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     Capitani, G., Tschopp, M.,. Eliot, A. C., Kirsch, J. F., and Grütter, M. G.: 
     Structure of ACC synthase Inactivated by the Mechanism-based Inhibitor L-vinylglycine. 
     FEBS Lett. 579, 2458-2462 (2005).

     Sivaraman, S. and Kirsch, J. F.: 
     The narrow substrate specificity of human tyrosineaminotransferase - 
     the enzyme deficient in tyrosinemia type II. 
     FEBS Journal. 273, 1920-1929 (2006).

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

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

     Chow, M. A., McElroy, K. E., Corbett, K. D., Berger, J. M., and Kirsch, J.F.:
     Narrowing substrate specificity in a directly evolved enzyme: The A293D mutant of aspartate aminotransferase.
     Biochemistry 43, 12780-12787 (2004).

     McCarter, J. D., Stephens, D, Shoemaker, K. Rosenberg, S., Kirsch, J. F., and Georgiou, G.: 
     Substrate Specificity of the E. coli Outer Membrane Protease OmpT.J. Bact.186, 5919-5925 (2004).

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

     Eliot, A. C. and Kirsch, J. F.: Pyridoxal Phosphate Enzymes: Mechanistic, Structural and 
     Evolutionary Considerations.  Ann. Revs. Biochem. 73, 383-415 (2004).
     Sandmark, J., Eliot, A. C., Famm H. J. K., Schneider, G., and Kirsch, J. F.: Conserved 
     and Non-conserved Residues in the Substrate Binding Site of 7,8-Diaminopelargonic 
     Acid Synthase from Escherichia coli are Essential for Catalysis. Biochemistry 43, 
     1213-1222 (2004). 

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

     Ko, SH., Eliot, A. C., and Kirsch, J. F.: S-Methylmethionine is Both a Substrate and an
     Inactivator of 1-Aminocyclopropane-1-carboxylate Synthase. Arch. Biochem. Biophys. 421 85-90

     Aitken, S. M., Kim, D. H., and Kirsch, J. F.: E. coli Cystathionine g-Synthase does not 
     Obey Ping-Pong Kinetics. Novel Continuous Assays for the Elimination and Substitution 
     Reactions. Biochemistry 42 11297-11306 (2003). 

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

     Capitani, G., Eliot, A. C., Gut, H., Khomutov, R. M., Kirsch, J. F., and Grütter, M. G.: 
     Structure of 1-Aminocyclopropane-1-Carboxylate Synthase in Complex with an Amino-Oxy 
     Analogue of the Substrate: Implications for Substrate Binding. Biochim. Biophys. Acta 1647, 
     55-60 (2003). 

     Rothman, S. C. and Kirsch, J. F.: How Does an Enzyme Evolved in vitro Compare to Naturally 
     Occurring Homologs Possessing the Targeted Function? Tyrosine Aminotransferase from Aspartate 
     Aminotransferase. Journal of Molecular Biology., 327 593-608 (2003). 

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

     Eliot, A. E., Sandmark, J., Schneider, G., and Kirsch, J.F.: The Dual-Specific Active of 
     7,8-Diaminopelargonic-Acid Synthase and the Effect of the R391A Mutation. Biochemistry, 
     41, 12582-12589 (2002). 

     Shaffer, W. A. Luong, T. N., Rothman, S. C. and Kirsch, J. F.: Quantitative Chimeric Analysis of 
     Six Specificity Determinants that Differentiate E. coli Aspartate from Tyrosine Aminotransferase. 
     Protein Science, 11, 2848-2859 (2002). 

     Capitani, G., McCarthy, D. L., Gut, H., Grütter, M. G., and Kirsch, J. F.: Apple ACC Synthase in 
     Complex with the Inhibitor L-aminoethoxyvinylglycine: Evidence for a Ketimine Intermediate. 
     J. Biol. Chem., 277, 49735-49742 (2002). 

     Pons, J., Stratton, J.R. and Kirsch, J.F.: How Do Two Unrelated Antibodies, 
     Hyhel-10 and F9.13.7 Recognize the Same Epitope of Hen Egg-White
     Lysozyme?  Protein Science, 11, 2308-2315 (2002).

