Department of Chemical and Biological Engineering

Anson Marston Distinguished Professor in Engineering

2031 Sweeney Hall
Iowa State University
Ames, IA 50011-2230

Phone (515)294-5968
Fax (515)294-2689
reillyiastate.edu

Education
PhD, ChE, Pennsylvania, 1964
AB, Chemistry, Princeton, 1960

Teaching/Office Hour Schedule

Research Interests
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 seven enzyme groups that participate in the fatty acid/polyketide synthesis cycle. They determine the phylogenys 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.

Other Information
Coordinator, Iowa State University-Université de Lausanne-Ecole Polytechnique Fédérale de Lausanne All-University Exchange, 1985-present.

Research Projects

Computational Analysis of Hydrolase Mechanisms
We are studying 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 alo determining the kinetic properties of these enzymes, one of which catalyzes disproprotionation 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 Seven 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 seven 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.

Recent Publications
Weschayanwiwat, P., J. F. Scamehorn, and P. J. Reilly. Surfactant Properties of Low Molecular Weight Phospholipids. J. Surfact. Deterg., 8, 65 (2005).

Laederach, A., and P. J. Reilly. Protein Recognition of Carbohydrates. Proteins: Struct. Funct. Bioinf., 60, 591 (2005).

Mulakala, C., and P. J. Reilly. Hypocrea jecorina (Trichoderma reesei) Cel7A as a Molecular Machine: A Docking Study. Proteins: Struct. Funct. Bioinf., 60, 598 (2005).

Beisel, C. L., M. K. Dowd, and P. J. Reilly. Conformational Analysis of Gossypol and Its Derivatives by Molecular Mechanics. J. Mol. Struct. (Theochem), 730, 51 (2005).

Mertz, B., R. S. Kuczenski, R. T. Larsen, A. D. Hill, and P. J. Reilly. Phylogenetic Analysis of Family 6 Glycoside Hydrolases. Biopolymers, 79, 197 (2005).

Mulakala, C., and P. J. Reilly. Force Calculations in Automated Docking: Enzyme-Substrate Interactions in Fusarium oxysporum Cel7B. Proteins: Struct. Funct. Bioinf., 61, 590 (2005).

Glatz, C. E., R. Gonzalez, M. E. Huba, S. K. Mallapragada, B. Narasimhan, P. J. Reilly, K. P. Saunders, and J. V. Shanks. Problem-Based Learning Biotechnology Courses in Chemical Engineering. Biotechnol. Prog., 22, 173 (2006).

Hill, A. D. and P. J. Reilly. Comparing Programs for Rigid-Body Multiple Structural Superposition of Proteins.  Proteins: Struct. Funct. Bioinf., 64, 219 (2006)

Mulakala, C., W. Nerinckx, and P. J. Reilly. Docking Studies on Glycoside Hydrolase Family 47 Endoplasmic Reticulum α-(1→2)-Mannosidase I to Elucidate the Pathway to the Substrate Transition State. Carbohydr. Res., 341, 2233 (2006).

Reilly, P. J. Amylase and Cellulase Structure and Function. Chapter 5. Bioprocessing for Value-Added Products from Renewable Resources. S. T. Yang, ed., Elsevier, Amsterdam, pp. 119-130 (2006).

Mulakala, C., W. Nerinckx, and P. J. Reilly. The Fate of β-D-Mannopyranose after Its Formation By Endoplasmic Reticulum α-(1→2)-Mannosidase I Catalysis. Carbohydr. Res., 342, 163 (2007).

Hill, A. D., and P. J. Reilly. Puckering Coordinates of Monocyclic Rings by Triangular Decomposition. J. Chem. Informat. Model., 47, 1031 (2007).

Trabue, S., K. Scoggin, S. Tjandrakusuma, M. A. Rasmussen, and P. J. Reilly. Ruminal Fermentation of Propylene Glycol and Glycerol. J. Agric. Food Chem., 55, 743 (2007).

Mertz, B., A. D. Hill, C. Mulakala, and P. J. Reilly. Automated Docking to Explore Subsite Binding by Glycoside Hydrolase Family 6 Cellobiohydrolases and Endoglucanases. Biopolymers, 87, 249 (2007).

Hill, A. D., and P. J. Reilly. A Gibbs Free Energy Correlation for Automated Docking of Carbo-hydrates. J. Comput. Chem., 29, 1131 (2008).

Fushinobu, S., B. Mertz, A. D. Hill, M. Hidaka, M. Kitaoka, and P. J. Reilly. Computational Analyses of the Conformational Itinerary along the Reaction Pathway of GH94 Cellobiose Phosphorylase. Carbohydr. Res., 343, 1023 (2008).

Cantú, D., W. Nerinckx, and P. J. Reilly. Theory and Computation Show That Asp463 Is the Catalytic Proton Donor in Human Endoplasmic Reticulum α-1,2-Mannosidase I. Carbohydr. Res., 343, 2235 (2008).

Hill, A. D., and P. J. Reilly. Computational Analysis of Glycoside Hydrolase Family 1 Specificities. Biopolymers, 89, 1021 (2008).

Mertz, B., X. Gu, and P. J. Reilly. Analysis of Functional Divergence within Two Structurally Related Glycoside Hydrolase Families. Biopolymers, 91, 478 (2009).

Petersen, L., A. Ardèvol, C. Rovira, and P. J. Reilly. Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study. J. Phys. Chem. B, 113, 7331 (2009).

Johnson, G. P., L. Petersen, A. D. French, and P. J. Reilly. Twisting of Glycosidic Bonds by Hydrolases. Carbohydr. Res., 344, 2157 (2009).

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