Predicting the Solvent Accessibility of Transmembrane Residues from Protein Sequence

In this study, we propose a novel method to predict the solvent accessible surface areas of
transmembrane residues. For both transmembrane α-helix and β-barrel residues, the correlation
coefficients between the predicted and observed accessible surface areas are around 0.65. On the basis
of predicted accessible surface areas, residues exposed to the lipid environment or buried inside a
protein can be identified by using certain cutoff thresholds. We have extensively examined our approach
based on different definitions of accessible surface areas and a variety of sets of control parameters.
Given that experimentally determining the structures of membrane proteins is very difficult and
membrane proteins are actually abundant in nature, our approach is useful for theoretically modeling
membrane protein tertiary structures, particularly for modeling the assembly of transmembrane
domains. This approach can be used to annotate the membrane proteins in proteomes to provide extra
structural and functional information.
Keywords: lipid exposed residues • transmembrane helix protein • transmembrane β-barrel protein • protein
sequence analysis • support vector regression