Secondary structure formation in model polypeptide chains

Abstract

Model polypeptide chains were folded into 3-D compact conformations using distance geometry techniques. Interresidue distances were predicted from the hydrophobicity of the monomers and were refined by repeated projections into lower-dimensional spaces. Main-chain hydrogen bond networks were constructed and propagated through the structure by adjusting local conformations to comply with ideal distance constraints around hydrogen bonds. The resulting folds were compact globules with distinct hydrophobic cores and contained secondary structure elements like real protein molecules. Apart from similarity in appearance, several properties of the model chains were also very close to those of native folded polypeptides. The method in its present form can serve as a starting point for the development of a novel structure prediction algorithm.