedral plant virus, was resolved to 8.5 by cryoelectron microscopy. The virion capsid has prominent surface protrusions and subunits with a clearly defined shell and protruding domains. The structures of both the individual capsid protein (CP) subunits and the entire virion capsid are consistent with other species in the Tombusviridae family. Within the RCNNW capsid, there is a clearly defined inner cage formed by complexes of genomic RNA and the amino termini of CP subunits. An RCNNW virion has approximately 390 +/- 30 Ca2+ ions bound to the capsid and 420 +/- 25 Mg2+ ions thought to be in the interior of the capsid. Depletion of both Ca2+ and Mg2+ ions from RCNMV leads to significant structural changes, including (i) formation of 11- to 13-A-diameter channels that extend through the capsid and (ii) significant reorganization within the interior of the capsid. Genomic RNA within native capsids containing both Ca2+ and Mg2+ ions is extremely resistant to nucleases, but depletion of both of these cations results in nuclease sensitivity, as measured by a significant reduction in RCNMV infectivity. These results indicate that divalent cations play a central role in capsid dynamics and suggest a mechanism for the release of viral RNA in low-divalent-cation environments such as those found within the cytoplasm of a cell.

    DOI: 10.1128/JVI.01137-06

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  64. Model of the toxic complex of anthrax: Responsive conformational changes in both the lethal factor and the protective antigen heptamer 査読有り

    Florence Tama, Gang Ren, Charles L. Brooks, Alok K. Mitra

    PROTEIN SCIENCE   15 巻 ( 9 ) 頁: 2190 - 2200   2006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)   出版者・発行元:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT  

    The toxic complex of anthrax is formed when the monomeric protective antigen (PA) (83 kDa), while bound to its cell-surface receptor, is first converted to PA63 heptamers (PA63h) following N-terminal proteolytic cleavage, and then lethal (LF) (90 kDa) or edema factor (EF) binds to the heptamer. We report a "pseudoatomic'' model for the complex of PA63h and full-length LF determined by applying the normal-mode flexible fitting procedure to a similar to 18 angstrom cryo-electron microscopy (EM) density map of the complex. The model describes the interacting surface that buries a total area of similar to 10,140 angstrom(2) comprising; similar to 40% charged, and; 30% each of polar and hydrophobic residues. For the heptamer, the buried surface, composed of similar to 110 residues, involves primarily three monomers and includes for two, similar stretches of the polypeptide chain from domain 1. For LF, the interface again involves; 110 residues, mostly from the N-terminal domain I (LFN), and the structurally homologous C-terminal domain IV. Most interestingly, bound LF displays a marked conformational change resulting from a ``collapse'' of domains I, III, and IVon domain II, with the largest movement of similar to 9 angstrom noted for domain I. On the other hand, primarily, rigid-body movements, larger than; 10 A for three PA63 monomers, cause the hourglass-shaped heptamer lumen to enlarge by as much as similar to 50% near the middle of the molecule. Such concerted structural rearrangements in LF and the heptamer can facilitate ingress of the ligand into the heptamer lumen prior to unfolding and release through the PA63h channel formed in the acidic late endosomal membrane.

    DOI: 10.1110/ps.062293906

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  65. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids 査読有り

    R Konecny, J Trylska, F Tama, DQ Zhang, NA Baker, CL Brooks, JA McCammon

    BIOPOLYMERS   82 巻 ( 2 ) 頁: 106 - 120   2006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:JOHN WILEY & SONS INC  

    Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium-binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca2+ can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca2+ ions can induce the capsid contraction and stabilize the native form. (c) 2005 Wiley Periodicals, Inc.

