Understanding and prediction of membrane protein structures requires knowledge of the physical forces that drive the polypeptide sequence to fold into its native conformation. One such physical potential - the hydrophobic effect – describes the free energy of transferring a protein moiety from water to the bilayer and is thought to make major contributions to the assembly and function of membrane proteins. Many hydrophobicity scales can be found in the literature, yet their accuracy is uncertain because these scales use mimics of the bilayer, mimics of the protein or mimics of both. Using equilibrium protein folding methods, we engineered the outer membrane protein phospholipase A (OmpLA) into a host-guest system to measure the transfer free energies of the twenty natural amino acid side chains from water to phospholipid bilayers. Our results represent the first water-to-bilayer hydrophobicity scale measured in the context of a native transmembrane protein using a phospholipid bilayer. Our side chain partitioning free energies reveal parity for apolar side-chain contributions between soluble and membrane proteins and can be used to accurately predict the helices of alpha-helical proteins such as rhodopsin. We further demonstrate that an arginine side-chain placed near the middle of a lipid bilayer is easily accommodated.
We recently extended our studies to include novel results on the free energy of folding and the m value for several additional membrane proteins. We found that the sensitivity of these membrane proteins to chemical denaturation (as judged by their m values) was consistent with the trends of water-soluble proteins having comparable differences in the solvent-exposure between their folded and unfolded states. Moreover, the stability measurements for all of our membrane proteins were accomplished in the same lipid bilayer system, which offers opportunities for extracting information on sequence–structure–energy relationships for these sequences.