Application of density similarities to predict membrane protein types based on pseudo-amino acid composition

Abstract

Cell membranes provide integrity of living cells. Although the stability of biological membrane is maintained by the lipid bilayer, membrane proteins perform most of the specific functions such as signal transduction, transmembrane transport, etc. Then it is plausible membrane proteins being attractive drug targets. In this article, based on the concept of using the pseudo-amino acid composition to define a protein, three different density similarities are developed for predicting the membrane protein type. The predicted results showed that the proposed approach can remarkably improve the accuracy, and might become a useful tool for predicting the other attributes of proteins as well.

Fig. 1

Schematic drawing showing the following five types of membrane proteins: (1) type I transmembrane, (2) type II transmembrane, (3) multipass transmembrane, (4) lipid-chain-anchored membrane, and (5) GPI-anchored membrane. Reproduced from Chou (2001) with permission.

Fig. 2

Schematic drawing showing the following five types of membrane proteins: (1) type I transmembrane, (2) type II, (3) type III, (4) type IV, (5) multipass transmembrane, (6) lipid-chain-anchored membrane, (7) GPI-anchored membrane, and (8) peripheral membrane. Reproduced from Chou and Shen (2007) with permission. see Spiess (1995) for a detailed description about their difference.