     Eliot, A. C., and Kirsch, J. F.:  Modulation of the Internal Aldimine pKa's of
     of 1-Aminocyclopropane-1-carboxylate Synthase and Aspartate Aminotransferase
     by Specific Active Site Residues.
     Biochemistry, 41, 3836-3842 (2002).

     Deu, E., Koch, K. A., and Kirsch, J. F.:  The Role of the Conserved Intersubunit
     Salt Bridge, Lys68*:Glu265 in Aspartate Aminotransferase Kinetics.  Multiple 
     Forced Covariant Amino Acid Substitutions in Natural Variants.
     Protein Science, 11, 1062-1073 (2002).

     McCarthy, D. L., Capitani, G., Feng, L., Gruetter, M. G. and Kirsch, J. F.:
     Glutamate 47 in 1-Aminocyclopropane-1-carboxylate Synthase is a Major 
     Specificity Determinant. 
     Biochemistry, 40, 12276-12284 (2001).

     Stratton, J. R., Pelton, J. G., and Kirsch, J. F.:  The Low Barrier Hydrogen 
     Bond in Subtilisin Contributes Less than 2.2 kcal/mol to kcat/Km.  
     Biochemistry, 40, 10411-10416 (2001).

     Koch, K.A., Capitani, G., Grueter, M. G., and Kirsch, J. F.: The Human cDNA for 
     a homologue of the plant enzyme 1-aminocyclopropane-1-carboxylate sythase 
     encodes a protein lacking that activity.  
     Gene, 272, 75-84 (2001).

     Luong, T. N., and Kirsch, J. F.: A general method for the quantitative analysis
     of functional chimeras: Applications from site-directed mutagenesis and 
     macromolecular association.
     Protein Science, 10, 581-591(2001)

     Feng, L., Geck, M. K., Eliot, A. C., and Kirsch, J. F.: Aminotransferase Activity
     and Bioinformatic Analysis of 1-Aminocyclopropane-1-carboxylate Synthase.
     Biochemistry (2000)

     Rajpal A., Kirsch, J. F.: Role of the minor energetic determinants of chicken egg 
     white lysozyme(HEWL) to the stability of the HEWL.antibody scFv-10 complex.
     Proteins, 40, 49-57(2000).

     Feng L., Kirsch, J. F.: L-Vinylglycine is an alternative substrate as well as a 
     mechanism-based inhibitor of 1-aminocyclopropane-1-carboxylate synthase.
     Biochemistry, 39, 2436-44 (2000) 
     Capitani, G., Hohenester, E., Feng, L., Storici, P., Kirsch, J. F., and 
     Jansonius, J. N.: Structure of 1-Aminocyclopropane-1-carboxylate Synthase,
     a Key Enzyme in the Biosynthesis of the Plant Hormone Ethylene. Journal of
     Molecular Biology, 294, 743-756 (1999).
     Geck, M. K., and Kirsch, J. F.: A novel, definitive test for substrate
     channeling illustrated with the aspartate aminotransferase/malate 
     dehydrogenase system. Biochemistry, 22, 8032-7 (1999).
     Pons, J., Rajpal, A., and Kirsch, J. F.: Energetic analysis of an 
     antigen/antibody interface: alanine scanning mutagenesis and double
     mutant cycles on the  HyHEL-10/lysozyme interaction. Protein Science, 8,
     958-968 (1999).

     Feng, L., Li, Y., and Kirsch, J. F.: Genetic Engineering Approaches to 
     Enzyme Design and Mechanism. Journal of Physical Organic Chemistry, 11,
     536-539 (1998).     

     Taylor, M. G., Rajpal, A., and Kirsch, J. F.: Kinetic Epitope Mapping
     of the Chicken Lysozyme HyHel-10 Fab Complex: Delineation of Docking
     Trajectories. Protein Science, 7, 1857-1867 (1998).

