Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
文献类型：期刊论文
| 作者 | Fleishman, SJ ; Whitehead, TA ; Strauch, EM ; Corn, JE ; Qin, SB ; Zhou, HX ; Mitchell, JC ; Demerdash, ONA ; Takeda-Shitaka, M ; Terashi, G ; Moal, IH ; Li, XF ; Bates, PA ; Zacharias, M ; Park, H ; Ko, JS ; Lee, H ; Seok, C ; Bourquard, T ; Bernauer, J ; Poupon, A ; Aze, J ; Soner, S ; Ovali, SK ; Ozbek, P ; Ben Tal, N ; Haliloglu, T ; Hwang, H ; Vreven, T ; Pierce, BG ; Weng, ZP ; Perez-Cano, L ; Pons, C ; Fernandez-Recio, J ; Jiang, F ; Yang, F ; Gong, XQ ; Cao, LB ; Xu, XJ ; Liu, B ; Wang, PW ; Li, CH ; Wang, CX ; Robert, CH ; Guharoy, M ; Liu, SY ; Huang, YY ; Li, L ; Guo, DC ; Chen, Y ; Xiao, Y ; London, N ; Itzhaki, Z ; Schueler-Furman, O ; Inbar, Y ; Potapov, V ; Cohen, M ; Schreiber, G ; Tsuchiya, Y ; Kanamori, E ; Standley, DM ; Nakamura, H ; Kinoshita, K ; Driggers, CM ; Hall, RG ; Morgan, JL ; Hsu, VL ; Zhan, J ; Yang, YD ; Zhou, YQ ; Kastritis, PL ; Bonvin, AMJJ ; Zhang, WY ; Camacho, CJ ; Kilambi, KP ; Sircar, A ; Gray, JJ ; Ohue, M ; Uchikoga, N ; Matsuzaki, Y ; Ishida, T ; Akiyama, Y ; Khashan, R ; Bush, S ; Fouches, D ; Tropsha, A ; Esquivel-Rodriguez, J ; Kihara, D ; Stranges, PB ; Jacak, R ; Kuhlman, B ; Huang, SY ; Zou, XQ ; Wodak, SJ ; Janin, J ; Baker, D |
| 刊名 | JOURNAL OF MOLECULAR BIOLOGY
 |
| 出版日期 | 2011 |
| 卷号 | 414期号:2页码:289 |
| 关键词 | COMPUTATIONAL DESIGN BINDING DOCKING ANTIBODY |
| ISSN号 | 0022-2836 |
| 通讯作者 | Baker, D: Univ Washington, Dept Biochem, Seattle, WA 98195 USA. |
| 中文摘要 | 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. (C) 2011 Elsevier Ltd. All rights reserved. |
| 收录类别 | SCI |
| 资助信息 | Human Frontier Science Program; Canadian Institutes of Health Research; Howard Hughes Medical Institute; Defense Advanced Research Projects Agency; National Institutes of Health Yeast Resource Center; Defense Threat Reduction Agency |
| 语种 | 英语 |
| 公开日期 | 2013-09-17 |
| 源URL | [http://ir.iphy.ac.cn/handle/311004/34924]  |
| 专题 | 物理研究所_物理所公开发表论文_物理所公开发表论文_期刊论文 |
| 推荐引用方式 GB/T 7714 | Fleishman, SJ,Whitehead, TA,Strauch, EM,et al. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology[J]. JOURNAL OF MOLECULAR BIOLOGY,2011,414(2):289. |
| APA | Fleishman, SJ.,Whitehead, TA.,Strauch, EM.,Corn, JE.,Qin, SB.,...&Baker, D.(2011).Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.JOURNAL OF MOLECULAR BIOLOGY,414(2),289. |
| MLA | Fleishman, SJ,et al."Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology".JOURNAL OF MOLECULAR BIOLOGY 414.2(2011):289. |
入库方式： OAI收割
来源：物理研究所
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