Understanding the chemical perspectives of enzymes and their medical applications

Publications


 

2018

135. Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools, Kholodar, S. A., Ghosh, A. K., Świderek, K., Moliner, V., & Kohen, A.,*  PNAS, 2018, 201811059.

134. Experimental and computational studies delineate the role for asparagine 177 in hydride transfer for E. coli thymidylate synthase, Gurevic, I., Islam, Z., Świderek, K., Trepka, K., Ghosh, A. K., Moliner, V., & Kohen, A.,* ACS Catalysis.

133. Effect of Asp122 Mutation on the Hydride Transfer in E. coli DHFR Demonstrates the Goldilocks of Enzyme Flexibility, Mhashal, A. R., Pshetitsky, Y., Eitan, R., Cheatum, C. M., Kohen, A., & Major, D. T., The Journal of Physical Chemistry B, 2018, 122, 8006-8017.

132. Chemo-enzymatic synthesis of the exocyclic olefin isomer of thymidine monophosphate,Mondal, D., Koehn, E. M., Yao, J., Wiemer, D. F., & Kohen, A.,*  Bioorganic & medicinal chemistry, 2018, 26, 2365-2371.

131. Bacterial versus human thymidylate synthase: Kinetics and functionality, Islam, Z., Gurevic, I., Strutzenberg, T.S, Ghosh, A.K., Iqbal, T., Kohen, A.,*  PloS one2018, 13.5, e0196506.

2017

130. Protein Mass Effects on Formate Dehydrogenase, Ranasinghe, C., Guo, Q., Sapienze, P.J., Lee, A.L., Quinn, D.M., Cheatum, C.M., Kohen, A.,*  J. Am. Chem. Soc.2017, 139, 17405-17413.

129. Flavin-dependent Thymidylate Synthase: N5 of Flavin as a Methyene Carrier, Karunaratne, K., Luedtke, N., Quinn, D.M., Kohen, A.,* Arch. Biochem. Biophys., 2017, 632, 11-19.

128. The Role of the M20 Loop in the Hydride Transfer in E. Coli Dihydrofolate Reductase, Mhashal, A., Vardi-Kilshtain, A., Kohen, A. Major, D.,* J. Biol. Chem., 2017, M117, 777136.

127. Measurement of Enzyme Isotope Effects, Kholodar, S., Ghosh, A., Kohen, A.,*  Methods in Enzymology, 2017, 596, 43-48.

126. Chemoenzymatic Synthesis of Ubiquitous Biological Redox Cofactors, Singh, P., Guo, Q., Kohen, A.,*  SYNLETT2017, 28(10), 1151-1159.

125. Benchmarking QM/MM Methods on the Thymidylate Synthase Catalyzed Hydride Transfer, Świderek, K., Arafet, K., Kohen, A., Moliner, V.,*  J. Chem. Theory Comput.201713, 1375–1388.

2016

124. The enigmatic conservation of enzyme dynamics in evolution, Kohen, A., Perspectives in Science, Accepted for Publication, Sept. 14, 2016. A STRENDA and Beilstein book, Eds. Cornish-Bowden, A., and Cattenr, C., Pub. Elsevir, Perspectives in Science, 2016, 9, 60-66.

123. Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations, Pshetitsky, Y., Eitan, R., Verner, G., Kohen, A., Major, D.,* J. Chem. Theory Comput., 2016, 12, 5179-5189.

122. Examinations of the Chemical Steps in Enzyme Catalysis, Singh, P., Islam, Z., Kohen, A.,* Methods in Enzymology, Chapter 11, Ed. Voth, G.A., Pub. Elsevier, Cambridge, MA, ISBN: 978-0-12-805347-8, 2016, 577, 287-318.

121. Preserved Hydride Transfer Mechanism in Evolutionary Divergent Thymidylate Synthases, Abeysinghe, T., Hong, B., Wang, Z., Kohen, A.,* Current Topics in Biochem. Res., 2016. 17, 19-30,

120. Noncovalent Intermediate of Thymidylate Synthase: Fact or Fiction?, Kholodar, S., Kohen, A.,* J. Am. Chem. Soc.2016,138, 8056-8059. (Communication)

119. Oscillatory Enzyme Dynamics Revealed by Two-Dimensional Infrared Spectroscopy, Pagano, P., Guo, Q., Kohen, A., Cheatum, C.M,* J. Phys. Chem. Lett.2016, 7, 2507-2511.

118. Flavin dependent thymidylate synthase as a new antibiotic target, Choi, M.A., Karunaratne, K., Kohen, A.,* Molecules, 2016, 21, 654-664. 

117. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii, Guo, Q., Gakhar., L., Wickersham., K., Francis, K., Vardi-Kilshtain., A., Major, T.D., Cheatum, C.M., Kohen, A.,* Biochemistry, 2016, 55, 2760-2771.

116. The Effect of the Protein Mass Modulation on Human Dihydrofolate Reductase, Francis, K., Sapienza, P.J., Lee, A.L., Kohen, A.,* Biochemistry2016, 33, 1100-1106.

115. An Unprecedented Mechanism of Nucleotide Methylation in Organisms Containing ThyX, Mishanina, T.V., Yu, L., Karunaratne, K., Mondal, D., Corcoran, J.M., Choi, M.A., Kohen, A.,*Science, 2016, 351, 507-510.

114. Dihydrofolate Reductase as a Model for Enzyme Catalysis, Francis,K., Kohen, A.,* Current Biotech., 2016, 4, 77-86.

2015

113. Dihydrofolate Reductase as a Model for Studies of Enzyme Dynamics and Catalysis, Kohen, A.,* F1000Research, 2015, 4 (F1000 Faculty Rev):1464. (Invited Review).

112. Activation of Two Sequential H-Transfers in the Thymidylate Synthase Catalyzed Reaction, Islam, Z., Strutzenberg, S.T., Ghosh, K.A.and Kohen, A.,* ACS Cat., 2015, 5, 6061-6068.

111. Synthesis and application of isotopically labeled flavin nucleotides, Mishanina, T., Kohen, A.,* J. Labeled Comp. Radiopharma., 2015, 58, 370–375.

110. The General Base in the Thymidylate Synthase Catalyzed Proton Abstraction, Ghosh, A.K., Islam, Z., Kruger, J.D., Abeysinghe, D. T., Kohen, A.,* Phys. Chem. Chem. Phys., 2015, 17, 30867-30875.

109. Network of remote and local protein dynamics in dihydrofolate reductase catalysis, Singh, P., Francis, K., and Kohen, A.,* ACS Cat., 2015, 5, 3067–3073.

108. A calibration curve for immobilized dihydrofolate reductase activity assay, Singh, P., Morris, H., Tivanski, A.V., Kohen, A.,* Data in Brief, 2015, 4, 19-21.

107. Line Shape Analysis of Two-dimensional Infrared Spectra, Guo, Q., Pagano, P., Li, Y., Kohen, A., Cheatum, C.M.,* J. Chem. Phys., 2015, 142, 212427.

106.  Influence of Active Site Conformations on the Hydride Transfer step of the Thymidylate Synthase Reaction Mechanism, Świderek, K., Kohen, A., Moliner, V.,* Phys. Chem. Chem. Phys., 2015, 17, 30793—30804.

105. Role of Long-Range dynamics in Different Thymidylate Synthase Catalyzed Reactions, Abeysinghe, T., and Kohen, A., Int. J. Mol. Sci. 2015, 16, 7304-7319.

104. Determination of concentration and activity of immobilized enzymes, Singh, P., Morris, H., Tivanski, A.V., and Kohen, A.,* Anal., Biochem. 2015, 484, 169­172.

103. Role of Dynamics in Enzyme Catalysis: Substantial vs. Semantic Controversies, Kohen, A.,* Acc. Chem. Res.,  2015, 48, 466-473.

102. Targeting the de novo Biosynthesis of Thymidylate for the Development of PET Probe for Pancreatic Cancer Imaging, Nilaweera, T., Saeed, M. and Kohen, A.* Biochemistry, 2015, 54, 1287–1293.

101. Linking Protein Motion to Enzyme Catalysis, Singh, P., Abeysinghe, T., Kohen, A.,* Molecules, 2015, 20, 1192-1209.

100. Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase, Doron, D., Stojković, V., Gakhar, L., Kohen, A., Major,D.,*   J. Phys. Chem. B., 2015, 119, 906–916.


2014


99. The Escherichia coli Dihydrofolate Reductase Catalyzed Proton and Hydride Transfers: Order and the Roles of Asp27 and Tyr100, Liu, C.T., Francis, K., Layfield , J., Huang, X., Hammes-Schiffer, S., Kohen, A.,* Benkovic, S.J.,*  Proc. Nat., Acad. Sci. USA, 2014, 111, 18231–18236.

98. Evoluntionalry Aspects of Enzyme Dynnamics, Klinman, J.P.* and Kohen. A.,* J. Biol. chem.2014, 289, 30205-30212.

97. Substrate Activation in Flavin-Dependent Thymidylate Synthase, Mishanina, T.V, Corcoran, J.M. and Kohen, A.,* J. Am. Chem. Soc. 2014, 136, 10597–10600.