     Rajpal, A, Taylor, M. G., and Kirsch, J. F. : Quantitative Evaluation of
     the Chicken Lysozyme Epitope in the HyHel-10 Fab Complex: Free Energies 
     and Kinetics. Protein Science, 7, 1868-1874 (1998).
     Li Y., Feng L., and Kirsch, J.F.:Kinetic and spectroscopic investigations 
     of wild-type and mutant forms of apple 1-aminocyclopropane-1-carboxylate
     synthase. Biochemistry, 36, 15477-15488 (1997). 

     Luong T., and Kirsch J.F.: A continuous coupled spectrophometric
     assay for tyrosine aminotransferase activity with aromatic and other
     nonpolar amino acids. Analytical Biochemistry, 253, 46-49 (1997). 
     Park Y., Luo J., Schultz P.G., and Kirsch J.F.: Noncoded amino acid
     replacement probes of the aspartate aminotransferase mechanism.
     Biochemistry, 36, 10517-10525 (1997).

     Ramjee M.K., Petithory J.R., McElver J., Weber S.C., and Kirsch J.F.: 
     A novel yeast expression/secretion system for the recombinant plant 
     thiol endoprotease propapain. Protein Engineering, 9,1055-1061 (1996) 

     Wolf, A.,  Lee,  K. C.,  Kirsch,  J. F.,  and  Ames,  G. F. : 
     Ligand-dependent conformational plasticity of the periplasmic 
     histidine-binding protein HisJ.  Involvement in transport specificity. 
     Journal Of Biological Chemistry,  271, 21243-21250 (1996).

     Goldberg, J. M. and Kirsch, J. F.: The Reaction Catalyzed by
     Escherichia coli  Aspartate Aminotransferase has Multiple Partially
     Rate-Determining Steps, While that Catalyzed by the Y225F Mutant is
     Dominated by Ketimine Hydrolysis. Biochemistry, 35,  5280-5291 (1996).

     Matsumura, I and Kirsch, J. F.: Synergistic Contributions of
     Asparagine 46 and Aspartate 52 to the Catalytic Mechanism of
     Chicken Egg White Lysozyme. Biochemistry, 35, 1890-1896 (1996).

     Matsumura, I and Kirsch, J. F.: Is Aspartate 52 Essential for
     Catalysis by Chicken Egg White Lysozyme?  The Role of Natural
     Substrate-Assisted Hydrolysis. Biochemistry, 35, 1881-1890 (1996).

     Gloss, L. M., Spencer, D. E. and Kirsch, J. F.: Cysteine-191 in
     Aspartate Aminotransferases Appears to be Conserved Due to the Lack
     of a Neutral Mutation Pathway to the Functional Equivalent,
     Alanine-191.  Proteins: Structure, Function and Genetics, 24, 195-208  
     Shih, P., and Kirsch, J. F.: Design and Structural Analysis of an
     Engineered Thermostable Chicken Lysozyme. Protein Science, 14,
     2063-2072 (1995).

     Shih, P., Holland, D. R. and Kirsch, J. F.: Thermal Stability
     Determinants of Chicken Egg-White Lysozyme Core Mutants:
     Hydrophobicity, Packing Volume, and Conserved Buried Water
     Molecules. Protein Science, 14, 2052-2062 (1995).

     Onuffer, J. J. and Kirsch, J. F.: Redesign of the Substrate
     Specificity of Escherichia coli Aspartate Aminotransferase to that 
     of Escherichia coli Tyrosine Aminotransferase by Homology Modeling 
     and Site-directed Mutagenesis. Protein Science 4, 1750-1757 

     Onuffer, J. J., Ton, B. T., Klement, I., and Kirsch, J. F.: The 
     Use of Natural and Unnatural Amino Acid Substrates to Define the 
     Substrate Specificity Differences of Escherichia coli Aspartate 
     and Tyrosine Aminotransferases. Protein Science 4, 1743-1749 

     Gloss, L. M. and Kirsch, J. F.: Examining the Structural and 
     Chemical Flexibility of the Active site Base, Lys-258, of 
     Escherichia coli Aspartate Aminotransferase by Replacement with 
     Unnatural Amino Acid Biochemistry 34, 12323-12332 (1995).

