A natural coarse graining for simulating large biomolecular motion.
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.
Gohlke
Holger
H
Department of Biological Sciences, J. W. Goethe-University, Frankfurt, Germany.
Thorpe
M F
MF
D001426:Bacterial Proteins; D002352:Carrier Proteins / Q000737:chemistry; D003198:Computer Simulation; D029968:Escherichia coli Proteins / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D033902:Periplasmic Binding Proteins; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry
D001426:Bacterial Proteins; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; C461619:MalE protein, E coli; D033902:Periplasmic Binding Proteins; D011506:Proteins; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease