Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.

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; Jérôme Azé; Seren Soner; Sefik Kerem Ovalı; Pemra Ozbek; Nir Ben Tal; Türkan Haliloglu; Howook Hwang; Thom Vreven; Brian G Pierce; Zhiping Weng; Laura Pérez-Cano; Carles Pons; Juan Fernández-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-Rodríguez; Daisuke Kihara; P Benjamin Stranges; Ron Jacak; Brian Kuhlman; Sheng-You Huang; Xiaoqin Zou; Shoshana J Wodak; Joel Janin; David Baker

inria-00637848, version 1

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.

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 ¹, Julie Bernauer ², Anne Poupon ³, Jérôme Azé ², Seren Soner, Sefik Kerem Ovalı, Pemra Ozbek, Nir Ben Tal, Türkan Haliloglu, Howook Hwang, Thom Vreven, Brian G Pierce, Zhiping Weng, Laura Pérez-Cano, Carles Pons, Juan Fernández-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-Rodríguez, Daisuke Kihara, P Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J Wodak, Joel Janin ⁴, David Baker

Journal of Molecular Biology (2011) in press

1 : ORPAILLEUR (INRIA Lorraine - LORIA)
INRIA – CNRS : UMR7503 – Université Henri Poincaré - Nancy I – Université Nancy II – Institut National Polytechnique de Lorraine (INPL) France
2 : AMIB (INRIA Saclay - Ile de France)
http://www.inria.fr/recherche/equipes/amib.fr.html
INRIA – Polytechnique - X – CNRS : UMR8623 – Université Paris XI - Paris Sud LIX Route de Saclay 91128 PALAISEAU CEDEX France
3 : Physiologie de la reproduction et des comportements (PRC)
CNRS : UMR6175 – Institut national de la recherche agronomique (INRA) : UR0085 – Université François Rabelais - Tours Centre de Recherches de Tours 37380 NOUZILLY France
4 : Yeast Structural Genomics
CNRS : UMR8619 – Université Paris XI - Paris Sud IBBMC UMR 8619, bâtiment 430, Université Paris-Sud, 91405 Orsay France

Références bibliographiques

inria-00637848, version 1
http://hal.inria.fr/inria-00637848
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Soumis le : Jeudi 3 Novembre 2011, 10:20:27
Dernière modification le : Samedi 12 Mai 2012, 10:12:27

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PubMed : 22001016

DOI : 10.1016/j.jmb.2011.09.031

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%% inria-00637848, version 1
%% http://hal.inria.fr/inria-00637848
@article{fleishman:inria-00637848,
    hal_id = {inria-00637848},
    url = {http://hal.inria.fr/inria-00637848},
    title = {{Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.}},
    author = {Fleishman, Sarel J and Whitehead, Timothy A and Strauch, Eva-Maria and Corn, Jacob E and Qin, Sanbo and Zhou, Huan-Xiang and Mitchell, Julie C and Demerdash, Omar N A and Takeda-Shitaka, Mayuko and Terashi, Genki and Moal, Iain H and Li, Xiaofan and Bates, Paul A and Zacharias, Martin and Park, Hahnbeom and Ko, Jun-Su and Lee, Hasup and Seok, Chaok and Bourquard, Thomas and Bernauer, Julie and Poupon, Anne and Az{\'e}, J{\'e}r{\^o}me and Soner, Seren and Ovalı, Sefik Kerem and Ozbek, Pemra and Tal, Nir Ben and Haliloglu, T{\"u}rkan and Hwang, Howook and Vreven, Thom and Pierce, Brian G and Weng, Zhiping and P{\'e}rez-Cano, Laura and Pons, Carles and Fern{\'a}ndez-Recio, Juan and Jiang, Fan and Yang, Feng and Gong, Xinqi and Cao, Libin and Xu, Xianjin and Liu, Bin and Wang, Panwen and Li, Chunhua and Wang, Cunxin and Robert, Charles H and Guharoy, Mainak and Liu, Shiyong and Huang, Yangyu and Li, Lin and Guo, Dachuan and Chen, Ying and Xiao, Yi and London, Nir and Itzhaki, Zohar and Schueler-Furman, Ora and Inbar, Yuval and Patapov, Vladimir and Cohen, Mati and Schreiber, Gideon and Tsuchiya, Yuko and Kanamori, Eiji and Standley, Daron M and Nakamura, Haruki and Kinoshita, Kengo and Driggers, Camden M and Hall, Robert G and Morgan, Jessica L and Hsu, Victor L and Zhan, Jian and Yang, Yuedong and Zhou, Yaoqi and Kastritis, Panagiotis L and Bonvin, Alexandre M J J and Zhang, Weiyi and Camacho, Carlos J and Kilambi, Krishna P and Sircar, Aroop and Gray, Jeffrey J and Ohue, Masahito and Uchikoga, Nobuyuki and Matsuzaki, Yuri and Ishida, Takashi and Akiyama, Yutaka and Khashan, Raed and Bush, Stephen and Fouches, Denis and Tropsha, Alexander and Esquivel-Rodr{\'\i}guez, Juan and Kihara, Daisuke and Stranges, P Benjamin and Jacak, Ron and Kuhlman, Brian and Huang, Sheng-You and Zou, Xiaoqin and Wodak, Shoshana J and Janin, Joel and Baker, David},
    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.}},
    language = {Anglais},
    affiliation = {ORPAILLEUR - INRIA Lorraine - LORIA , AMIB - INRIA Saclay - Ile de France , Physiologie de la reproduction et des comportements - PRC , Yeast Structural Genomics},
    publisher = {Elsevier},
    pages = {in press},
    journal = {Journal of Molecular Biology},
    audience = {internationale },
    doi = {10.1016/j.jmb.2011.09.031 },
    year = {2011},
    month = Sep,
}