    DOI: 10.1002/bip.20409

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  66. Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines 査読有り

    Florence Tama, Charles L. Brooks

    ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE   35 巻   頁: 115 - 133   2006年

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    記述言語:英語   掲載種別:論文集(書籍)内論文   出版者・発行元:ANNUAL REVIEWS  

    Computational studies of large macromolecular assemblages have come a long way during the past 10 years. With the explosion of computer power and parallel computing, timescales of molecular dynamics simulations have been extended far beyond the hundreds of picoseconds timescale. However, limitations remain for studies of large-scale conformational changes occurring on timescales beyond nanoseconds, especially for large macromolecules. In this review, we describe recent methods based on normal mode analysis that have enabled us to study dynamics on the microsecond timescale for large macromolecules using different levels of coarse graining, from atomically detailed models to those employing only low-resolution structural information. Emerging from such studies is a control principle for robustness in Nature's machines. We discuss this idea in the context of large-scale functional reorganization of the ribosome, virus particles, and the muscle protein myosin.

    DOI: 10.1146/annurev.biophys.35.040405.102010

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  67. Structure of the E-coli protein-conducting channel bound to a translating ribosome 査読有り

    K Mitra, C Schaffitzel, T Shaikh, F Tama, S Jenni, CL Brooks, N Ban, J Frank

    NATURE   438 巻 ( 7066 ) 頁: 318 - 324   2005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)   出版者・発行元:NATURE PUBLISHING GROUP  

    Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia coli PCC, SecYEG, complexed with the ribosome and a nascent chain containing a signal anchor. This reconstruction shows a messenger RNA, three transfer RNAs, the nascent chain, and detailed features of both a translocating PCC and a second, non-translocating PCC bound to mRNA hairpins. The translocating PCC forms connections with ribosomal RNA hairpins on two sides and ribosomal proteins at the back, leaving a frontal opening. Normal mode-based flexible fitting of the archaeal SecYE beta structure into the PCC electron microscopy densities favours a front-to-front arrangement of two SecYEG complexes in the PCC, and supports channel formation by the opening of two linked SecY halves during polypeptide translocation. On the basis of our observation in the translocating PCC of two segregated pores with different degrees of access to bulk lipid, we propose a model for co-translational protein translocation.

    DOI: 10.1038/nature04133

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  68. The 13 angstrom structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy 査読有り

    S Falke, F Tama, CL Brooks, EP Gogol, MT Fisher

    JOURNAL OF MOLECULAR BIOLOGY   348 巻 ( 1 ) 頁: 219 - 230   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)   出版者・発行元:ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

    The 13 angstrom resolution structures of GroEL bound to a single monomer of the protein substrate glutamine synthetase (GS(m)), as well as that of unliganded GroEL have been determined from a heterogeneous image population using cryo-electron microscopy (cryo-EM) coupled with single-particle image classification and reconstruction techniques. We combined structural data from cryo-EM maps and dynamic modeling, taking advantage of the known X-ray crystallographic structure and normal mode flexible fitting (NMFF) analysis, to describe the changes that occur in GroEL structure induced by GS(m) binding. The NMFF analysis reveals that the molecular movements induced by GS(m) binding propagate throughout the GroEL structure. The modeled molecular motions show that some domains undergo en bloc movements, while others show more complex independent internal movements. Interestingly, the substrate-bound apical domains of both the cis (GS(m)-bound ring) and trans (the opposite substrate-free ring) show counterclockwise rotations, in the same direction (though not as dramatic) as those documented for the ATP-GroEL-induced structure changes. The structural changes from the allosteric substrate protein-induced negative cooperativity between the GroEL rings involves upward concerted movements of both cis and trans equatorial domains toward the GS(m)-bound ring, while the inter-ring distances between the heptamer contact residues are maintained. Furthermore, the NMFF analysis identifies the secondary structural elements that are involved in the observed similar to 5 angstrom reduction in the diameter of the cavity opening in the unbound trans ring. Understanding the molecular basis of these substrate protein-induced structural changes across the heptamer rings provides insight into the origins of the allosteric negative cooperative effects that are transmitted over long distances (similar to 140 angstrom). (c) 2005 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.jmb.2005.02.027

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  69. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis 査読有り