     Malashkevich, V. N., Onuffer, J. J., Kirsch, J. F., and Jansonius, 
     J. N.: Alternating, Arginine-modulated Substrate Specificity in an 
     Engineered Tyrosine Aminotransferase Nature Struct. Biol. 2, 548-
     553 (1995).

     Furumo, N.C. and Kirsch, J. F.: Accumulation of the Quinonoid 
     Intermediate in the Reaction Catalyzed by Aspartate 
     Aminotransferase with Cysteine Sulfinic Acid. Arch. Biochem. 
     Biophys. 319, 49-54 (1995).

     Apicella, C. A. and Kirsch, J. F. : Site Directed Mutagenesis and 
     Chemical Modification of Asp 222 of Aspartate Aminotransferase. 
     Abst. 1295, ASBMB meeting San Francisco.(1995).

     Gloss, L. M. and Kirsch, J. F.: Probing the Roles of the Active 
     Site Base, Lys-258, of E. coli Aspartate Aminotransferase by 
     Replacement with Unnatural Amino Acids.  Abst. 1292, ASBMB meeting 
     San Francisco.(1995).

     Gloss, L. M. and Kirsch, J.F.: Use of Site-directed
     Mutagenesis and Alternative Substrates to Assign the Prototropic
     Groups Important to Catalysis by Escherichia coli Aspartate
     Aminotransferase. Biochemistry 34, 3999-4007 (1995).

     Gloss, L. M. and Kirsch, J.F.: Decreasing the Basicity of the 
     Active Site Base, Lys-258, of Escherichia coli Aspartate 
     Aminotransferase by Replacement with g-thia-Lysine. Biochemistry 
     34,3990-3998 (1995).

     White, M. F., Vasquez, J., Yang, S-F., and Kirsch, J. F.: 
     Expression of Apple 1-aminocyclopropane-1-carboxylate Synthase in 
     E. coli: Kinetic Characterization of Wild-type and Active-site 
     Mutant Forms. Proc. Natl. Acad. Sci USA. 91, 12428-12432 (1994).

     Kirsch, J. F. and Onuffer, J. J.: Redesign of Aspartate 
     Aminotransferase Specificity to that of Tyrosine Aminotransferase. 
     in Biochemistry of Vitamin B6 and PQQ. Eds. F. Bossa, G. Marino 
     and G. Sannia. BirkhSuser. (1994). pp. 37-41.

     Hohenester, E., White, M. F., Kirsch, J. F., and Jansonius, J. N.: 
     Crystallization and Preliminary X-ray Analysis of Recombinant 1-
     Aminocyclopropane-1-carboxylate Synthase from Apple, a Key Enzyme 
     in the Biosynthesis of the Plant Hormone Ethylene. J. Mol. Biol. 
     243, 947-949 (1994).

     Onuffer, J. J. and Kirsch, J. F.: Characterization of the Apparent 
     Negative Cooperativity Induced in Escherichia coli Aspartate 
     Aminotransferase by the Replacement of Aspartate 222 with Alanine. 
     Evidence for an Extremely Slow Conformational Change. Protein 
     Engineering 7, 413-424 (1994).

     Shih, P., Malcolm, B. A., Rosenberg, S., Kirsch, J. F., and 
     Wilson, A. C.: Reconstruction and Testing of Ancestral Lysozymes. 
     Methods in Enzymology 224, 576-589 (1993).

     Kam-Morgan, L. N. W., Lavoie, T. B., Smith-Gill, S. J., and 
     Kirsch, J. F.: Site-Directed Mutagenesis as a Tool in the Analysis 
     of Protein-Protein Interactions. Methods in Enzymology 224, 503-
     516 (1993).

     Deng, H., Goldberg, J. M., Kirsch, J. F., and Callender, R.: 
     Elucidation of the Solution Structure of the Escherichia Coli a-
     Methyl-L-Aspartate Aminotransferase Complex by Isotope Edited 
     Classical Raman Difference Spectroscopy. J. Amer. Chem. Soc. 115, 
     8869-8870 (1993).

