Relationships between protein structure and dynamics from a database of NMR-derived backbone order parameters

Joshua L. Goodman, Mark D. Pagel, Martin J. Stone

Research output: Contribution to journalArticle

74 Scopus citations

Abstract

The amplitude of protein backbone NH group motions on a time-scale faster than molecular tumbling may be determined by analysis of 15N NMR relaxation data according to the Lipari-Szabo model free formalism. An internet-accessible database has been compiled containing 1855 order parameters from 20 independent NMR relaxation studies on proteins whose three-dimensional structures are known. A series of statistical analyses has been performed to identify relationships between the structural features and backbone dynamics of these proteins. Comparison of average order parameters for different amino acid types indicates that amino acids with small side-chains tend to have greater backbone flexibility than those with large side-chains. In addition, the motions of a given NH group are also related to the sizes of the neighboring amino acids in the primary sequence. The secondary structural environment appears to influence backbone dynamics relatively weakly, with only subtle differences between the order parameter distributions of loop structures and regular hydrogen bonded secondary structure elements. However, NH groups near helix termini are more mobile on average than those in the central regions of helices. Tertiary structure influences are also relatively weak but in the expected direction, with more exposed residues being more flexible on average than residues that are relatively inaccessible to solvent. (C) 2000 Academic Press.

Original languageEnglish (US)
Pages (from-to)963-978
Number of pages16
JournalJournal of Molecular Biology
Volume295
Issue number4
DOIs
StatePublished - Jan 28 2000

Keywords

  • Database
  • NMR
  • Order parameter
  • Protein dynamics
  • Structure-dynamics relationships

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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