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Energetics and stability of transmembrane helix packing: A replica‐exchange simulation with a knowledge‐based membrane potential

The energetics and stability of the packing of transmembrane helices were investigated by Monte Carlo simulations with the replica‐exchange method. The helices were modeled with a united atom representation, and the CHARMM19 force field was employed. Based on known experimental structures of membrane proteins, an implicit knowledge‐based potential was developed to describe the helix–membrane interactions at the residue level, whose validity was tested through prediction of the orientations when single helices were inserted into a membrane. Two systems were studied in this article, namely the glycophorin A dimer, and helices A and B of Bacteriorhodopsin. For the glycophorin A dimer, the most stable structure (0.5 Å away from the experimental structure) is mainly stabilized by the favorable helix–helix interactions, and has the most population regardless of the helix–membrane interaction. However, for helices A and B of Bacteriorhodopsin, it was found that the packing determined by helix–helix interactions is nonspecific, and a native‐like structure (0.2 Å from the experimental one) can be identified from several structural analogs as the most stable one only after applying the membrane potential. Our results suggest that the contribution from the helix–membrane interaction could be critical in the correct packing of transmembrane helices in the membrane. Proteins 2006. © 2005 Wiley‐Liss, Inc.