Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

ABSTRACT: We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplex

SUBMITTER: Aliev AE 

PROVIDER: S-EPMC4282583 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature