A natural coarse graining for simulating large biomolecular motion

Biophys J. 2006 Sep 15;91(6):2115-20. doi: 10.1529/biophysj.106.083568. Epub 2006 Jun 30.

Abstract

Various coarse graining schemes have been proposed to speed up computer simulations of the motion within large biomolecules, which can contain hundreds of thousands of atoms. We point out here that there is a very natural way of doing this, using the rigid regions identified within a biomolecule as the coarse grain elements. Subsequently, computer resources can be concentrated on the flexible connections between the rigid units. Examples of the use of such techniques are given for the protein barnase and the maltodextrin binding protein, using the geometric simulation technique FRODA and the rigidity enhanced elastic network model RCNMA to compute mobilities and atomic displacements.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins
  • Carrier Proteins / chemistry
  • Computer Simulation*
  • Escherichia coli Proteins / chemistry
  • Models, Molecular*
  • Motion
  • Periplasmic Binding Proteins
  • Proteins / chemistry*
  • Ribonucleases / chemistry

Substances

  • Bacterial Proteins
  • Carrier Proteins
  • Escherichia coli Proteins
  • MalE protein, E coli
  • Periplasmic Binding Proteins
  • Proteins
  • Ribonucleases
  • Bacillus amyloliquefaciens ribonuclease