Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations.

ABSTRACT: The brevity of molecular dynamics simulations often limits their utility in developing and evaluating structural models of proteins. The duration of simulations can be increased greatly using discrete molecular dynamics (DMD). However, the trade off is that coarse graining, implicit solvent, and other time-saving procedures reduce the accuracy of DMD simulations. Here we address some of these issues by comparing results of DMD and conventional all atom MD simulations on proteins of known structure and misfolded proteins. DMD simulations were performed at a range of temperatures to identify a 'physiological' temperature for DMD that mimicked molecular motions of conventional MD simulations at 310K. We also compared results obtained with a new implicit solvent model developed here based on M

SUBMITTER: Yun S 

PROVIDER: S-EPMC3104411 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature