Prediction of rotational orientation of transmembrane helical segments of integral membrane proteins using new environment-based propensities for amino acids derived from structural analyses

Alpha-helical integral-membrane proteins (IMPs) play a key role in many biological processes, such as signal transduction, and are targets for >50% of current therapeutic drugs. In contrast to their significant abundance and biological importance, they comprise <1% of structurally solved proteins. In the absence of experimental evidence, molecular modeling of IMP structures is an alternative for providing structural information and aiding further experimental design. In the current work, we propose two new amino acid lipid-facing propensity scales derived from the structural analysis of a nonredundant set of water-soluble proteins. The new scales, pi and delta, perform as well or better than published scales (Carugo's hydrophobicity and kPROT scales) in predicting the lipid-facing side of helical segments of a set of structurally solved IMPs, thus indicating (a) that the folding properties of water-soluble proteins and IMPs are similar, and (b) that the new scales will prove useful in modeling the transmembrane segments of IMPs.