title: Predicting enzyme functional surfaces and locating key residues automatically from structures.
abstract: Locating functionally important protein surfaces and identifying the catalytic site residues are critical for studying enzyme functions. Here, we present a method for predicting and characterizing catalytic sites of enzymes that is fold-independent. By extract atomic patterns of catalytic residues in surface pockets computed geometrically, we develop a library of atomic patterns on protein functional surfaces of ca 700 structures. Together with propensities of secondary structures and residue occurrence in active sites, we develop a method to identify functionally important surfaces on protein structures and to locate key residues. We discuss application of our methods to amylase, dioxygenase, deaminase, dehalogenase, and hydratase. A large scale cross-validated prediction study shows that our method is sensitive and specific. Our method can used to study enzyme function, drug design, and engineering novel biochemical function.
authors.affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607-7052, USA.
authors.forename: Yan Yuan
authors.initials: YY
authors.lastname: Tseng
authors.forename: Jie
authors.initials: J
authors.lastname: Liang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D002384:Catalysis; D003198:Computer Simulation; D004789:Enzyme Activation; D004798:Enzymes / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
chemical_list: D000596:Amino Acids; D004798:Enzymes