    F Tama, CL Brooks

    JOURNAL OF MOLECULAR BIOLOGY   345 巻 ( 2 ) 頁: 299 - 314   2005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 LTD ELSEVIER SCIENCE LTD  

    We analyze the mechanical properties and putative dynamical fluctuations of a variety of viral capsids comprising different sizes and quasi-equivalent symmetries by performing normal mode analysis using the elastic network model. The expansion of the capsid to a swollen state is studied using normal modes and is compared with the experimentally observed conformational change for three of the viruses for which experimental data exist. We show that a combination of one or two normal modes captures remarkably well the overall translation that dominates the motion between the two conformational states, and reproduces the overall conformational change. We observe for all of the viral capsids that the nature of the modes is different. In particular for the T=7 virus, HK97, for which the shape of the capsid changes from spherical to faceted polyhedra, two modes are necessary to accomplish the conformational transition. In addition, we extend our study to viral capsids with other T numbers, and discuss the similarities and differences in the features of virus capsid conformational dynamics. We note that the pentamers generally have higher flexibility and propensity to move freely from the other capsomers, which facilitates the shape adaptation that may be important in the viral life cycle. (C) 2004 Elsevier ttd. All rights reserved.

    DOI: 10.1016/j.jmb.2004.10.054

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  70. The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function 査読有り

    F Tama, M Feig, J Liu, CL Brooks, KA Taylor

    JOURNAL OF MOLECULAR BIOLOGY   345 巻 ( 4 ) 頁: 837 - 854   2005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 LTD ELSEVIER SCIENCE LTD  

    A combination of experimental structural data, homology modelling and elastic network normal mode analysis is used to explore how coupled motions between the two myosin heads and the dimerization domain (S2) in smooth muscle myosin 11 determine the domain movements required to achieve the inhibited state of this ATP-dependent molecular motor. These physical models rationalize the empirical requirement for at least two heptads of non-coiled a-helix at the junction between the myosin heads and S2, and the dependence of regulation on S2 length. The results correlate well with biochemical data regarding altered conformational-dependent solubility and stability. Structural models of the conformational transition between putative active states and the inhibited state show that torsional flexibility of the S2 a-helices is a key mechanical requirement for myosin 11 regulation. These torsional motions of the myosin heads about their coiled coil a-helices affect the S2 domain structure, which reciprocally affects the motions of the myosin heads. This inter-relationship may explain a large body of data on function of molecular motors that form dimers through a coiled-coil domain. (C) 2004 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.jmb.2004.10.084

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  71. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM 査読有り

    F Tama, O Miyashita, CL Brooks

    JOURNAL OF STRUCTURAL BIOLOGY   147 巻 ( 3 ) 頁: 315 - 326   2004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)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    A new method for the flexible fitting of high-resolution structures into low-resolution maps of macromolecular complexes from electron microscopy has been recently described in applications to simulated electron density maps. This method uses a linear combination of low-frequency normal modes in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. Gradient-following techniques in the coordinate space of collective normal modes are used to optimize the overall correlation coefficient between computed and measured electron densities. With this approach, multi-scale flexible fitting can be performed using all-atoms or Cot atoms. In this paper, illustrative studies of normal mode based flexible fitting to experimental cryo-EM maps are presented for three different systems. Large, functionally relevant conformational changes for elongation factor G bound to the ribosome, Escherichia coli RNA polymerase and cowpea chlorotic mottle virus are elucidated as the result of the application of NMFF from high-resolution structures to cryo-electron microscopy maps. (C) 2004 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.jsb.2004.03.002

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  72. Ribosome motions modulate electrostatic properties 査読有り

    J Trylska, R Konecny, F Tama, CL Brooks, JA McCammon

    BIOPOLYMERS   74 巻 ( 6 ) 頁: 423 - 431   2004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:WILEY-BLACKWELL  

