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論文・著書情報
| タイトル |
| 和文: | |
| 英文: | Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology |
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| 著者 |
| 和文: |
Sarel J. Fleishman,
Timothy A. Whitehead,
Eva-Maria Strauch,
Jacob E. Corn,
Sanbo Qin,
Huan-Xiang Zhou,
Julie C. Mitchell,
Omar N. A. Demerdash,
Mayuko Takeda-Shitaka,
Genki Terashi,
Iain H. Moal,
Xiaofan Li,
Paul A. Bates,
Martin Zacharias,
Hahnbeom Park,
Jun-su Ko,
Hasup Lee,
Chaok Seok,
Thomas Bourquard,
Julie Bernauer,
Anne Poupon,
Jerome Aze,
Seren Soner,
Sefik Kerem Oval.,
Pemra Ozbek,
Nir Ben Tal,
Turkan Haliloglu,
Howook Hwang,
Thom Vreven,
Brian G. Pierce,
Zhiping Weng,
Laura Perez-Cano,
Carles Pons,
Juan Fernandez-Recio,
Fan Jiang,
Feng Yang,
Xinqi Gong,
Libin Cao,
Xianjin Xu,
Bin Liu,
Panwen Wang,
Chunhua Li,
Cunxin Wang,
Charles H. Robert,
Mainak Guharoy,
Shiyong Liu,
Yangyu Huang,
Lin Li,
Dachuan Guo,
Ying Chen,
Yi Xiao,
Nir London,
Zohar Itzhaki,
Ora Schueler-Furman,
Yuval Inbar,
Vladimir Patapov,
Mati Cohen,
Gideon Schreiber,
Yuko Tsuchiya,
Eiji Kanamori,
Daron M. Standley,
Haruki Nakamura,
木下 賢吾,
Camden M. Driggers,
Robert G. Hall,
Jessica L. Morgan,
Victor L. Hsu,
Jian Zhan,
Yuedong Yang,
Yaoqi Zhou,
Panagiotis L. Kastritis,
Alexandre M. J. J. Bonvin,
Weiyi Zhang,
Carlos J. Camacho,
Krishna P. Kilambi,
Aroop Sircar,
Jeffrey J. Gray,
大上 雅史,
Nobuyuki Uchikoga,
松崎 由理,
石田 貴士,
秋山 泰,
Raed Khashan,
Stephen Bush,
Denis Fouches,
Alexander Tropsha,
Juan Esquivel-Rodriguez,
Daisuke Kihara,
P. Benjamin Stranges,
Ron Jacak,
Brian Kuhlman,
Sheng-You Huang,
Xiaoqin Zou,
Shoshana J. Wodak,
Joel Janin,
David Baker.
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| 英文: |
Sarel J. Fleishman,
Timothy A. Whitehead,
Eva-Maria Strauch,
Jacob E. Corn,
Sanbo Qin,
Huan-Xiang Zhou,
Julie C. Mitchell,
Omar N. A. Demerdash,
Mayuko Takeda-Shitaka,
Genki Terashi,
Iain H. Moal,
Xiaofan Li,
Paul A. Bates,
Martin Zacharias,
Hahnbeom Park,
Jun-su Ko,
Hasup Lee,
Chaok Seok,
Thomas Bourquard,
Julie Bernauer,
Anne Poupon,
Jerome Aze,
Seren Soner,
Sefik Kerem Oval.,
Pemra Ozbek,
Nir Ben Tal,
Turkan Haliloglu,
Howook Hwang,
Thom Vreven,
Brian G. Pierce,
Zhiping Weng,
Laura Perez-Cano,
Carles Pons,
Juan Fernandez-Recio,
Fan Jiang,
Feng Yang,
Xinqi Gong,
Libin Cao,
Xianjin Xu,
Bin Liu,
Panwen Wang,
Chunhua Li,
Cunxin Wang,
Charles H. Robert,
Mainak Guharoy,
Shiyong Liu,
Yangyu Huang,
Lin Li,
Dachuan Guo,
Ying Chen,
Yi Xiao,
Nir London,
Zohar Itzhaki,
Ora Schueler-Furman,
Yuval Inbar,
Vladimir Patapov,
Mati Cohen,
Gideon Schreiber,
Yuko Tsuchiya,
Eiji Kanamori,
Daron M. Standley,
Haruki Nakamura,
Kengo Kinoshita,
Camden M. Driggers,
Robert G. Hall,
Jessica L. Morgan,
Victor L. Hsu,
Jian Zhan,
Yuedong Yang,
Yaoqi Zhou,
Panagiotis L. Kastritis,
Alexandre M. J. J. Bonvin,
Weiyi Zhang,
Carlos J. Camacho,
Krishna P. Kilambi,
Aroop Sircar,
Jeffrey J. Gray,
Masahito Ohue,
Nobuyuki Uchikoga,
Yuri Matsuzaki,
Takashi Ishida,
Yutaka Akiyama,
Raed Khashan,
Stephen Bush,
Denis Fouches,
Alexander Tropsha,
Juan Esquivel-Rodriguez,
Daisuke Kihara,
P. Benjamin Stranges,
Ron Jacak,
Brian Kuhlman,
Sheng-You Huang,
Xiaoqin Zou,
Shoshana J. Wodak,
Joel Janin,
David Baker.
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| 言語 |
English |
| 掲載誌/書名 |
| 和文: | |
| 英文: | Journal of Molecular Biology |
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巻, 号, ページ
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Volume 414
Issue 2
pp. 289-302
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| 出版年月 |
2011年11月25日 |
| 出版者 |
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| 会議名称 |
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| 開催地 |
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| 公式リンク |
https://www.sciencedirect.com/science/article/pii/S0022283611010552
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| DOI |
https://doi.org/10.1016/j.jmb.2011.09.031 |
| アブストラクト |
The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state of the art and spurring progress in the very challenging areas of protein docking and structure prediction. We sought to bring the power of community-wide experiments to bear on a very challenging protein design problem that provides a complementary but equally fundamental test of current understanding of protein-binding thermodynamics. We have generated a number of designed protein–protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments, suggesting that there may be important physical chemistry missing in the energy calculations. A total of 28 research groups took up the challenge of determining what is missing: we provided structures of 87 designed complexes and 120 naturally occurring complexes and asked participants to identify energetic contributions and/or structural features that distinguish between the two sets. The community found that electrostatics and solvation terms partially distinguish the designs from the natural complexes, largely due to the nonpolar character of the designed interactions. Beyond this polarity difference, the community found that the designed binding surfaces were, on average, structurally less embedded in the designed monomers, suggesting that backbone conformational rigidity at the designed surface is important for realization of the designed function. These results can be used to improve computational design strategies, but there is still much to be learned; for example, one designed complex, which does form in experiments, was classified by all metrics as a nonbinder. |
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