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• W2321080291 startingPage "1689" @default.
• W2321080291 abstract "Allostery is a ubiquitous process for protein regulatory activity in which a binding event can change a protein's function carried out at a distal site. Despite intensive theoretical and experimental investigation of protein allostery in the past five decades, effective methods have yet to be developed that can systematically identify key residues involved in allosteric mechanisms. In this study, we propose the rigid residue scan as a systematic approach to identify important allosteric residues. The third PDZ domain (PDZ3) in the postsynaptic density 95 protein (PSD-95) is used as a model system, and each amino acid residue is treated as a single rigid body during independent molecular dynamics simulations. Various indices based on cross-correlation matrices are used, which allow for two groups of residues with different functions to be identified. The first group is proposed as switches that are needed to turn on the binding effect of protein allostery. The second group is proposed as wire residues that are needed to propagate energy or information from the binding site to distal locations within the same protein. Among the nine residues suggested as important for PDZ3 intramolecular communication in this study, eight have been reported as critical for allostery in PDZ3. Therefore, the rigid residue scan approach is demonstrated to be an effective method for systemically identifying key residues in protein intramolecular communication and allosteric mechanisms." @default.
• W2321080291 created "2016-06-24" @default.
• W2321080291 creator A5010373442 @default.
• W2321080291 creator A5081800735 @default.
• W2321080291 creator A5085516115 @default.
• W2321080291 date "2014-12-11" @default.
• W2321080291 modified "2023-09-25" @default.
• W2321080291 title "Identifying Key Residues for Protein Allostery through Rigid Residue Scan" @default.
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• W2321080291 doi "https://doi.org/10.1021/jp5083455" @default.
• W2321080291 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/25437403" @default.
• W2321080291 hasPublicationYear "2014" @default.
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