Application of residue distribution along the sequence for discriminating outer membrane proteins

Abstract

Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important problem both for detecting outer membrane proteins from genomic sequences and for the successful prediction of their secondary and tertiary structures. In this work, we have systematically analyzed the distribution of amino acid residues in the sequences of globular and outer membrane proteins. We observed that the occurrence of two neighboring aliphatic and polar residues is significantly higher in outer membrane proteins than in globular proteins. From the information about the dipeptide composition we have devised a statistical method for discriminating outer membrane proteins from other globular and membrane proteins. Our approach correctly picked up the outer membrane proteins with an accuracy of 95% for the training set of 337 proteins. On the other hand, our method has correctly excluded the globular proteins at an accuracy of 79% in a non-redundant dataset of 674 proteins. Furthermore, the present method is able to correctly exclude α-helical membrane proteins up to an accuracy of 87%. These accuracy levels are comparable to other methods in the literature. The influence of protein size and structural class for discrimination is discussed.