A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.

ABSTRACT: An elastic network model (ENM), usually Cα coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three α-helix rich prote

SUBMITTER: Kim MH 

PROVIDER: S-EPMC3649262 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature