Use of a symmetry condition to compute the conformation of gramicidin S1

Abstract

Using an improved method for computing conformations of closed rings with symmetry, in conjunction with an improved empirical energy function, the conformational space of Gramicidin S is reexamined. The search for minimum energy conformations is confined to the subspace containing closed symmetric rings. A large number of initial conformations selected from that subspace is subjected to energy minimization or is eliminated in a sequence of steps designed to locate the global minimum-energy conformation. One conformation having distinctly low energy is found and is judged to be the global minimum-energy conformation. This conformation is of the beta-pleated sheet type and is in complete agreement with experimental data. Similar structures with beta-pleated sheet-type conformations have been proposed previously on the basis of less extensive examiniations of the conformational space; the condition of exact ring closure, and the extensive examination of conformational space, used here, establish this structure on a firm basis.