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- W2078705445 endingPage "e1004018" @default.
- W2078705445 startingPage "e1004018" @default.
- W2078705445 abstract "Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc–FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design." @default.
- W2078705445 created "2016-06-24" @default.
- W2078705445 creator A5008845398 @default.
- W2078705445 creator A5022643245 @default.
- W2078705445 creator A5053548009 @default.
- W2078705445 date "2014-12-11" @default.
- W2078705445 modified "2023-10-16" @default.
- W2078705445 title "Protein-Protein Docking with Dynamic Residue Protonation States" @default.
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- W2078705445 doi "https://doi.org/10.1371/journal.pcbi.1004018" @default.
- W2078705445 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4263365" @default.
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- W2078705445 hasPublicationYear "2014" @default.
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