REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.

ABSTRACT: Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is pre

SUBMITTER: Moritsugu K 

PROVIDER: S-EPMC2483758 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature