Motifs in outer membrane protein sequences: applications for discrimination.
Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important problem for predicting their secondary and tertiary structures and detecting outer membrane proteins from genomic sequences as well. In this work, we have systematically analyzed the distribution of amino acid residues in the sequences of globular and outer membrane proteins with several motifs, such as A*B, A**B, etc. We observed that the motifs E*L, A*K and L*E occur frequently in globular proteins while S*S, N*S and R*D predominantly occur in OMPs. We have devised a statistical method based on frequently occurring motifs in globular and OMPs and obtained an accuracy of 96% and 82% for correctly identifying OMPs and excluding globular proteins, respectively. Further, we noticed that the motifs of transmembrane helical (TMH) proteins are different from that of OMPs. While I*A, I*L and L*I prefer in TMH proteins S*S, N*S and N*N predominantly occur in OMPs. The information about the occurrence of A*B motifs in TMH and OMPs could discriminate them with an accuracy of 80% for excluding OMPs and 100% for identifying OMPs. The influence of protein size and structural class for discrimination is discussed.
Gromiha
M Michael
MM
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D019992:Databases as Topic; D004151:Dipeptides / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D010363:Pattern Recognition, Automated / Q000379:methods*; D017510:Protein Folding; D020539:Sequence Analysis, Protein; D013499:Surface Properties
D000596:Amino Acids; D004151:Dipeptides; D008565:Membrane Proteins