Normal mode analysis and applications in biological physics

J Phys Condens Matter. 2010 Oct 27;22(42):423202. doi: 10.1088/0953-8984/22/42/423202. Epub 2010 Oct 7.

Abstract

Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.

Publication types

  • Review

MeSH terms

  • ATP-Binding Cassette Transporters / chemistry
  • ATP-Binding Cassette Transporters / metabolism
  • Animals
  • Biophysics / methods*
  • Humans
  • Models, Molecular
  • Principal Component Analysis
  • Protein Conformation
  • Vibration
  • Virion / chemistry
  • Virion / metabolism

Substances

  • ATP-Binding Cassette Transporters