96. Concerted versus Step-Wise Mechanism in Thymidylate Synthase, Islam, Z., Strutzenberg, S.T., Gurevic, I. and Kohen, A.,* J. Am. Chem. Soc. 2014,136, 9850-9853.

95. Protein Mass-modulated Effects in the Catalytic Mechanism of Dihydrofolate Reductase: Beyond Promoting Vibrations, Wang, Z., Singh, P., Czekster, M.C., Kohen, A.,* and Schramm, V.L. J. Am. Chem. Soc. 2014, 136, 8333-8341

94. Standards for the Reporting of Kinetic Isotope Effects in Enzymology, Francis, K. and Kohen, A.,* Perspectives in Science. 2014, 1, 110–120.

93. Simulations of Remote Mutants of Dihydrofolate Reductase Reveal the Nature of a Network of Residues Coupled to Hydride Transfer, Roston, D., Kohen, A., Doron, D., Major, D.T., J. Comput. Chem. 2014, 35, 1411-1417.

92. How Accurate are Transition States from Simulations of Enzymatic Reactions? Doron, D., Kohen, A., Nam, K., Major, D.T.,* J. Chem. Theory Comput., 2014, 10, 1863–1871.

91. Protein Motions and the Activation of the C-H Bond Catalyzed by Dihydrofolate Reductase, Francis, K., Kohen, A.,* Curr. Opinion Chem. Biol., 2014, 21, 19–24.

90. Stereospecific Multiple Isotopic Labeling of Benzyl Alcohol, Roston, D., Kohen, A.,* J. Labeled Comp. Radiopharma., 2014, 57, 75-77.

89. Kinetic Isotope Effects as a Probe of Hydrogen Transfers to and from Common Enzymatic Cofactors, Roston, D., Islam, Z., and Kohen, A.,* Arch. Biochem. Biophys. 2014, 544, 96-104

88. Extension and limits of the network of couple motions correlated to hydride transfer in dihydrofolate reductase, Singh, P., Sen, A., Francis, K. and Kohen, A.,* J. Am. Chem. Soc. 2014,136, 2575-2582


2013


87. Preservation of Protein Dynamics in Enzyme Evolution, Francis, K., Stojković, V., and Kohen, A.,* J. Biol. Chem. 2013, 288, 35961-35968.

86. A critical test of the "Tunneling and Coupled Motion" Concept in Enzymatic Alcohol Oxidation, Roston, D. and Kohen, A.,* J. Am. Chem. Soc. 2013, 135, 13624-13627.

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

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

83. 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.

82. 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.

81.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


80. 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

79. 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

78. 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.

77. 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

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

75. 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.

74. 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.

73. 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

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

71. 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

70.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

69. 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

68. 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

67. 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.

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


2011


65. “Structural study of the mutants of FDTS from T. maritima”, Mathews, I.I.*, Fleischmann, T., Kohen, A., Lesley, S.A.,  Acta Cryst., 2011, A67, C781.

64. 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

63. 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

62. 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.

61. 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.

60. 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)

59. 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.

58. 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.

57. 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


56. 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).

55. 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

54. 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.

53. 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")

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

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

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


2009


49. Effect of electrostatic shielding on H-tunneling in R67 dihydrofolate, Yahashiri, A.; Nimrod, G.; Ben-Tal, N.; Howell, E.E.; and Kohen, A.*, ChemBioChem 2009, 10, 2620-2623

48. Exploring the Molecular Origins of Protein Dynamics in the Active Site of Human Carbonic Anhydrase II, Hill, S.E., Bandaria, J.N., Fox, M., Vanderah, E., Kohen A.,and Cheatum, C.M.*, J. Phys. Chem. B. 2009, 113, 11505 - 11510.

47. Microscale synthesis and kinetic isotope effect analysis of (4R)-[Ad-14C, 4-2H] NADPH and (4R)-[Ad-3H,4-2H] NADPH, Yahashiri, A.; Sen, A.; and Kohen, A.*, J. Labeled Comp. Radiopharma, 2009, 52, 463-466.

46. Examination of Enzymatic H-Tunneling through Kinetics and Dynamics, Bandaria, J.N., Cheatum, C.M., and Kohen, A.*, J. Am. Chem. Soc. 2009, 131, 10151-10155

45. An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene, Koehn, E.M., Fleischmann, T., Conrad, J.A., Palfey, B.A., Lesley, S.A., Mathews, I.I., and Kohen, A.*, Nature 2009, 458, 919-923.

