Predicting amino acid residues responsible for enzyme specificity solely from protein sequences.
We describe a general, modular method for developing protocols to identify the amino acid residues that most likely define the division of a protein superfamily into two subsets. As one possibility, we use PROBE to gather superfamily members and perform an ungapped alignment. We then use a modified BLOSUM62 substitution matrix to determine the discriminating power of each column of aligned residues. The overall method is particularly useful for predicting amino acids responsible for substrate or binding specificity when no structures are available. We apply our method to three pairs of protein classes in three different superfamilies, and present our results, some of which have been experimentally verified. This approach may accelerate the elucidation of enzymic substrate specificity, which is critical for both mechanistic insights into biocatalysis and ultimate application.
Department of Chemical Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, USA.
Eudean
E
Shaw
Jonathan S
JS
Dordick
D000262:Adenylyl Cyclases / Q000737:chemistry / Q000145:classification / Q000235:genetics; D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D016000:Cluster Analysis; D030562:Databases, Protein; D004122:Dimethylallyltranstransferase / Q000737:chemistry / Q000145:classification / Q000235:genetics; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D006162:Guanylate Cyclase / Q000737:chemistry / Q000145:classification / Q000235:genetics; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D051381:Rats; D012177:Retinol-Binding Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013379:Substrate Specificity
D002352:Carrier Proteins; C490174:Fabp7 protein, rat; D000071438:Fatty Acid-Binding Protein 7; D050556:Fatty Acid-Binding Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D011506:Proteins; D012177:Retinol-Binding Proteins; D004122:Dimethylallyltranstransferase; D000262:Adenylyl Cyclases; D006162:Guanylate Cyclase