Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: Molecular dynamics simulations of native and denatured staphylococcal nuclease

Research output: Contribution to journalArticle

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 S2 values. This result suggests that derived order parameters may be used to provide a reasonable estimate of the total conformational entropy change on protein folding.

Original languageEnglish (US)
Pages (from-to)123-133
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume38
Issue number2
DOIs
StatePublished - Feb 1 2000

Keywords

  • Conformational entropy
  • Molecular dynamics simulation
  • Order parameters
  • Protein folding
  • Staphylococcal nuclease

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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