Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
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Author(s)
Whitehead, Timothy A
Strauch, Eva-Maria
Corn, Jacob E
Qin, Sanbo
Zhou, Huan-Xiang
Mitchell, Julie C
Demerdash, Omar NA
Takeda-Shitaka, Mayuko
Terashi, Genki
Moal, Iain H
Li, Xiaofan
Bates, Paul A
Zacharias, Martin
Park, Hahnbeom
Ko, Jun-su
Lee, Hasup
Seok, Chaok
Bourquard, Thomas
Bernauer, Julie
Poupon, Anne
Aze, Jerome
Soner, Seren
Ovali, Sefik Kerem
Ozbek, Pemra
Ben Tal, Nir
Haliloglu, Turkan
Hwang, Howook
Vreven, Thom
Pierce, Brian G
Weng, Zhiping
Perez-Cano, Laura
Pons, Caries
Fernandez-Recio, Juan
Jiang, Fan
Yang, Feng
Gong, Xinqi
Cao, Libin
Xu, Xianjin
Liu, Bin
Wang, Panwen
Li, Chunhua
Wang, Cunxin
Robert, Charles H
Guharoy, Mainak
Liu, Shiyong
Huang, Yangyu
Li, Lin
Guo, Dachuan
Chen, Ying
Xiao, Yi
London, Nir
Itzhaki, Zohar
Schueler-Furman, Ora
Inbar, Yuval
Potapov, Vladimir
Cohen, Mati
Schreiber, Gideon
Tsuchiya, Yuko
Kanamori, Eiji
Standley, Daron M
Nakamura, Haruki
Kinoshita, Kengo
Driggers, Camden M
Hall, Robert G
Morgan, Jessica L
Hsu, Victor L
Zhan, Jian
Yang, Yuedong
Zhou, Yaoqi
Kastritis, Panagiotis L
Bonvin, Alexandre MJJ
Zhang, Weiyi
Camacho, Carlos J
Kilambi, Krishna P
Sircar, Aroop
Gray, Jeffrey J
Ohue, Masahito
Uchikoga, Nobuyuki
Matsuzaki, Yuri
Ishida, Takashi
Akiyama, Yutaka
Khashan, Raed
Bush, Stephen
Fouches, Denis
Tropsha, Alexander
Esquivel-Rodriguez, Juan
Kihara, Daisuke
Stranges, P Benjamin
Jacak, Ron
Kuhlman, Brian
Huang, Sheng-You
Zou, Xiaoqin
Wodak, Shoshana J
Janin, Joel
Baker, David
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Abstract
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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Journal of Molecular Biology
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414
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2
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Medicinal and biomolecular chemistry
Biochemistry and cell biology
Microbiology