HIGH COORDINATION LATTICE MODELS OF PROTEIN-STRUCTURE, DYNAMICS AND THERMODYNAMICS

A high coordination lattice discretization of protein conformational s pace is described. The model allows discrete representation of polypep tide chains of globular proteins and small macromolecular assemblies w ith an accuracy comparable to the accuracy of crystallographic structu res. Knowledge based force field, that consists of sequence specific s hort range interactions, cooperative model of hydrogen bond network an d tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution te rtiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when ev olutionary information is exploited or/and when sparse experimental da ta are available. The model responds correctly to sequence mutations a nd could be used at early stages of a computer aided protein design an d protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of p olypeptides and proteins and quite detailed theoretical studies of the rmodynamics of nontrivial protein models.