A method for evaluating binding free energy differences of protein-protein complex structures generated by protein docking was recently developed by some of us. The method, termed evERdock, combined short (2 ns) molecular dynamics (MD) simulations in explicit water and solution theory in the energy representation (ER) and succeeded in selecting the near-native complex structures from a set of decoys. In the current work, we performed longer (up to 100 ns) MD simulations before employing ER analysis in order to further refine the structures of the decoy set with improved binding free energies. Moreover, we estimated the binding free energies for each complex structure based on an average value from five individual MD snapshots. After MD simulations, all decoys exhibit a decrease in binding free energy, suggesting that proper equilibration in explicit solvent resulted in more favourably bound complexes. During the MD simulations, non-native structures tend to become unstable and in some cases dissociate, while near-native structures maintain a stable interface. The energies after the MD simulations show an improved correlation between similarity criteria (such as interface root-mean-square distance) to the native (crystal) structure and the binding free energy. In addition, calculated binding free energies show sensitivity to the number of contacts, which was demonstrated to reflect the relative stability of structures at earlier stages of the MD simulation. We therefore conclude that the additional equilibration step along with the use of multiple conformations can make the evERdock scheme more versatile under low computational cost.
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21 November 2018
Research Article|
November 19 2018
Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations
Ai Shinobu;
Ai Shinobu
1
School of Life Science and Technology, Tokyo Institute of Technology
, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
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Kazuhiro Takemura;
Kazuhiro Takemura
1
School of Life Science and Technology, Tokyo Institute of Technology
, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
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Nobuyuki Matubayasi
;
Nobuyuki Matubayasi
2
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University
, Toyonaka, Osaka 560-8531, Japan
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Akio Kitao
Akio Kitao
a)
1
School of Life Science and Technology, Tokyo Institute of Technology
, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
a)Author to whom correspondence should be addressed: [email protected]
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a)Author to whom correspondence should be addressed: [email protected]
J. Chem. Phys. 149, 195101 (2018)
Article history
Received:
September 11 2018
Accepted:
October 29 2018
Citation
Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao; Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations. J. Chem. Phys. 21 November 2018; 149 (19): 195101. https://doi.org/10.1063/1.5055799
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