Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.

ABSTRACT: Normal mode analysis (NMA) has received much attention as a direct approach to extract the collective motions of macromolecules. However, the stringent requirement of computational resources by classical all-atom NMA limits the size of the macromolecules to which the method is normally applied. We implemented a novel coarse-grained normal mode approach based on partitioning the all-atom Hessian matrix into relevant and nonrelevant parts. It is interesting to note that, using classical all-atom NMA results as a reference, we found that this method generates more accurate results than do other coarse-grained approaches, including elastic network model and block normal mode approaches. Moreover, this new method is effective in incorporating the energetic contributions from the nonrelevant ato

SUBMITTER: Zhou L 

PROVIDER: S-EPMC2292380 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature