title: 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.
mesh_terms: D003201:Computers; D006096:Gramicidin; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D006096:Gramicidin