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Predicting Enzyme Functional Surfaces and Locating Key Residues Automatically from Structures

2007; Springer Science+Business Media; Volume: 35; Issue: 6 Linguagem: Inglês

10.1007/s10439-006-9241-2

1573-9686

Yan Yuan Tseng, Jie Liang,

Enzyme Structure and Function

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.