Force field-dependent solution properties of glycine oligomers.

ABSTRACT: Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly(3) and Gly(10) in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly(3) and Gly(10) were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows u

SUBMITTER: Drake JA 

PROVIDER: S-EPMC4450816 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature