This address only accepts messages from caltech.edu email accounts. To block spam all other messages are deleted without warning - do not send from your gmail account! If homework is turned in by email please send it directly to the appropriate TA, not to the common TA address.
This link will only accept connections from on campus machines.
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.
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.
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.
Reader William P. Jencks. BINDING-ENERGY, SPECIFICITY, AND ENZYMIC CATALYSIS - THE CIRCE EFFECT Advances In Enzymology And Related Areas Of Molecular Biology, Vol 43, p219-410,1975.
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 Lizbeth Hedstrom, Laszlo Szilagyi, and William J. Rutter . Converting trypsin to chymotrypsin: the role of surface loops Science, Vol 255(5049), p1249-1253, 6 March 1992.
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.
link to PDF Carol A. Fierke, Kenneth A. Johnson, Stephen J. Benkovic. Drobnak I., Braselmann E., Clark P.L. Multiple driving forces required for efficient secretion of autotransporter virulence proteins. J Biol Chem, Vol 290(16), p10104-10116, Apr 17 2015.
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.
page with link to PDF Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela Röthlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas III, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, and David Baker. De Novo Computational Design of Retro-Aldol Enzymes Science, Vol 319(5868), p1387-1391, 7 March 2008.
PDF Lars Giger, Sami Caner, Richard Obexer, Peter Kast, David Baker, Nenad Ban & Donald Hilvert Evolution of a designed retro-aldolase leads to complete active site remodeling Nature Chemical Biology, Vol 9(8), p494-498 | August 2015
PDF Hilvert, D. Design of Protein Catalysts Ann. Rev. of Biochemistry, Vol 82, p447-470, June 2013.