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Role of the protein side‐chain fluctuations on the strength of pair‐wise electrostatic interactions: Comparing experimental with computed p K a s
Author(s) -
Alexov Emil
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10265
Subject(s) - side chain , chemical physics , chemistry , electrostatics , molecular dynamics , ion , lysozyme , statistical physics , molecular physics , physics , computational chemistry , biochemistry , organic chemistry , polymer
The effect of the protein side‐chain fluctuations on the strength of electrostatic interactions was studied. The effect was modeled on 7 different crystal structures on the same enzyme as well as on 20 molecular dynamics snapshot structures. It was shown that the side‐chain flexibility affects predominantly the magnitude of the strong pair‐wise interactions, that is, the pair‐wise interaction among ion pairs, and practically does not affect the interactions with the rest of the protein. This was used to suggest a correction function that should be applied to the original pair‐wise electrostatic interaction to mimic the effects of the fluctuations. The procedure is applied on three ion pairs identified in lysozyme. It was shown that sampling different side‐chain rotamers and modifying the strength of the pair‐wise interaction energies makes calculated p K a s less sensitive to the fluctuations of the structure and improves the prediction accuracy. Proteins 2003;50:94–103. © 2002 Wiley‐Liss, Inc.