Conformational heterogeneity and low-frequency vibrational modes of proteins

Erika Balog, Jeremy C. Smith, David Perahia

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm-1) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.

Original languageEnglish
Pages (from-to)5543-5548
Number of pages6
JournalPhysical Chemistry Chemical Physics
DOIs
Publication statusPublished - Jan 1 2006

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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