Directory

Peter J Reilly

  • Anson Marston Distinguished Professor Emeritus



Education

Ph.D. Chemical Engineering, University of Pennsylvania, 1964 A.B. Chemistry, Princeton University, 1960

Interest Areas

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. Research Projects Computational Analysis of Enzyme Mechanisms
 We have studied an α-1,2-mannosidase, a cellulase, a β-xylosidase, and a thioesterase 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.

Brief Biography

Teaching in Spring 2014 Semester CH E 382 - Chemical Reaction Engineering Other Information 1985-present; Coordinator, Iowa State University–Université de Lausanne–Ecole Polytechnique Fédérale de Lausanne All-University Exchange

Selected Publications

  • Warner, C. D., R. M. Go, C. García-Salinas, C. Ford, and P. J. Reilly. "Kinetic Characterization of a Glycoside Hydrolase Family 44 Endoglucanase from Ruminococcus flavefaciens FD-1," Enzyme Microb. Technol., 48, 27 (2011). http://dx.doi.org/10.1016/j.enzmictec.2010.08.009
  • Cantu, D. C., Y. Chen, M. L. Lemons, and P. J. Reilly. "ThYme: A Database for Thioester-Active Enzymes," Nucleic Acids Res., 39, D342 (2011). http://dx.doi.org/10.1093/nar/gkg1072
  • Jing, F., D C. Cantu, J. Tvaruzkova, J. P. Chipman, B. J. Nikolau, M. D. Yandeau-Nelson,  and P. J. Reilly. "Phylogenetic and Experimental Characterization of an Acyl-ACP Thioesterase Family Reveals Significant Diversity in Enzymatic Specificity and Activity," BMC Biochem., 12, 44 (2011). http://www.biomedcentral.com/1471-2091/12/44
  • Chen, Y., E. E. Kelly, R. P. Masluk, C. L. Nelson, D. C. Cantu, and P. J. Reilly. "Structural Classification and Properties of Ketoacyl Synthases," Protein Sci., 20, 1659 (2011). http:/dx.doi.org/10.1002/pro.712
  • Cantu, D. C., M. J. Forrester, K. Charov, and P. J. Reilly. "Acyl Carrier Protein Structural Classification and Normal Mode Analysis," Protein Sci., 21, 655 (2012). http://dx.doi.org/10.1002/pro.2050
  • Chen, Y., A. Elizondo-Noriega, D. C. Cantu, and P. J. Reilly. "Structural Classification of Biotin Carboxyl Carrier Proteins," Biotechnol. Lett., 34, 1869 (2012). http://dx.doi.org/10.1007/s10529-012-0978-4
  • Cantu, D. C., T. Dai, Z. S. Beversdorf, and P. J. Reilly. "Structural Classification and Properties of Ketoacyl Reductases, Hydroxyacyl Dehydratases, and Enoyl Reductases," Protein Eng. Des. Sel., 25, 803 (2012). http://dx.doi.org/10.1093/protein/gzs050
  • Warner, C. D., G. Camci-Unal, N. L. B. Pohl, C. Ford, and P. J. Reilly. "Substrate Binding by the Catalytic Domain and Carbohydrate Binding Module of Ruminococcus flavefaciens FD-1 Xyloglucan­ase/Endoglucanase," Ind. Eng. Chem. Res., 52, 30 (2013). http://dx.doi.org/10.1021/ie202988a
  • Hill, A. D., and P. J. Reilly. "Scoring Functions for AutoDock," Molecular Methods in Biochemistry. M. Frank and T. Lüttke, eds. Part III – Structural Bioinformatics. Springer. Accepted for publication.
  • Cantu, D. C., A. Ardèvol, C. Rovira, and P. J. Reilly. "Mechanism of a HotDog-fold Acyl-CoA Thioesterase by QM/MM Metadynamics Simulations," Chem. Eur. J., submitted for publication.
  • Carvalho, C. C, N. N. Phan, Y. Chen, and P. J. Reilly. "Carbohydrate Binding Module Clans," Carbohydr. Res., submitted for publication.