Energetics, stability, and prediction of transmembrane helices

We show that the peptide backbone of an oc-helix places a severe thermodyna mic constraint on transmembrane (TM) stability. Neglect of this constraint by commonly used hydrophobicity scales underlies the notorious uncertainty of TM helix prediction by sliding-window hydropathy plots of membrane prote in (MP) amino acid sequences. We find that an experiment-based whole-residu e hydropathy scale (WW scale), which includes the backbone constraint, iden tifies TM helices of membrane proteins with an accuracy greater than 99%. F urthermore, it correctly predicts the minimum hydrophobicity required for s table single-helix TM insertion observed in Escherichia coli. In order to i mprove membrane protein topology prediction further, we introduce the augme nted WW (aWW) scale, which accounts for the energetics of salt-bridge forma tion. An important issue for genomic analysis is the ability of the hydropa thy plot method to distinguish membrane from soluble proteins. We find that the method falsely predicts 17 to 43% of a set of soluble proteins to be M Ps, depending upon the hydropathy scale used. (C) 2001 Academic Press.