     Goldberg, J. M., Zheng, J., Deng, H., Chen, Y. Q., Callender, R., 
     and Kirsch, J. F.: The Structure of the Complex Between Pyridoxal 
     5'-Phosphate and the Tyrosine-225 to Phenylalanine Mutant of 
     Escherichia Coli Aspartate Aminotransferase Determined by Isotope 
     Edited Classical Raman Difference Spectroscopy. Biochemistry 
     32,8092-8097 (1993).

     Kam-Morgan, L N. W, Smith-Gill, S. J, Taylor, M.G., Zhang, L, 
     Wilson, A. C., and Kirsch, J. F.: High Resolution Mapping of the 
     HyHEL-10 Epitope of Hen Lysozyme by Site-Directed Mutagenesis. 
     Proc. Natl. Acad. Sci. USA. 90, 3958-3962 (1993).

     Toney, M. D. and  Kirsch, J. F.: Lysine 258 in Aspartate     
     Aminotransferase Enforcer of the Circe Effect for Amino Acid 
     Substrates and the General Base Catalyst for the 1,3-Prototropic 
     Shift. Biochemistry 32, 1471-1479 (1993).

     P.W.W. White and J.F. Kirsch: Sequential Site-directed 
     Mutagenesis and Chemical Modification to Convert the Active Site 
     Arginine 292 of Aspartate Aminotransferase to Homoarginine. J. 
     Amer. Chem. Soc. 114, 3567-3568 (1992).

     L.M. Gloss, A. Planas, and J. F. Kirsch: The Contribution to 
     Catalysis and Stability of the Five Cysteines in E. coli 
     Aspartate Aminotransferase; Preparation and Properties of a 
     Cysteine-Free Enzyme. Biochemistry 31, 32-39 (1992).

     J.R. Petithory, F.R. Masiarz, J.F. Kirsch, D.V. Santi, and B.A. 
     Malcolm: A Rapid Method for the Determination of Endoproteinase 
     Specificity: Specificity of the 3C Proteinase from Hepatitus-A 
     Virus. Proc. Natl. Acad. Sci. USA 88, 11510-11514 (1991).

     J.M. Goldberg, R.V. Swanson, H.S. Goodman, and J.F. Kirsch: The 
     Tyr 225 Phe Mutation of Escherichia coli Aspartate 
     Aminotransferase Results in an Alkaline Transition in the 
     Spectrophotometric and Kinetic pKa Values and Reduced Values of 
     Both kcat and Km. Biochemistry 30, 305-312 (1991).

     A. Planas and J.F. Kirsch: Re-Engineering the Catalytic Lysine 
     of Aspartate Aminotransferase by Chemical Elaboration of a 
     Genetically Introduced Cysteine. Biochemistry 30, 8268-8276 

     B.A. Malcolm, K.P. Wilson, B.W. Matthews, J.F. Kirsch, and A.C. 
     Wilson: Hydrocarbon, Packing, Thermostability, and X-ray 
     Structures of Ancestral Lysozymes. Nature 345, 86-89 (1990).

     M.D. Toney and J.F. Kirsch: Direct Bronsted Analysis of the 
     Restoration of Activity to a Mutant Enzyme by Exogenous Amines.  
     Science 243, 1485-1488 (1989).

     B.A. Malcolm, S. Rosenberg, M.J. Corey, J.S. Allen, A. 
     deBaetselier, and J.F. Kirsch: Site-Directed Mutagenesis of the 
     Catalytic Residues Asp-52 and Glu-35 of Chicken Egg-White 
     Lysozyme," Proc. Natl. Acad. Sci. USA 86, 133-137 (1989).

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Departments of Molecular and Cell Biology and Chemistry
University of California, Berkeley
and Materials Sciences Division
Lawrence Berkeley National Laboratory
Berkeley, California 94720
jfkirsch uclink4.berkeley.edu
copyright 1996 University of California
page maintained by Stacy Du
created by Alan D. Miller