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
(2004).
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
(1996).
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
(1995).
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
(1995).
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
(1991).
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).
[Home] [The Boss] [Research] [Publications] [Links] [The Group] [For Students]
Departments of Molecular and Cell Biology and Chemistry University of California, Berkeley and Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley, California 94720 +1-510-642-6368 jfkirsch  uclink4.berkeley.edu |
copyright 1996 University of
California page maintained by Stacy Du created by Alan D. Miller  |