Molecular Dynamics of Coat Proteins of the Human Rhinovirus

Wan F. Lau, Bernard Pettitt, Terry P. Lybrand

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

The effects of the oxazole antiviral WIN 52084 on the thermal vibrations of the coat proteins of the human rhinovirus were studied by means of a comparison of two molecular dynamics simulations. One simulation involved only a protomeric unit (cluster of four proteins) of the viral coat, while the other included the antiviral drug bound to the protein cluster. Analysis of the RMS fluctations for all atoms indicates that the drug did not cause any statistically significant global changes in the amplitude of atomic motion. However, the RMS fluctuation of seventeen residues in the vicinity of the drug decreased by about 11%. Two global effects were observed. Most importantly, the drug was found to make the decay times of the atomic fluctuations more uniform. Also, the drug lowered the average correlation time for displacements of atoms in the drug-bound cluster. Finally, a comparison of the differences in the normalized cross-correlation functions of residues close to the binding site showed that the residues move more collectively and in phase in the presence of the ligand. These results indicate that the drug has a global effect on the dynamics of the protein cluster and suggest a simple mechanical model for the action of the drug.

Original languageEnglish (US)
Pages (from-to)385-398
Number of pages14
JournalMolecular Simulation
Volume1
Issue number6
DOIs
StatePublished - 1988
Externally publishedYes

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Keywords

  • atomic trajectories
  • Langevin dynamics
  • Molecular dynamics
  • soft-spheres
  • time-dependent properties

ASJC Scopus subject areas

  • Chemical Engineering(all)
  • Information Systems
  • Materials Science(all)
  • Modeling and Simulation
  • Condensed Matter Physics
  • Chemistry(all)

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