44. Oxidase Activity of a Flavin-Dependent Thymidylate Synthase, Wang, Z., Chernyshev, A., Koehn, E.M., Manuel, A., Lesley, S.A., and Kohen A.*, FEBS J. 2009, 276 (10), 2801-2810.

43. Enzymatic H-transfers: Quantum Tunneling and Coupled Motion from Kinetic Isotope Effect Studies, Stojkovic, V., Kohen A.*, Isr. J. Chem. 2009, 49, 163-173 (Invited Review).

42. Quantum Effects in Enzyme Kinetics, Sen, A., and Kohen, A.*, in Quantum Tunnelling in Enzyme Catalyzed Reactions, Allemann, R. and Scrutton, N., Eds, Royal Society of Chemistry, London, UK, 2009, Ch. 7, pp.164-181. ISBN 978-0-85404-122-0

41. QM/MM study of Thymidylate Synthase: Enzymatic motions and the temperature dependence of the rate limiting step, Kanaan, N., Marti, S.*, Moliner, V.*, and Kohen, A., J. Phys. Chem. A. 2009, 113, 2176-2182 (Special Issue on Chemical Dynamics: Max Wolfsberg Festschrift, Sharon Hammes-Schiffer Ed.).


2008


40. Kohen A., Spotlight: "Deep Tunneling Dominates the Biologically Important Hydride Transfer Reaction from NADH to FMN in Morphinone Reductase" J. Am. Chem. Soc. 2008, (invited Spotlight on JACS 2008, 130, 7092).

39. Tuning of the H-Transfer Coordinate in Primitive versus Well-Evolved Enzymes, Yahashiri, A., Howell, E.E., and Kohen, A.*, ChemPhysChem 2008, 9, 980-982 (Communication). Supplementary Information.

38. Fast Enzyme Dynamics at the Active Site of Formate Dehydrogenase, Bandaria, J., Dutta, S., Hill, S., Kohen, A., and Cheatum, C.*, J. Am. Chem. Soc. 2008, 130, 22-23 (Communication).


2007


37. The Role of Y94 in Proton and Hydride Transfers Catalyzed by Thymidylate Synthase Hong, B., Maley, F., and Kohen, A.*, Biochemistry 2007, 46, 14188-14197.

36. The relationships between oxidase and synthase activities of flavin dependent thymidylate synthase (FDTS) Chernyshev, A., Fleischmann,T., Koehn, E.M., Lesley, S.A., and Kohen, A.*, Chem. Commun., 2007, 2861-2863.

35. A QM/MM Study of the catalytic mechanism of the thymidylate synthase, Kanaan, N., Mart�, S.*, Moliner, V.*, and Kohen, A., Biochemistry, 2007, 46, 3704-3713.

34. Thymidyl Biosynthesis Enzymes as Antibiotic Targets, Chernyshev, A., Fleischmann, T., and Kohen, A.*, Appl. Microbiol. Biotech., 2007, 74. 282-289 (review).

33. Probes for hydrogen tunneling and coupled motion in enzymatic systems, Kohen, A. in Hydrogen-Transfer Reactions, Vol; 4: Biological Aspect , Hynes, Klinman, Limbach, Schowen, Eds., Wiley_VCH, Weinheim, 2007, Chapter 12, pp. 1311-1340.


2006


32. Coordinated Effects of Distal Mutations on Environmentally Coupled Tunneling in Dihydrofolate Reductase, Wang, L., Goodey, N.M., Benkovic, S.J.*, and Kohen, A.*, Proc. Natl. Acad. Sci. USA 2006, 103, 15753-15758.

31. Analytical Procedures for the Preparation, Isolation, Analysis and Preservation of Reduced Nicotinamides Markham, K.A., and Kohen, A.*, Curr. Anal. Chem., 2006, 2, 379-388 (invited review).

30. Kinetic isotope effects as probes for hydrogen tunneling in enzyme catalysis Kohen, A., in Isotope Effects in Chemistry and Biology, Kohen, A. Limbach, H.H. Eds., Taylor & Francis -CRC Press, Boca Raton, FL, 2006, Ch. 28, pp-743-764. ISBN 0824724496.

29. Hydride transfer versus hydrogen radical transfer in thymidylate synthase Hong, B., Haddad, M., Maley, F., Jensen, J.H., and Kohen, A.* J. Am. Chem. Soc. (communication) 2006, 128, 5636 - 5637 Supplementary Information

28. A lag-phase in the reduction of flavin dependent thymidylate synthase (FDTS) revealed a mechanistic missing link Mason, A., Agrawal, N., Washington, T., Lesley, S.A., and Kohen, A.*, Chem. Comm. 2006, 1781�1783.

