Analytical rebridging Monte Carlo: Application to cis/trans isomerization in proline-containing, cyclic peptides

Abstract

We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/transisomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have previously been characterized by nuclear magnetic resonance methods. Our simulations achieve effective equilibration and agree well with experimental data in all cases. We discuss the importance of effective equilibration as well as the role of bond flexibility and solvent effects in the prediction of equilibrium properties.