Faculty Research Page

Jack F. Kirsch

Jack Kirsch

Professor of the Graduate School Division of Biochemistry, Biophysics and Structural Biology

Lab Homepage: http://mcb.berkeley.edu/labs/kirsch/

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Research Interests


We are currently engaged in collaborative research with Professor Steven Brenner, which is focused on developing improved methods for annotation of protein function from sequence and structural data.

Current Projects

In additon to the project listed above, we maintain an active interest in mechanistic enzymology, especially pyridoxal phosphate dependent enzymes.  Other interests include protein/protein and protein/ small molecule interactions, as well as quantitative analysis of drug/target interactions.

Selected Publications

Specificity and Cooperativity at ß-Lactamase Position 104 in TEM-1/BLIP and SHV-1/BLIP Interactions [M.S. Hanes, K.A. Reynolds, C. McNamara, P. Ghosh, R. A. Bonomo, J. F. Kirsch, T. M. Handel (2011) Proteins, Structure, Function and Genetics 79, 1267-1276]

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts [R. K. Shultzaberger, D. S. Malashock, J. F. Kirsch, M. B. Eisen (2010) PLoS Genet 6, e1001042]

Active Site Prediction using Evolutionary and Structural Information [S. Sankararaman, S. Fei, J. F. Kirsch, M. I. Jordan, K. Sjolander (2010)  Bioinformatics 26, 617-624]

The Partially Folded Homodimeric Intermediate of E. coli Aspartate Aminotransferase Contains a “Molten Interface” structure [E. Deu, J. Dhoot, J. F. Kirsch (2009) Biochemistry 48, 433-441]

Computational Redesign of the SHV-1 ß-lactamase/ß-lactamase Inhibitor Protein Interface [K. A. Reynolds, M. S. Hanes, J. M. Thomson, A. J. Antczak, J. M. Berger, R. A. Bonomo, J. F. Kirsch, T. M.  Handel (2008)  J. Molec. Biol. 382, 1265-1275]

Identification of Mutations that Shift Paralog Functions: Conversion of E. Coli Malate Dehydrogenase to a Lactate Dehydrogenase by Rational Design [Y. Yin  and J. F. Kirsch (2007) Proceedings of the National Academy of Sciences, USA 104, 17353-17357]

The Unfolding Pathway for Apo E. coli Aspartate Aminotransferase is Dependent on the Choice of Denaturant [E. Deu, and J. F. Kirsch (2007) Biochemistry 46, 5810-5818]

Free Energies of Protein-Protein Association Determined by Electrospray Ionization Mass Spectrometry Correlate Accurately with Values Obtained by Solution Methods. [S. R. Krishnaswamy, E. R. Williams, and J. F.  Kirsch (2006) Protein Science 15,1465-1475]

Directed Evolution Relieves Product Inhibition in a Rationally Designed Tyrosine Aminotransferase. [S. C. Rothman, M. Voorhies, and J. F. Kirsch (2004) Protein Science 13, 763-772]

Avoiding the Road Less Traveled: How the Topology of Enzyme-substrate Complexes Can Dictate Product Selection. [A. C. Eliot and J. F. Kirsch (2003) Accts. Chem. Res. 36, 757-765]

Pyridoxal Phosphate Enzymes: Mechanistic, Structural and Evolutionary Considerations. [A. C. Eliot, and J. F. Kirsch (2004) Ann. Revs. Biochem. 73, 383-415]

Photo credit: Mark Joseph Hanson of Mark Joseph Studio.

Last Updated 2011-08-12