Structural dynamics of protein backbone ψ angles: Extended molecular dynamics simulations versus experimental 3J scalar couplings

Phineus R.L. Markwick, Scott A. Showalter, Guillaume Bouvignies, Rafael Brüschweiler, Martin Blackledge

Research output: Contribution to journalArticle

30 Scopus citations

Abstract

3J scalar couplings report on the conformational averaging of backbone ψ angles in peptides and proteins, and therefore represent a potentially powerful tool for studying the details of both structure and dynamics in solution. We have compared an extensive experimental dataset with J-couplings predicted from unrestrained molecular dynamics simulation using enhanced sampling available from accelerated molecular dynamics or using long timescale trajectories (200 ns). The dynamic fluctuations predicted to be present along the backbone, in agreement with residual dipolar coupling analysis, are compatible with the experimental 3J scalar couplings providing a slightly better reproduction of these experimental parameters than a high-resolution static structure.

Original languageEnglish (US)
Pages (from-to)17-21
Number of pages5
JournalJournal of Biomolecular NMR
Volume45
Issue number1-2
DOIs
StatePublished - Jul 24 2009

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Spectroscopy

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