    The electrostatic properties of the 70S ribosome of Thermus thermophilus were studied qualitatively by solving the Poisson-Boltzmann (PB) equation in aqueous solution and with physiological ionic strength. The electrostatic potential was calculated for conformations of the ribosome derived by recent normal mode analysis (Tama, F., et al. Proc Natl Acad Sci USA 2003 1001, 9319-9323) of the ratchet-like reorganization that occurs during translocation (Frank, J.; Agrawal, R. K. Nature 2000 406, 318-322). To solve the PB equation, effective parameters (charges and radii), applicable to a highly charged backbone model of the ribosome, were developed. Regions of positive potential were found at the binding site of the elongation factors G and Tu, as well as where the release factors bind. Large positive potential areas are especially pronounced around the L11 and L6 proteins. The region around the L1 protein is also positively charged, supporting the idea that L1 may interact with the E-site tRNA during its release from the ribosome after translocation. Functional rearrangement of the ribosome leads to electrostatic changes which may help the translocation of the tRNAs during the elongation stage. (C) 2004 Wiley Periodicals, Inc.

    DOI: 10.1002/bip.20093

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  73. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis 査読有り

    F Tama, O Miyashita, CL Brooks

    JOURNAL OF MOLECULAR BIOLOGY   337 巻 ( 4 ) 頁: 985 - 999   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)   出版者・発行元:ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

    A novel method is presented for the quantitative flexible docking of high-resolution structure into low-resolution maps of macromolecular complexes from electron microscopy. This method uses a linear combination of low-frequency normal modes from elastic network description of the molecular framework in an iterative manner to deform the structure optimally to conform to the low-resolution electron density map. The methodology utilizes gradient following techniques in collective normal modes to locally optimize the overall correlation coefficient between computed and measured electron density. To evaluate the performance of our approach, several proteins, which undergo large conformational changes, have been studied. We demonstrate that refinement based on normal mode analysis provides an accurate and fast alternative for the flexible fitting of high-resolution structure into a low-resolution density map. Additionally, we show that lower resolution (multi-scale) structural models can be used for the normal mode searching in lieu of fully atomic models with little loss of overall accuracy. (C) 2004 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.jmb.2004.01.048

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  74. Topology representing neural networks reconcile biomolecular shape, structure, and dynamics 査読有り

    W Wriggers, P Chacon, JA Kovacs, F Tama, S Birmanns

    NEUROCOMPUTING   56 巻   頁: 365 - 379   2004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:ELSEVIER SCIENCE BV  

    Topology-representing networks (TRNs) generate reduced models of biomolecules and thereby facilitate the fitting of molecular fragments into large macromolecular complexes. The components of such complexes undergo a wide range of motions, and shapes observed at low resolution often deviate from the known atomic structures. What is required for the modeling of such motions is a combination of global shape constraints based on the low-resolution data with a local modeling of atomic interactions. We present a novel Motion Capture Network that freezes inessential degrees of freedom to maintain the stereochemistry of an atomic model. TRN-based deformable models retain much of the mechanical properties of biological macromolecules. The elastic models yield a decomposition of the predicted motion into vibrational normal modes and are amenable to interactive manipulation with haptic rendering software. (C) 2003 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.neucom.2003.09.007

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  75. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy 査読有り

    F Tama, M Valle, J Frank, CL Brooks

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   100 巻 ( 16 ) 頁: 9319 - 9323   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)   出版者・発行元:NATL ACAD SCIENCES  

    Combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. The dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70S ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that either facilitate the conformational switching or maintain structural integrity of the 50S/30S interface. Motions of the tRNAs residing in the A and P sites also suggest the early stages of tRNA translocation as a result of this ratchet-like movement. Displacement of the L1 stalk, alternately closing and opening the intersubunit space near the E site, is observed in the dynamic model, in line with growing experimental evidence for the role of this structural component in facilitating the exiting of tRNA. Finally, a hinge-like transition in the 30S ribosomal subunit, similar to that observed in crystal structures of this complex, is also manifest as a dynamic mode of the ribosome. The coincidence of these dynamic transitions with the individual normal modes of the ribosome and the good correspondence between these motions and those observed in experiment suggest an underlying principle of nature to exploit the shape of molecular assemblies such as the ribosome to provide robustness to functionally important motions.

