title: Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.
abstract: A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.
authors: Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany.
authors: Katja
authors: K
authors: Ostermeir
authors: Martin
authors: M
authors: Zacharias
mesh_terms: D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics; D018909:src Homology Domains
chemical_list: D009842:Oligopeptides; D010455:Peptides; C508725:Trp-cage peptide; C506175:chignolin
keywords: accelerated sampling; conformational sampling; force field calculation; molecular dynamics simulations; peptide and protein folding; potential scaling