An investigation into the ability to define transmembrane protein spans using the biophysical properties of amino acid residues.

A key question associated with topology predictions for membrane proteins is whether there is sufficient variation in the biophysical properties of residues at the membrane interface to enable identification of TM spans in a robust and efficient manner using relatively simple methods of analysis. Here, a test for the homogeneity of multinomial populations is used to identify statistical differences between the residue compositions of windows within datasets of aligned non-homologous TM alpha-helices. Using this approach, the accuracy and robustness of the predicted boundaries for datasets of uncleaved signal (US) sequences and stop transfer sequences (ST) is tested. The validity of the 21 residue length, which is generally assumed for TM spans in membrane protein topology prediction is also investigated and it is suggested that ST sequences may be better represented by a length of 22 residues.