The University of Iowa

Amnon Kohen

Amnon Kohen
Professor
Phone: 
319-335-0234
Office: 
E274 CB
Biosketch: 
  • B.Sc., Hebrew University in Jerusalem, Israel (1989)
  • D.Sc., Technion - Israel Institute of Technology (1994)
  • Postdoctoral Research Associate, University of California at Berkeley (1995-1999)
Keywords: 

Bioorganic Chemistry; studying the mechanisms by which enzymes activate C-H and N2 bonds. Examination of protein structure, dynamics and function relationship. Pursuing medical and technological applications of biological catalysts.

Research Interests: 

We study enzymes that are important in many biological processes such as de novo DNA synthesis. Many antibiotic and chemotherapeutic drugs target these enzymes. We employ an interdisciplinary approach to study enzyme mechanisms using various techniques in chemistry and molecular biology. Our group has a broad research interest in various aspects of enzyme catalysis: (1) we develop experimental methods to investigate the role of protein motions and quantum mechanics in enzyme catalyzed reactions; (2) we study molecular mechanisms of the recently discovered enzymes as attractive targets for novel antibiotic drugs; (3) we develop clinical applications of enzyme mechanisms, such as development of new P.E.T. imaging probes based on in vivo enzyme activities.

In addition to common kinetic assays (e.g. UV-Vis spectroscopy, quench-flow experiments), we often use kinetic isotope effects (KIEs), structure and dynamics measurements (e.g. X-ray crystallography, NMR, 2D-IR measurements), and computer simulations to study enzymes. Students in the group will gain knowledge and hands-on experience in organic synthesis, molecular biology and protein purification, structural biology and drug design, enzyme assays and kinetics, isotope effect measurements, and theoretical calculations on enzyme catalysis.

Recent Publications: 

2013


A critical test of the "Tunneling and Coupled Motion" Concept in Enzymatic Alcohol Oxidation, Roston, D. and Kohen, A.,* J. Am. Chem. Soc. 2013 (Just Accepted)

Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis Klinman, J.P. and Kohen. A.,* Annu. Rev. Biochem., 2013, 82, 471-496

Isotope Effects As probe For Enzyme Catalyzed Hydrogen-Transfer Reactions, Roston, D., Islam, Z., and Kohen, A.,* Molecules, 2013, 18, 5543-5567

Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site, Wang, Z., Sapienza, P.J., Abeysinghe, T., Luzum, C., Lee, A.L., Finer-Moore, J.S., Stroud, R.M., and Kohen, A.,* J. Am. Chem. Soc.2013, 135, 7583-7592.

Relationship of Femtoseconds Dynamics to the Catalyzed Hydrogen Transfer, Cheatum, C.M.,* and Kohen, A,* Topics in Current Chemistry, Special issue on "Macromolecular Dynamics in Biological Catalysis", Eds, Hammes-Schiffer, S. & Klinman, J.P., Pub: Elsevier, 2013, pp 1-13.

QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase, Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A.,*  Biochemistry 2013, 52, 2348-2358 


2012


A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase, Wang, Z., Abeysinghe, T., Finer-Moore, J.S., Stroud, R.M., and Kohen, A.,* J. Am. Chem. Soc., 2012134, 17722-17730   

Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface, Vardi-Kilshtain, A., Major, D.T.,* Kohen, A., Engel, H., and Doron, D., J. Chem. Theory Comput., 2012, 8, 4786–4796

Folate binding site of flavin-dependent thymidylate synthase, Koehn, E.M., Perissinotti, L.L., Moghram, S., Prabhakar, A., Lesley, S.A., Mathews, I.I.,* and Kohen, A.,* Proc. Nat. Acad. Sci. USA, 2012, 109, 15722-15727.

Synthesis of radiolabeled nicotinamide cofactors from labeled pyridines: versatile probes for enzyme kinetics, Sen, A., Stojković, V., and Kohen, A.* Anal. Biochem., 2012, 430, 123-129

Hydrogen Donor-Acceptor Fluctuations from Kinetic Isotope Effects: A Phenomenological Model, Roston, D., Cheatum, C.M., and Kohen, A.,* Biochemistry, 2012, 51, 6860-6870

A Model Reaction Assesses Contribution of H-Tunneling and Coupled Motions to Enzyme Catalysis, Liu, Q., Zhao, Y., Hammann, B., Eilers, J., Lu, Y.,* and Kohen, A.,* J. Org. Chem., 2012, 77, 6825-6833.

Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase, Engel, H., Doron, D. Kohen, A., and Major, D.T.,* J. Chem. Theory Comput., 2012, 8, 1223-1234.

Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase, Doron, D., Kohen, A., and Major, D.T.,* J. Chem. Theory Comput., 2012, 8, 2484-2496

Enzyme Dynamics: Consensus and Controversy, Kohen, A., J. Biocatal. Biotransformation 2012, 1:1, doi: 10.4172/jbcbt.1000e103 (Editorial).

