Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

J Mol Biol. 2005 Jan 14;345(2):299-314. doi: 10.1016/j.jmb.2004.10.054.

Abstract

We analyze the mechanical properties and putative dynamical fluctuations of a variety of viral capsids comprising different sizes and quasi-equivalent symmetries by performing normal mode analysis using the elastic network model. The expansion of the capsid to a swollen state is studied using normal modes and is compared with the experimentally observed conformational change for three of the viruses for which experimental data exist. We show that a combination of one or two normal modes captures remarkably well the overall translation that dominates the motion between the two conformational states, and reproduces the overall conformational change. We observe for all of the viral capsids that the nature of the modes is different. In particular for the T=7 virus, HK97, for which the shape of the capsid changes from spherical to faceted polyhedra, two modes are necessary to accomplish the conformational transition. In addition, we extend our study to viral capsids with other T numbers, and discuss the similarities and differences in the features of virus capsid conformational dynamics. We note that the pentamers generally have higher flexibility and propensity to move freely from the other capsomers, which facilitates the shape adaptation that may be important in the viral life cycle.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Bacteriophages / chemistry
  • Capsid / chemistry*
  • Capsid Proteins / chemistry
  • Macromolecular Substances
  • Models, Molecular
  • Models, Statistical
  • Protein Conformation
  • Viruses / metabolism*
  • X-Rays

Substances

  • Capsid Proteins
  • Macromolecular Substances