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Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease
Author(s) -
Wrabl James O.,
Shortle David,
Woolf Thomas B.
Publication year - 2000
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/(sici)1097-0134(20000201)38:2<123::aid-prot2>3.0.co;2-h
Subject(s) - conformational entropy , nuclease , molecular dynamics , entropy (arrow of time) , chemistry , configuration entropy , thermodynamics , statistical physics , molecule , computational chemistry , physics , biochemistry , dna , organic chemistry
Abstract Recent work has suggested that changes in NMR order parameters may quantitatively reflect changes in the conformational entropy of a protein ensemble. The extent of the mathematical relationship between local entropy changes as seen by NMR order parameters and the full protein entropy change is a complex issue. As a step towards a fuller understanding of this problem, molecular dynamics calculations of both native and denatured staphylococcal nuclease were performed. The N‐H bond vector motion, in both explicit and implicit solvent, was analyzed to estimate local and global entropy changes. The calculated N‐H bond vector order parameters from simulation agreed on average with experimental values for both native and denatured structures. However, the inverted‐U profile of order parameters versus residue number observed experimentally for denatured nuclease was only partially reproduced by simulation of compact denatured structures. Comparisons made across the full set of simulations revealed a correlation between the N‐H order parameter‐based conformational entropy change and the total quasiharmonic‐based conformational entropy change between the native and denatured structures. The calculations showed that about 25% of the total entropy change was reflected by changes in simulated S 2 values. This result suggests that NMR‐derived order parameters may be used to provide a reasonable estimate of the total conformational entropy change on protein folding. Proteins 2000;38:123–133. © 2000 Wiley‐Liss, Inc.