    DOI: 10.1073/pnas.1632476100

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  76. Normal mode analysis with simplified models to investigate the global dynamics of biological systems 査読有り

    F Tama

    PROTEIN AND PEPTIDE LETTERS   10 巻 ( 2 ) 頁: 119 - 132   2003年4月

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    記述言語:英語   出版者・発行元:BENTHAM SCIENCE PUBL LTD  

    Dynamical properties of macromolecules are increasingly being recognized as significantly contributing to biological functions, including catalysis, regulation of activity, etc. In this review, theoretical approaches to the study of dynamics of biological systems and their application are discussed. In particular, simplified models for the normal mode analysis are described.

    DOI: 10.2174/0929866033479077

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  77. Mega-Dalton biomolecular motion captured from electron microscopy reconstructions 査読有り

    P Chacon, F Tama, W Wriggers

    JOURNAL OF MOLECULAR BIOLOGY   326 巻 ( 2 ) 頁: 485 - 492   2003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:ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

    The vibrational analysis of elastic models suggests that the essential motions of large biomolecular assemblies can be captured efficiently at an intermediate scale without requiring knowledge of the atomic structure. While prior work has established a theoretical foundation for this analysis, we demonstrate here on experimental electron microscopy maps that vibrational modes indeed describe functionally relevant movements of macromolecular machines. The clamp closure in bacterial RNA polymerase, the ratcheting of 30 S and 50 S subunits of the ribosome, and the dynamic flexibility of chaperonin CCT are extracted directly from single electron microscopy structures at 15-27 Angstrom resolution. The striking agreement of the presented results with experimentally observed motions suggests that the motion of the large scale machinery in the cell is surprisingly independent of detailed atomic interactions and can be quite reasonably described as a motion of elastic bodies. (C) 2003 Elsevier Science Ltd. All rights reserved.

    DOI: 10.1016/S0022-2836(02)01426-2

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  78. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory 査読有り

    F Tama, W Wriggers, CL Brooks

    JOURNAL OF MOLECULAR BIOLOGY   321 巻 ( 2 ) 頁: 297 - 305   2002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:ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

    A theory of elastic normal modes is described for the exploration of global distortions of biological structures and their assemblies based upon low-resolution image data. Structural information at low resolution, e.g. from density maps measured by cryogenic electron microscopy (cryo-EM), is used to construct discrete multi-resolution models for the electron density using the techniques of vector quantization. The elastic normal modes computed based on these discretized low-resolution models are found to compare well with the normal modes obtained at atomic resolution. The quality of the normal modes describing global displacements of the molecular system is found to depend on the resolution of the synthetic EM data and the extent of reductionism in the discretized representation. However, models that reproduce the functional rearrangements of our test set of molecules are achieved for realistic values of experimental resolution. Thus large conformational changes as occur during the functioning of biological macromolecules and assemblies can be elucidated directly from low-resolution structural data through the application of elastic normal mode theory and vector quantization. (C) 2002 Elsevier Science Ltd. All rights reserved.

    DOI: 10.1016/S0022-2836(02)00627-7

    Web of Science

  79. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus 査読有り

    F Tama, CL Brooks

    JOURNAL OF MOLECULAR BIOLOGY   318 巻 ( 3 ) 頁: 733 - 747   2002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:ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD  

