A RAPID AND EFFICIENT ALGORITHM FOR PACKING POLYPEPTIDE-CHAINS BY ENERGY MINIMIZATION

An improved algorithm for packing polypeptide chains with fixed geometry, which converges to a local energy minimum rapidly and efficiently, is described. The speed of convergence of the new algorithm is comparable to that of existing algorithms for minimizing the energies of single polypeptide chains, and it is several times greater than the speed of convergence of previous algorithms for minimizing the energy of structures consisting of several poly-peptide chains. The algorithm has been used to minimize the energy of three-stranded (L-Ala)(8) beta-sheets, three-stranded (L-Val)(6) beta-sheets, and five-stranded (L-Ile)(6) beta-sheets, starting from regular structures found previously; of the three-stranded regular and truncated (Gly-L-Pro-L-Pro)(4) structures used in earlier work to model collagen; and of the stacked beta-sheet(L-Ala-GLy)(6) structures used to model silk. The antiparallel L-Ala beta-sheet, and Gly-Pro-Pro triple helices, and the silk II structure remained nearly regular after energy minimization, but by contrast with results from earlier computations the other structures became significantly irregular. (C) 1994 by John Wiley and Sons, Inc.