Experimental and theoretical studies of enzyme-catalyzed hydrogen transfer reactions, Wang, Z., Roston, D., and Kohen, A.,* in Structural and Mechanistic Enzymology: Bringing together Experiments and Computing, Vol. Eds. Christov, C.Z. and Karabencheva, T., in series entitled Advances in Protein Cheistry and Structural Biology, Ed. Donev, R., Burlington, Academic Press, Elsevier Inc., Vol. 87, pp. 155-180, 2012.  ISBN: 978-0-12-398312-1

Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase (FDTS),Mishanina, T.V., Koehn, E.M., Conrad, J.A., Palfey, B., Lesley, S.A., and Kohen, A.*, J. Am. Chem. Soc., 2012, 134, 4442-4448

Effects of the donor acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction, Stojkoviç, V., Perissinotti, L., Willmer, D., Benkovic, S., and Kohen, A.,* J. Am. Chem. Soc., 2012, 134, 1738-1745

A fast chemo-enzymatic synthesis of [11C]-N5,N10-methylenetetrahydrofolate as a potential PET tracer for proliferating cells, Saeed, M., Tewson, T.J., Erdahl, C.E., and Kohen, A.,* Nucl. Med. Biol., 2012, 39, 697-701

3-Picolyl Azide Adenine Dinucleotide as a Probe of Femtosecond to Picosecond Enzyme Dynamics, Dutta, S., Li, Y-L., Rock, W., Houtman, J.C., Kohen, A., and Cheatum, C.M.,* J. Phys. Chem. B., 2012, 116, 542-548.

Mechanisms and inhibition of uracil methylating enzymes, Mishanina, T.V., Koehn, E., and Kohen, A.,* Bioorg. Chem. 2012, 43, 37–43


2011


Comparative Hydrogen-Deuterium Exchange for a Mesophilic vs Thermophilic Dihydrofolate Reductase at 25 °C: Identification of a Single Active Site Region with Enhanced Flexibility in the Mesophilic Protein, Oyeyemi, O.A., Sours, K.M., Lee, T., Kohen, A., Resing, K.A., Ahn, N.G., and Klinman, J.P.,* Biochemistry, 2011, 50, 8251-8260

Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface, Doron, D., Major, D.T.,* Kohen, A., Thiel, W., and Wu, X., J. Chem. Theory Comput., 2011, 7, 3420–3437

Self-assembled enzymatic monolayer directly bound to a gold surface: Activity and molecular recognition force spectroscopy studies, Ditzler, L., Sen, A., Gannon, M., Kohen, A.,* and Tivanski, A.,* J. Am. Chem. Soc. (Communication), 2011,133, 13284-13287.

A novel positron emission tomography tracer distinguishes normal from cancerous cells, Saeed, M., Sheff, D, and Kohen, A.*, J. Biol. Chem., 2011, 286, 33872-33878.

Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water, Dutta, S., Rock, W., Cook, R. J. Kohen, A., and Cheatum C. M.*, J. Chem. Phys., 2011, 135, 055106. (Published on line Aug 5, 2011)

Triple isotopic labeling and kinetic isotope effects: a sensitive and accurate method for exposing H-transfer steps in enzymatic systems, Sen, A., Yahasiri, A., and Kohen, A.*, Biochemistry, 2011, 50, 6462–6468.

Temperature Dependence of the Kinetic Isotope Effects in Thymidylate Synthase, A Theoretical Study, Kanaan, N., Ferrer, S., Martí, S, Garcia-Viloca, M., and Kohen, A., and Moliner, V.*, J. Am. Chem. Soc., 2011, 133, 6692-6702.

Kinetic Isotope Effect in Enzymology, Kohen, A.,* Roston, D., Stojkovic, V., and Wang, Z, in Encyclopedia of Anlytical Chemistry, R. A. Meyers, Ed.; John Wiley & Sons, Ltd: Chichester, UK, 2011; Vol. S1-S3, pp 77-99, ISBN: (978-0-470-97333-2).


2010


The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer, Stojkovic, V., Perissinotti, L.L., Lee, J., Benkovic, S.J., and Kohen, A.*, Chem. Commun., 2010, 46, 8974-8976 (Communication).

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase, Bandaria, J.N., Dutta, S., Nydegger, M.W., Rock, W., Kohen, A., and Cheatum, C.M.*, Proc. Natl. Acad. Sci. USA 2010, 107, 17974-17979

Characterization of azo-NAD to assess its potential as a two-dimensional infrared probe of enzyme dynamics, Dutta, S., Cook, R.J., Houtman, J.C.D., Kohen, A.*, and Cheatum, C.M.*, Anal. Biochem., 2010, 407, 241-246.

Enzymatic tunneling and kinetic isotope effects: chemistry at the crossroads, Sen, A., and Kohen, A.*, J. Phys. Org. Chem. 2010, 23, 613-619 (invited review for a special issue entitled "Symposium in Print on Tunneling")

Thymidylate Synthase Catalyzed H-transfers: Two Chapters in One Tale, Wang, Z. and Kohen, A.*, J. Am. Chem. Soc. 2010, 132, 9820-9825.

Elusive Transition State of Alcohol Dehydrogenase Unveiled , Roston, D. and Kohen, A.*, Proc. Natl. Acad. Sci. USA 2010, 107, 9572-9577

Flavin-dependent thymidylate synthase: A novel pathway towards thymine, Koehn, E.M. and Kohen, A.*, Arch Biochem Biophys. 2010, 493, 96-102.