    Normal mode analysis based on a simplified energy function was used to study the swelling process of the icosahedral virus, cowpea chlorotic mottle virus (CCMV). Native state virus particles (coat proteins) of this T = 3 icosahedral virus have been shown to undergo a large conformational change to a swollen state when metal ions are removed or the pH is raised. A normal mode analysis based on the native state capsid showed one preferential direction, a breathing mode, that explains the majority of the structural rearrangement necessary to bring the native structure close to the swollen state.
    From the native form of CCMV, the structure can be displaced along the direction of a single breathing mode by different amounts to create several candidate swollen structures and a putative pathway for virus expansion. The R-factor between these predicted swollen capsid structures and experimental electron density from cryoelectron microscopy (cryo-EM) measurements is then calculated to indicate how well each structure satisfies the experimental measurements on the swollen capsid state. A decrease of the crystallographic R-factor value from similar to72% to similar to49% was observed for these simple incremental displacements along the breathing mode. The simultaneous displacement of the native structure along other relevant (symmetric, non-degenerate) modes produce a structure with an R-factor of 45%, which is further reduced to 43.9% after minimization: a value in good accord with models based on the EM data at 28 Angstrom resolution.
    Based on the incrementally expanded structures, a pathway for the swelling process has been proposed. Analysis of the intermediate structures along this pathway indicates a significant loss of interactions at the quasi-3-fold interfaces occurs in the initial stages of the swelling process and this serves as a trigger for the compact to swollen transition. Furthermore, the pH dependent swelling appears to be triggered by the titration of a single residue with an anomalous pK(a) value in the unswollen particle. (C) 2002 Elsevier Science Ltd. All rights reserved.

    DOI: 10.1016/S0022-2836(02)00135-3

    Web of Science

  80. Conformational change of proteins arising from normal mode calculations 査読有り

    F Tama, YH Sanejouand

    PROTEIN ENGINEERING   14 巻 ( 1 ) 頁: 1 - 6   2001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:OXFORD UNIV PRESS  

    A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.

    DOI: 10.1093/protein/14.1.1

    Web of Science

  81. Building-block approach for determining low-frequency normal modes of macromolecules 査読有り

    F Tama, FX Gadea, O Marques, YH Sanejouand

    PROTEINS-STRUCTURE FUNCTION AND GENETICS   41 巻 ( 1 ) 頁: 1 - 7   2000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)   出版者・発行元:WILEY-LISS  

    Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed method that rests on the hypothesis that low-frequency normal modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino-acid residues. Such a hypothesis is strongly supported by our results, because we show that the latter method, named RTB, yields very accurate approximations for the low-frequency normal modes of all proteins considered. Moreover, the quality of the normal modes thus obtained depends very little on the way the polypeptidic chain is split into blocks, Noteworthy, with six aminoacids per block, the normal modes are almost as accurate as with a single amino-acid per block. In this case, for a protein of n residues and N atoms, the RTB method requires the diagonalization of an n x n matrix, whereas standard procedures require the diagonalization of a 3N x 3N matrix. Being a fast method, our approach can be useful for normal mode analyses of large systems, paving the way for further developments and applications in contexts for which the normal modes are needed frequently, as for example during molecular dynamics calculations. Proteins 2000;41:1-7. (C) 2000 Wiley-Liss, Inc.

    Web of Science

  82. Molecular dynamics simulation shows large volume fluctuations of proteins 査読有り

    F Tama, O Miyashita, A Kitao, N Go

    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS   29 巻 ( 7 ) 頁: 472 - 480   2000年

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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:SPRINGER-VERLAG  

    In this paper we present a new approach to study the volume fluctuations of proteins. From a 1 ns molecular dynamics simulation, the volume fluctuation of human lysozyme has been calculated. We used two different ways for the calculation. In the first one, the volume fluctuation is extracted directly from the trajectory. For the second one, a newly developed formalism based on principal component analysis is used. The r.m.s. volume fluctuations obtained from the two analyses agree well with each other. The isothermal intrinsic compressibility was found to be larger than the one reported by experiment. The difference is discussed and suggested to exist in the assumed uncertainty of the compressibility of hydrated water to deduce the isothermal intrinsic compressibility from the experimental value. Spectral analysis shows that low-frequency dynamics dominate the total volume fluctuation. The same aspect is found in the study using principal component analysis. This low-frequency region is related to large and slow motions of proteins. Therefore a long time dynamics simulation is necessary to describe the volume fluctuations of proteins.

