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PETER REILLY'S RESEARCH PAGE

Peter Reilly and his research group work in biochemical engineering, and more specifically in using molecular mechanics, molecular dynamics and quantum mechanics to explore the interactions between substrates and enzyme active sites. They construct and maintain the database that lists the amino acid sequences and three-dimensional (tertiary) structures of the members of the eight enzyme groups that participate in the fatty acid/polyketide synthesis cycle. They determine the phylogenetics of members of these enzyme groups and of the families that comprise them. They also produce, purify and crystallize cellulases to obtain their tertiary structures and kinetic properties.

Research Projects

Computational Analysis of Hydrolase Mechanisms


We have studied an α-1,2-mannosidase, a cellulase, and a β-xylosidase by advanced modeling methods, using available tertiary structures as templates, with molecular mechanics, molecular dynamics, and quantum mechanics computational methods. Studying complexes of carbohydrates in the active sites of these hydrolases yields various optimal and suboptimal protein–carbohydrate conformations, and this allows an advanced understanding of protein structure–function relationships and of pathways to and from the transition states of these complexes.

Production, Crystallization, and Structural Characterization of Bacterial Cellulases


We are producing, purifying, crystallizing, and determining the tertiary structures of two bacterial cellulases that convert cellulose to various cellooligosaccharides and are therefore classified as endoglucanases. We are also determining the kinetic properties of these enzymes, both of which catalyze disproportionation reactions. We collaborate with Clark Ford of the Department of Food Science and Human Nutrition and Richard Honzatko of the Department of Biochemistry, Biophysics, and Molecular Biology on this project.

Construction and Use of a Database of the Eight Enzyme Groups in the Fatty Acid/Polyketide Synthesis Cycle


We use data-mining techniques to find amino acid sequences and tertiary structures of members of the eight enzyme groups that make up the fatty acid/polyketide synthesis cycle and include them in a major database called ThYme (Thioester-active enzYmes). We arrange these members into families unrelated to each other by sequence similarity. We group families into clans related by tertiary structure and mechanism. Furthermore, we divide families into subfamilies by differences in their sequences. This allows an intimate understanding how enzymes produced by different organisms having the same substrate specificities are related to each other.