期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 50, 期 1, 页码 94-103出版社
WILEY
DOI: 10.1002/prot.10265
关键词
pH; pK(a)s; Boltzmann distribution; Poisson-Boltzmann equation; DelPhi; MCCE; sidechain flexibility; conformation changes; ion pairs; salt bridges
资金
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R37GM030518, R01GM030518] Funding Source: NIH RePORTER
- NIGMS NIH HHS [GM-30518] Funding Source: Medline
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 pK(a)s less sensitive to the fluctuations of the structure and improves the prediction accuracy.
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