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REVIEW: Bioinformatics and Molecular Modeling in Chemical Enzymology. Active Sites of Hydrolases

S. D. Varfolomeev*, I. V. Uporov, and E. V. Fedorov

School of Chemistry, Lomonosov Moscow State University, Moscow, Russia; fax: 939-3589; E-mail: sdvarf@enzyme.chem.msu.ru

* To whom correspondence should be addressed.

Received April 26, 2002; Revision received June 17, 2002
Comparison and multiple alignments of amino acid sequences of a representative number of related enzymes demonstrate the existence of certain positions of amino acid residues which are permanently reproducible in all members of the whole family. The use of the bioinformatic approach revealed conservative residues in each of the related enzymes and ranked amino acid conservatism for the overall enzymatic catalysis. Glycine and aspartic acid residues were shown to be the most essential for structure and catalytic activity of enzymes. Amino acid residues forming catalytic subsite of the active site of enzymes are always highly conservative. Analysis revealed that aspartic acid carboxyl group is the most frequently employed nucleophilic (in deprotonated form) and electrophilic (in protonated form) agent involved in activation of molecules by the mechanism of general base and acidic catalyses in the catalytic sites of enzymes. Glycine is a unique amino acid possessing the highest possibilities for rotation along C-C and C-N bonds of the polypeptide chain. The conservative fixation of the glycine residue in polypeptide chains of related enzymes provides a possibility for directed assembly of amino acid residues into the catalytic subsite structure. It is possible that the conservative glycines provide known conformational mobility of the protein and the active site. Methods of molecular modeling were used for analysis of structural substitutions of conservative and non-conservative glycines and their effects on geometry of catalytic site of typical hydrolases. The substitution of glycine(s) for alanine significantly altered the catalytic site structures.
KEY WORDS: bioinformatics, molecular modeling, multiple alignment, glycine, aspartic acid, alpha-chymotrypsin, pepsin, alkaline phosphatase, inorganic pyrophosphatase, computer mutations, RMSD