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PDF Daniel A. Kraut, Kate S. Carroll, and Daniel Herschlag CHALLENGES IN ENZYME MECHANISM AND ENERGETICS Ann. Rev. Biochem. Vol 72, p517-571, 2003.
PDF Gustav E. Lienhard Enzymatic catalysis and transition state theory Science, Vol 180(4082), p149-154, 13 April 1973.
PDF Richard Wolfenden and Warren M. Kati. Testing the Limits of Protein-Ligand Binding Discrimination with Transition-State Analogue Inhibitors Accounts Chemical Research, Vol 24, p209-215, 1991.
PDF Andreas Matouschek, James T. Kellis Jr, Luis Serrano & Alan R. Fersht. Mapping the transition state and pathway of protein folding by protein engineering Nature, Vol 340, p122-126, July 13 1989.
Class Handout Eric Furfine. A Brief Outline of Organic Chemistry for Biochemists and Molecular Biologists Glaxo Wellcome Inc. May 1996
PDF Suzanne J. Admiraal, Benoit Schneider, Philippe Meyer, Joel Janin, Michel Veron, Dominique Deville-Bonne, and Daniel Herschlag. Nucleophilic Activation by Positioning in Phosphoryl Transfer Catalyzed by Nucleoside Diphosphate Kinase Biochemistry, Vol 38, p4701-4711, 1999.
PDF Jeremy R. Knowles and William P. Jencks. The Intrinsic PkA-Values of Functional Groups in Enzymes: Improper Deductions from the Ph-Dependence of Steady-State Parameters Critical Reviews in Biochemistry and Molecular Biology, Vol 4(2), p165-173, 1976.
PDF Q. Wang, D. Trimbur, R. Graham, R.A.J. Warren, and S.G. Withers. Identification of the Acid/Base Catalyst in Agrobacterium faecalis β-Glucosidase by Kinetic Analysis of Mutants Biochemistry, Vol 34(44), p14554-14562, 1995.
PDF Shu-ou Shan, Aiichiro Yoshida, Sengen Sun, Joseph A. Piccirilli, and Daniel Herschlag. Three metal ions at the active site of the Tetrahymena group I ribozyme PNAS Vol 96(22), p12299-12304, October 26 1999.
PDF Alan R. Fersht, Jian-Ping Shi, Jack Knill-Jones, Denise M. Lowe, Anthony J. Wilkinson, David M. Blow, Peter Brick, Paul Carter, Mary M. Y. Waye & Greg Winter Hydrogen Bonding and biological specificity analysed by protein engineering Nature, Vol 314(6008), p235-238, March 21 1985.
PDF Michael I. Page and William P. Jencks. Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect PNAS, Vol 68, p1678-1683, August 1971.
PDF Geeta J. Narlikar and Daniel Herschlag. Direct Demonstration of the Catalytic Role of Binding Interactions in an Enzymatic Reaction Biochemistry,Vol 37(28), p9902-9911, June 20 1998.
PDF Xin Zhang, et al. Sequential Checkpoints Govern Substrate Selection During Cotranslational Protein Targeting" Science 328(5979) p757-760, 2010
PDF Yuxin Zhai and Susan A. Martinis. Two Conserved Threonines Collaborate in the Escherichia coli Leucyl-tRNA Synthetase Amino Acid Editing Mechanism Biochemistry, 44(47), p15437-15443, 2005.
Page with link to PDF Patrick J O'Brien, Daniel Herschlag. Catalytic promiscuity and the evolution of new enzymatic activities Chemistry & Biology, Vol 6(4), pR91-R105, April 1999.
page with link to PDF D. Blangy, H. Buc and J. Monod. Kinetics of the allosteric interactions of phosphofructokinase from Escherichia coli Journal of Molecular Biology, Vol 31(1), p13-35, 14 January 1968.
PDF Jan Pieter Abrahams, Andrew G. W. Leslie, René Lutter & John E. Walker . Structure at 2.8 Å resolution of F1-ATPase from bovine heart mitochondria Nature, Vol 370(6491), p621-628, 25 August 1994.
PDF William J. Ray Jr.. Rate-limiting step: a quantitative definition. Application to steady-state enzymic systems Biochemistry,Vol 22(20), p4625-4637, September 1983.
PDF Antoon C. Brouwer and Jack F. Kirsch. Investigation of diffusion-limited rates of chymotrypsin reactions by viscosity variation Biochemistry,Vol 21(6), p1302-1307, March 1982.
PDF C.F. Midelfort and I.A. Rose. A stereochemical method for detection of ATP terminal phosphate transfer in enzymatic reactions. Glutamine synthetase. Journal of Biological Chemistry, Vol 251(19), p5881-5887, October 10 1976.
PDF W.W. Cleland. Partition analysis and concept of net rate constants as tools in enzyme kinetics Biochemistry, Vol 14(14), p3220-3224, 1975.
PDF Carol A. Fierke, Kenneth A. Johnson, Stephen J. Benkovic. Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli Biochemistry, Vol 26(13), p4085-4092, 1987.
PDF Smita S. Patel, Isaac Wong, Kenneth A. Johnson. Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant Biochemistry, Vol 30(2), p511-525, 1991.
PDF Jon R. Lorsch and Daniel Herschlag. Kinetic dissection of fundamental processes of eukaryotic translation initiation in vitro The EMBO Journal, Vol 18(23), p 6705-6717, 1999.
PDF Chirlmin Joo, Hamza Balci, Yuji Ishitsuka, Chittanon Buranachai, and Taekjip Ha. Advances in Single-Molecule Fluorescence Methods for Molecular Biology Ann. Rev. of Biochemistry, Vol 77, p51-76, 2008.
PDF Cecconi, C., Shank, E.A., Marqusee, S., and C. Bustamante. Studying protein folding with laser tweezers Proceedings of the International School Enrico Fermi, Società Italiana di Fisica: p145-160, October 2007.
PDF Andreas Engel and Hermann E. Gaub. Structure and Mechanics of Membrane Proteins Ann. Rev. of Biochemistry, Vol 82, p127-148, July 2008.
1. Enzyme mechanisms PDF Jonathan K. Lassila, David Baker, and Daniel Herschlag. Origins of catalysis by computationally designed retroaldolase enzymes. PNAS Vol 107(11), p4937-4942, March 16 2010.
2. Enzyme mechanisms PDF Charlotte M. Miton et al, Evolutionary repurposing of a sulfatase: A new Michaelis complex lead to efficient transition state charge offset PNAS 115(31), E7293-E7302 July 31 2018.
3. Allostery PDF D.Blangy, H.Buc, J.Monod. Kinetics of the allosteric interactions of phosphofructokinase from Echerichia coli JMB Volume 31, Issue 1, 14 January 1968, Pages 13-35
4. Steady-state and pre-steady-state kinetics PDF Isabel Strohkendl et al. Kinetic basis for DNA target specificity of CRISPR-Cas12a. Mol Cell 71(5), 816-824 September 6 2018)
5. Molecular machines, steady-state kinetics PDF Jon A. Kenniston, Tania A. Baker, Julio M. Fernandez, Robert T. Sauer Linkage between ATP consumption and mechanical unfolding during the protein processing reaction of an AAA+ degradation machine. Cell 114, 511-520 August 23 2003.
6. Single Molecule kinetics. PDF Marie-Eve Aubin-Tam, Adrian O. Olivares, Robert T.Sauer, Tania A.Baker, Matthew J.Lang. Single-Molecule protein unfolding and translocation by an ATP-fueled proteolytic machine Cell Volume 145(2), p257-267, 15 April 2011