Efficient sampling in collective coordinate space.
Collective motions in biological macromolecules have been shown to be important for function. The most important collective motions occur on slow time scales, which poses a sampling problem in dynamic simulation of biomolecules. We present a novel method for efficient conformational sampling. The method combines the simulation of an ensemble of concurrent trajectories with restraints acting on the ensemble of structures as a whole. Two properties of the ensemble may be restrained: (i) the variance of the ensemble and (ii) the average position of the ensemble. Both properties are defined in a subspace of collective coordinate space spanned by an arbitrary number of modes. We show that weak restraints on the ensemble variance suffice for an increase in sampling efficiency along soft modes by two orders of magnitudes. The resulting trajectories exhibit virtually the same structural quality as trajectories generated by restraint-free-molecular dynamics simulation, as judged by standard structure validation tools. The method is used to probe the resistance of a structure against conformational changes along collective modes and clearly distinguishes soft from stiff modes. Further applications are discussed. Proteins 2000;39:82-88.
Abseher
R
R
European Molecular Biology Laboratory, Heidelberg, Germany. abseher@embl-heidelberg.de
Nilges
M
M
D003198:Computer Simulation; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D015983:Selection Bias; D013049:Spectrin / Q000737:chemistry / Q000235:genetics
D011506:Proteins; D013049:Spectrin