MODELING OF FOLDING OF ALPHA-HELICAL PROTEINS WITH KNOWN SECONDARY STRUCTURE

A folding model based on an annealing algorithm is proposed for a prot ein with known secondary structure and minimal architecture graph. The model differs from most others known by taking into account, when cal culating the globule energy, not only the energy of residue-residue in teractions but also the energy of residue-solvent interactions acid th e conformational energy of loops. This is accomplished by introducing the statistical potentials of pairwise residue-residue and residue-sol vent interactions. The conformational space of loops is determined by modeling free polypeptide loop behavior. Using four-helix proteins as an example, it is shown that the model allows one to predict the posit ions of the helices in the globule with sufficient precision: the rms deviation of the predicted structures versus the native one is about 1 .5 Angstrom.