%F inria-00637848, version 1
%0 Journal Article
%U http://hal.inria.fr/inria-00637848
%2 SDV:BBM:BS
%T Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology.
%A Fleishman, Sarel J
%A Whitehead, Timothy A
%A Strauch, Eva-Maria
%A Corn, Jacob E
%A Qin, Sanbo
%A Zhou, Huan-Xiang
%A Mitchell, Julie C
%A Demerdash, Omar N A
%A Takeda-Shitaka, Mayuko
%A Terashi, Genki
%A Moal, Iain H
%A Li, Xiaofan
%A Bates, Paul A
%A Zacharias, Martin
%A Park, Hahnbeom
%A Ko, Jun-Su
%A Lee, Hasup
%A Seok, Chaok
%A Bourquard, Thomas
%A Bernauer, Julie
%A Poupon, Anne
%A Azé, Jérôme
%A Soner, Seren
%A Ovalı, Sefik Kerem
%A Ozbek, Pemra
%A Tal, Nir Ben
%A Haliloglu, Türkan
%A Hwang, Howook
%A Vreven, Thom
%A Pierce, Brian G
%A Weng, Zhiping
%A Pérez-Cano, Laura
%A Pons, Carles
%A Fernández-Recio, Juan
%A Jiang, Fan
%A Yang, Feng
%A Gong, Xinqi
%A Cao, Libin
%A Xu, Xianjin
%A Liu, Bin
%A Wang, Panwen
%A Li, Chunhua
%A Wang, Cunxin
%A Robert, Charles H
%A Guharoy, Mainak
%A Liu, Shiyong
%A Huang, Yangyu
%A Li, Lin
%A Guo, Dachuan
%A Chen, Ying
%A Xiao, Yi
%A London, Nir
%A Itzhaki, Zohar
%A Schueler-Furman, Ora
%A Inbar, Yuval
%A Patapov, Vladimir
%A Cohen, Mati
%A Schreiber, Gideon
%A Tsuchiya, Yuko
%A Kanamori, Eiji
%A Standley, Daron M
%A Nakamura, Haruki
%A Kinoshita, Kengo
%A Driggers, Camden M
%A Hall, Robert G
%A Morgan, Jessica L
%A Hsu, Victor L
%A Zhan, Jian
%A Yang, Yuedong
%A Zhou, Yaoqi
%A Kastritis, Panagiotis L
%A Bonvin, Alexandre M J J
%A Zhang, Weiyi
%A Camacho, Carlos J
%A Kilambi, Krishna P
%A Sircar, Aroop
%A Gray, Jeffrey J
%A Ohue, Masahito
%A Uchikoga, Nobuyuki
%A Matsuzaki, Yuri
%A Ishida, Takashi
%A Akiyama, Yutaka
%A Khashan, Raed
%A Bush, Stephen
%A Fouches, Denis
%A Tropsha, Alexander
%A Esquivel-Rodríguez, Juan
%A Kihara, Daisuke
%A Stranges, P Benjamin
%A Jacak, Ron
%A Kuhlman, Brian
%A Huang, Sheng-You
%A Zou, Xiaoqin
%A Wodak, Shoshana J
%A Janin, Joel
%A Baker, David
%+ ORPAILLEUR - INRIA Lorraine - LORIA , AMIB - INRIA Saclay - Ile de France , Physiologie de la reproduction et des comportements - PRC , Yeast Structural Genomics
%X 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.
%G Anglais
%J Journal of Molecular Biology
%8 2011-09-29
%2 internationale
%I Elsevier
%P in press
%R 10.1016/j.jmb.2011.09.031

Journal of Molecular Biology (J Mol Biol)
Publisher	Elsevier
ISSN	0022-2836 (eISSN : 1089-8638)