    DOI: 10.1007/s002490000103

    Web of Science

▼全件表示

科研費 3

  1. コンピューティングを活用した寄生植物ストライガを抑制する生命機能分子の探索

    研究課題/研究課題番号:17F17819  2017年11月 - 2018年3月

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    担当区分:その他 

    Based on X-ray crystal structure of Striga receptor ShHTL5, homology models of ShHTL7 were developed and validated. In addition, models of a collection of experimentally investigated HTL7 mutants (amino acid residue changes in the receptor’s active site) were created. These structures were submitted to MD simulations to explore their structural flexibility. The analyses of resulting MD trajectories showed significantly higher plasticity of HTL7 protein helices that surround the active site of HTLs compared to HTL5. The degree of flexibility decreases with increasing number of single residue changes from HTL7 towards HTL5. The increased flexibility in HTL7 is found to be in accordance with experimental assay results that indicate that HTL7 is more promiscuous with regard to ligand binding compared to other HTLs.
    The developed homology models of HTL7 and the published structure of HTL5 were further used as basis for induced fit docking studies with experimentally validated active molecules. The purpose of these docking studies was to (i) computationally assess the structure-activity relationship of tested small molecules and Striga receptors and to identify essential protein-ligand interactions that lead to receptor modulation, and (ii) to create an ensemble of structural complexes with highly potent molecules for subsequent protein-ligand MD simulations. These could be used for the development of 3D dynophore models that would allow virtual screening of chemical libraries.
    29年度が最終年度であるため、記入しない。
    29年度が最終年度であるため、記入しない。

  2. Database of Molecular Shapes and Diffraction Patterns for X-ray Free Electron Laser Data Analysis

    研究課題/研究課題番号:17K07305  2017年4月 - 2020年3月

    TAMA FLORENCE

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    担当区分:研究代表者 

    配分額:4810000円 ( 直接経費:3700000円 、 間接経費:1110000円 )

    本研究ではクライオ電子顕微鏡やX線自由電子レーザーにより得られる少数の画像データから大まかな構造を推定するアルゴリズムを開発した。この手法では既知の生体分子の形に関するデータベースを構築し、その中からインプット画像と一致度の高い構造を選択、提案する。
    まず、電子顕微鏡データによりこの手法の実現性を検討し、少数の画像から比較的正確に正しい形の情報を選択できることを示した。次に、X線自由電子レーザーデータの解析を高速化するためにGaussian mixture modelで粗視的にモデルを表現する手法を開発した。また、画像比較の精度を高めるために最適な画像領域を自動的に選択する手法を開発した。
    生体分子の構造に関する情報はそれらの機能を理解して医薬などの応用に活用するために重要である。本研究ではデータベースを活用することによりクライオ電子顕微鏡やX線自由電子レーザーによる観測データからターゲットの形を素早く推定するための手法を開発した。

  3. 動的構造生命科学研究領域における海外ネットワーク形成を目指した支援活動

    研究課題/研究課題番号:15K21711  2015年11月 - 2019年3月

    新学術領域研究(研究領域提案型)

    神田 大輔

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    担当区分:研究分担者 

    新学術領域研究「動的構造生命」の学術活動の範囲を国際的に広げることを目指した.4年間の活動期間中に,海外からの講演者の招聘4件5人,海外からの共同研究者やポスドク,学生の受入13件13人,サバティカル教員の受入1件1人,共同実験のための教員や学生の派遣1件4人,国内国際学会への日本在住外国籍学生の派遣1件3人,国際版の技術講習会への海外からの参加の支援6件31人,公募班員に対する旅費支援11件11人を行った.
    当初は海外からの優れた研究者による講演のための日本への招聘旅費を中心に考えていたが,実際に運用すると国際連携に実質的に役立つ運用ができた.教員や大学院生の海外研究室での実験のための旅費支援や,海外からの研究者の短期および長期滞在(2週間-1年間)のサポートなど,通常の研究費では難しい活動を支援できた.本新学術研究により開発・改良された新測定技術を実際の研究現場に取り入れてもらうことの重要性をかんがみて,国際的にも普及活動ができた.