Support vector machines for predicting membrane protein types by using functional domain composition

Abstract

Membrane proteins are generally classified into the following five types: 1), type I membrane protein; 2), type II membrane protein; 3), multipass transmembrane proteins; 4), lipid chain-anchored membrane proteins; and 5), GPI-anchored membrane proteins. In this article, based on the concept of using the functional domain composition to define a protein, the Support Vector Machine algorithm is developed for predicting the membrane protein type. High success rates are obtained by both the self-consistency and jackknife tests. The current approach, complemented with the powerful covariant discriminant algorithm based on the pseudo-amino acid composition that has incorporated quasi-sequence-order effect as recently proposed by K. C. Chou (2001), may become a very useful high-throughput tool in the area of bioinformatics and proteomics.

FIGURE 1

Schematic drawing showing the following five types of membrane proteins: (a) type I transmembrane, (b) type II transmembrane, (c) multipass transmembrane, (d) lipid-chain anchored membrane, and (e) GPI-anchored membrane. As shown from the figure, although both type I and type II membrane proteins are of single-pass transmembrane, type I has a cytoplasmic C-terminus and an extracellular or luminal N-terminus for plasma membrane or organelle membrane, respectively, while the arrangement of N- and C-termini in type II membrane proteins is the reverse. No such distinction was drawn between the extracellular (or luminal) and cytoplasmic sides for the other three types in the current classification scheme. Reproduced from Chou (2001) with permission.

FIGURE 2

A schematic drawing to show (a) the first rank, (b) the second rank, and (c) the third-rank sequence-order correlation mode along a protein sequence. (a) Reflects the correlation mode between all the most contiguous residues, (b) that between all the secondmost contiguous residues, and (c) that between all the thirdmost contiguous residues.