FOLDING POLYPEPTIDE ALPHA-CARBON BACKBONES BY DISTANCE GEOMETRY METHODS

Polypeptide alpha-carbon backbones were modeled as freely rotating chains made up of spherical monomers. The monomers were assigned an abstract binary ''hydrophobicity'' property that could be either present or absent. Under the assumption that ''hydrophobic'' residues tend to cluster together, away from the polar solvent, three-dimensional conformations of random copolymers of ''hydrophobic'' and ''hydrophilic'' monomers were calculated by a novel algorithm based on distance geometry techniques. The simulated molecules were globular and compact in shape, and possessed distinct hydrophobic cores, indicating that our method was capable of reproducing some of the important global features of real polypeptides. (C) 1994 John Wiley & Sons, Inc.