Lattice model simulations of polypeptide chain folding.
Simulated annealing methods are applied to simple cubic lattice C alpha models of eight small monomeric globular proteins and their transition from a random chain to a low energy compact state is examined. The lowest energy structures are compared to their crystal forms using coordinate distance deviations, dRMS and RMS, and by distance contact maps. Analysis of the transition region indicates that, for this model, collapse begins with a rapid decline in radius of gyration followed continuously by chain repackings that lead to progressively lower values of chain energy. Chain repackings represent a highly cooperative interplay between the formation of local and non-local interactions. The components of this transition are characterized by rapid relaxation of shorter chain segments to form local contacts and slower relaxations of longer chain segments to form non-local contacts. Final structures obtained with this procedure contain many of the gross topologies of their native structures.
Covell
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DG
Frederick Biomedical Supercomputing Center, PRI/Dyncorp, FCRDC, NCI, MD 21702.
D003198:Computer Simulation; D003461:Crystallography; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature; D013816:Thermodynamics