Predicting protein quaternary structure by pseudo amino acid composition

In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, that associate through noncovalent interactions and, occasionally, disulfide bonds. With the number of protein sequences entering into data banks rapidly increasing, we are confronted with a challenge: how to develop an automated method to identify the quaternary attribute for a new polypeptide chain (i.e., whether it is formed just as a monomer, or as a dimer, trimer, or any other oligomer). This is important, because the functions of proteins are closely related to their quaternary attribute. For example, some critical ligands only bind to dimers but not to monomers; some marvelous allosteric transitions only occur in tetramers but not other oligomers; and some ion channels are formed by tetramers, whereas others are formed by pentamers. To explore this problem, we adopted the pseudo amino acid composition originally proposed for improving the prediction of protein subcellular location (Chou, Proteins, 2001; 43:246-255). The advantage of using the pseudo amino acid composition to represent a protein is that it has paved a way that can take into account a considerable amount of sequence-order effects to significantly improve prediction quality. Results obtained by resubstitution, jack-knife, and independent data set tests, have indicated that the current approach might be quite promising in dealing with such an extremely complicated and difficult problem.