An algorithm for packing regular multistrand polypeptide structures by energy minimization

Abstract

AbstractAn algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum‐energy regular structures of three‐stranded (L‐Ala)8, three‐stranded (L‐Val)6, five‐stranded (L‐Ile)6, and the regular and truncated three‐stranded (Gly‐L‐Pro‐L‐Pro)4 triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.