Prediction of membrane protein types by incorporating amphipathic effects.

According to their intramolecular arrangement and position in a cell, membrane proteins are generally classified into the following six types: (1) type I transmembrane, (2) type II transmembrane, (3) multipass transmembrane, (4) lipid chain-anchored membrane, (5) GPI-anchored membrane, and (6) peripheral membrane. Situated in a heteropolar environment, these six types of membrane proteins must have quite different amphiphilic sequence-order patterns in order to stabilize their respective frameworks. To incorporate such a feature into the predictor, the amphiphilic pseudo amino acid composition has been formulated that contains a series of hydrophobic and hydrophilic correlation factors. The success rates thus obtained have been remarkably enhanced in identifying the types of membrane proteins, as demonstrated by the jackknife test and independent data set test, respectively.