Monte carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane

Jakob P. Ulmschneider ^{1 *}, Martin B. Ulmschneider ², Alfredo Di Nola ¹

¹Department of Chemistry, University of Rome La Sapienza, Rome, Italy
²Department of Biochemistry, University of Oxford, Oxford, United Kingdom

email: Jakob P. Ulmschneider (Jakob@ulmschneider.com)

Keywords

peptide folding � Monte Carlo � generalized Born � implicit membrane

Abstract

An efficient Monte Carlo (MC) algorithm using concerted backbone rotations is combined with a recently developed implicit membrane model to simulate the folding of the hydrophobic transmembrane domain M2TM of the M2 protein from influenza A virus and Sarcolipin at atomic resolution. The implicit membrane environment is based on generalized Born theory and has been calibrated against experimental data. The MC sampling has previously been used to fold several small polypeptides and been shown to be equivalent to molecular dynamics (MD). In combination with a replica exchange algorithm, M2TM is found to form continuous membrane spanning helical conformations for low temperature replicas. Sarcolipin is only partially helical, in agreement with the experimental NMR structures in lipid bilayers and detergent micelles. Higher temperature replicas exhibit a rapidly decreasing helicity, in agreement with expected thermodynamic behavior. To exclude the possibility of an erroneous helical bias in the simulations, the model is tested by sampling a synthetic Alanine-rich polypeptide of known helicity. The results demonstrate there is no overstabilization of helical conformations, indicating that the implicit model captures the essential components of the native membrane environment for M2TM and Sarcolipin. Proteins 2007. © 2007 Wiley-Liss, Inc.