Mary Jo Ondrechen

About

Prof. Ondrechen’s research group specializes in theoretical and computational chemistry and computational biology. Areas of interest include: 1) Understanding the fundamental basis for enzyme catalysis; 2) Functional genomics – prediction of the functional roles of gene products (proteins); 3) Modeling of enzyme-substrate interactions; 4) Drug discovery; and 5) Bioinformatics.

With the sequencing of the human genome and the genomes of hundreds of species of interest, Structural Genomics (SG) projects have now reported over 12,000 new protein structures. The next question is: What do these structures actually do? Prof. Ondrechen’s group is developing methods to predict protein function from structure. Our THEMATICS (see Ondrechen et al., Proc. Natl. Acad. Sci. USA 98, 12473, 2001) and POOL (see Tong, Wei, Murga, Ondrechen and Williams, PLoS Computational Biology, 2009) methods predict the residues involved in biochemical function, require only the structure of the query protein, and thus work for proteins that bear no resemblance to previously characterized proteins. Our SALSA method (see Wang, Yin, et al. 2013) uses these predicted functional residues to determine biochemical function.

Another current project explores the multilayer nature of enzyme active sites – we are able to predict when remote amino acid residues are involved in catalysis. We work in collaboration with experimentalists to test and verify our predictions pertaining to multilayer active sites.

Selected Publications

• L. Ngu, J.N. Winters, K. Nguyen, K.E. Ramos, N.A. DeLateur, L. Makowski, P.C. Whitford, M.J Ondrechen, P.J. Beuning, Probing Remote Residues Important for Catalysis In Escherichia Coli Ornithine Transcarbamoylase, PLoS ONE 15(2), 2020, e0228487
• R.N. Hanson, E. McCaskill, E. Hua, P. Tongcharoensirikul, R. Dilis, J.L. Silver, T.A. Coulther, M.J. Ondrechen, D. Labaree, R.B. Hochberg, Synthesis of Benzoylbenzamide Derivatives of 17α-E- Vinyl Estradiol and Evaluation as Ligands for the Estrogen Receptor-a Ligand Binding Domain, Steroids, 144, 2019, 15-20
• D.J. MacPherson, C.L. Mills, M.J. Ondrechen, J.A. Hardy Tri-Arginine Exosite Patch of Caspase-6 Recruits Substrates for Hydrolysis, Journal of Biological Chemistry, 294(1), 2019, 71-88
• C.L. Mills, R. Garg, J.S. Lee, L. Tian, A. Suciu, G. Cooperman, P.J. Beuning, M.J. Ondrechen, Functional Classification of Protein Structures by Local Structure Matching in Graph Representation, Protein Science, 27, 2018, 1125-1135

Faculty

May 20, 2020

REU Award for Modeling SARS-CoV-2 Proteins

BioE Affiliated Faculty Mary Jo Ondrechen, Assistant Professor Mona Minkara, and COS Assistant Professor Steven Lopez were awarded a $73K NSF RAPID grant for “Undergraduate Research in Modeling and Computation for Discovery of Molecular Probes for SARS-CoV-2 Proteins.”

Faculty

Jun 27, 2019

Predicting Protein Functions from 3D Structures

ECE Professor Deniz Erdogmus (co-PI) and affiliated BioE Professors Mary Jo Ondrechen (PI) and Penny Beuning (co-PI) were awarded a $600K NSF grant for “Mining for mechanistic information to predict protein function”.

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