Comparison of a Monte Carlo Strategy with a Combined DG/MDSA Method for Structure Determination of Bicyclic Peptides

Abstract

The MC simulation program MOCCA and the combined methods of Distance Geometry and Molecular Dynamics are utilised for structural studies of four isomers of the bee venom toxin apamin. For the MC strategy the conformational space is reduced to torsional degrees of freedom. The study compares the efficiency of both simulation strategies for structure determination of bicyclic peptides and examines the limits of the Monte Carlo method. MOCCA shows a lower efficiency as compared to the combined methods of Distance Geometry and Molecular Dynamics for the structure determination of the bicyclic isomers of apamin.