Home Faculty and Research Faculty by Name Jack Kirsch

Jack Kirsch

Professor of the Graduate School Division of Biochemistry and Molecular Biology

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

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Research Interests

PLEASE NOTE.  PROFESSOR KIRSCH IS RETIRED AND IS NO LONGER ACCEPTING NEW STUDENTS OR POSTDOCTORAL FELLOWS.

We are interested in understanding quantitatively the effects of single and multiple amino acid substitutions on: 1. enzyme activity, 2. the relationship between sequence and function, and 3. protein-protein complexes. We recently introduced a method for the quantitative analysis of chimeric constructs (Luong and Kirsch (2001)) and the use of Venn Diagrams from set theory (Deu and Kirsch (2002)), Rothman and Kirsch (2003) to help to understand how amino acid replacements change enzyme specificity. We are using directed evolution and phylogenetic approaches to the above problems. 

Current Projects

PLP enzymology. The laboratory has a long-standing interest in the biochemistry of enzymes that utilize the cofactor pyridoxal phosphate (PLP), which is essential for the catalysis of the major reactions involved in amino acid transformations. Projects 1-4 illustrate some of our current pursuits in PLP enzymology: 1) The best understood of these enzymes is aspartate aminotransfersase. The three-dimensional structure of this enzyme has guided these experiments, and has aided greatly in the interpretation of the mechanistic studies carried out in our laboratory. We are currently employing directed evolution by DNA shuffling to explore the sets of mutations that govern specificity for different amino acid substrates. 2) The enzyme aminocyclopropane carboxylate synthase (ACCS) is the committed enzyme in the biosynthetic pathway to the important plant hormone, ethylene. Our laboratory, in a collaboration, has solved the crystal structure, and we are currently involved in a detailed study of the mechanism of action of this enzyme. 3) It has been estimated that approximately 40% of the genome has been mis annotated.  We have elected to characterize a number of new aminotransferases, whose annotation is uncertain in order to discover genome wide specifictiy determinants for this group of enzymes. 4) Directed evolution is being used to narrow enzyme selectivity and to change reaction type. 

Protein/protein recognition. We have used high resolution epitope mapping to understand how specific contacts at interfaces effect both the stability and kinetics of these interactions. We recently devised an experimental approach that reveals details about docking trajectories of interacting proteins. (Tayloret al, 1998). This method is being adapted to evaluate subunit associations in oligomeric proteins. Protein stability and protein-protein interactions are being examined by mass spectrometry in collaboration with Professor E. Williams of this university.

Selected Publications

The Narrow Substrate Specificity of Human Tyrosineaminotransferase – The Enzyme Deficient in Tyrosinemia Type II [ S. Sivaraman and J. F.  Kirsch (2006) FEBS Journal 273, 1920–1929]

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] 

The Enzymology of Cystathionine Biosynthesis: Strategies for the Control of Substrate and Reaction Specificity. [S. M. Aitken and J. F.  Kirsch (2005) Arch. Biochem. Biophys. 433, 166-175]

Structure of ACC synthase Inactivated by the Mechanism-based Inhibitor L-vinylglycine. [G. Capitani, M. Tschopp, A. C.  Eliot, J. F.  Kirsch, and M. G. Grütter (2005) FEBS Lett. 579, 2458-2462]
 
Conserved and Non-conserved Residues in the Substrate Binding Site of 7,8-Diaminopelargonic Acid Synthase from Escherichia coli are Essential for Catalysis. [J.  Sandmark, A. C.  Eliot, H. J. K. Famm, G. Schneider, and J. F.  Kirsch (2004) Biochemistry 43, 1213-1222]

The Role of Active-Site Residues Thr81, Ser82, Thr85, Gln157, and Tyr158 in Yeast Cystathionine β-Synthase Catalysis and Reaction Specificity. [S. M. Aitken and J. F. Kirsch (2004) Biochemistry 43, 1963-1971]

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]

The Kinetics of the Yeast Cystathionine-β-Synthase Forward and Reverse Reactions. Continuous Assays and the Equilibrium Constant for the Reaction. [S. M. Aitken and J. F. Kirsch (2003) Biochemistry 42, 571-578]

How Does an Enzyme Evolved in vitro Compare to Naturally Occurring Homologs Possessing the Targeted Function? Tyrosine Aminotransferase from Aspartate Aminotransferase. [S. C. Rothman and J. F. Kirsch (2003) J. Mol. Biol. 327 593-608]

 

Last Updated 2006-08-18