High coordination lattice models of protein structure, dynamics and thermodynamics.

Abstract

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force field, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and 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 tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.