title: Time-averaged order parameter restraints in molecular dynamics simulations.
abstract: A method is described that allows experimental S(2) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland, hansen@itt.uni-stuttgart.de.
authors.forename: Niels
authors.initials: N
authors.lastname: Hansen
authors.forename: Fabian
authors.initials: F
authors.lastname: Heller
authors.forename: Nathan
authors.initials: N
authors.lastname: Schmid
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D013997:Time Factors; D054159:Torsion, Mechanical
chemical_list: D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D010455:Peptides