27. Arrhenius curves of hydrogen transfers: Tunnel effects, isotope effects, and effects of pre-equilibria Limbach, H.H., Lopez, J.M., and Kohen, A., Phyl. Trans. R. Soc. B., 2006, 361,1399 - 1415.

26. The role of enzyme dynamics and tunneling in catalyzing hydride transfer: Studies of distal mutants of dihydrofolate reductase Wang, L., Goodey, N.M., Benkovic, S.J., and Kohen, A., Phyl. Trans. R. Soc. B., 2006, 361, 1307-1215. Supplementary Information

25. Effects of a distal mutation on active site chemistry Wang, L., Tharp, S., Selzer, T., Benkovic, S.J., and Kohen, A., Biochemistry, 2006, 45, 1383-1392. Supplementary Information


2005


24. Nonperfect synchronization of reaction center rehybridization in the transition state of the hydride transfer catalyzed by dihydrofolate reductase Pu, J., Ma, S., Garcia-Viloca, M., Gao, J., Truhlar, D.G., and Kohen, A., J. Am. Chem. Soc., 2005, 127, 14879-14886.

23. Microscale synthesis of isotopically labeled 6R-N5, N10 methylene-5, 6, 7, 8-tetrahydrofolate Hong, B. and Kohen, A., J. Label Compd. Radiopharm. 2005, 48, 759�769.

22. Competitive 15N kinetic isotope effects of nitrogenase catalyzed dinitrogen reduction Sra, A.K., Hu, Y. Martin, G.E., Snow, D.D., Ribbe, M.W., and Kohen, A. J. Am. Chem. Soc. 2004, 126, 12768-12769; Supplementary Information

 


2004


21. Mechanistic studies of a flavin-dependent thymidylate synthase Agrawal, N., Lesley, S.A., Kuhn, P., Kohen, A. Biochemistry, 2004, 43, 10295-10301, Accelarated Publication; Supplementary Information.

20. Tunneling and coupled motion in the E. coli dihydrofolate reductase catalysis R. Steven Sikorski, Lin Wang, Kelli A. Markham, P. T. Ravi Rajagopalan, Stephen J. Benkovic, and Amnon Kohen J. Am. Chem. Soc. 2004, 126, 4778-4779; Supplementary Information

19. Microscale synthesis of isotopically labeled R-[6-XH]-N5,N10-methlene 5,6,7,8-tetrahydrofolate as a cofactor for thymidylate synthase Agrawal, N., Mihai, C., Kohen, A. Anal. Biochem.2004 328, 44-50.

18. Vibrationally enhanced hydrogen tunneling in the E. coli thymidylate synthase catalyzed reaction Agrawal, N., Hong, B., Mihai, C., and Kohen, A. Biochemistry, 2004, 43, 1998-2006.

17. Synthesis and utility of 14C-nicotinamide cofactors Markham, K., Sikorski, R.S., and Kohen, A. Anal. Biochem. 2004, 325, 62-67


2003


16. Synthesis of R and S tritiated reduced b-nicotinamide adenine dinucleotide 2' phosphate McCracken, J. A., Wang, L., Kohen, A. Anal. Biochem 2003, 324, 131-136

15. Microscale synthesis of 2-tritiated isopropanol and 4-R tritiated reduced nicotinamide adenine dinucleotide phosphate Agrawal, N. and Kohen, A. Anal. Biochem. 2003, 322, 179-184

14. Purification, analysis and preservation of reduced nicotinamide adenine dinucleotide 2'-phosphate Markham, K.A., Sikorski, R.S., and Kohen, A. Anal. Biochem. 2003, 322, 26-32

13. Kinetic isotope effects as probes for hydrogen tunneling, coupled motion and dynamics contributions to enzyme catalysis, A. Kohen Prog. React. Kinet. Mech. 2003 28, 119-156


2002


12. Nitrogenase catalyzed dinitrogen reduction -a new mechanistic approach, Sra, A.K.; Kohen, A., Nitrogen Fixation, Global Perspective, 2002, (eds. T Finan, M O'Brian, D Layzell, K Vessey, W Newton), CABI Publishing, London, p 371.

11. Boundary Conditions for the Swain-Schaad Relationship as a Criterion for Hydrogen Tunneling, Kohen, A.; Jensen, J. J. Am. Chem. Soc., 2002,124(15); 3858-3864.


1995-2001


10. Convex Arrhenius plots and their interpretation, Truhlar, D. G., and Kohen, A. Proc. Natl. Acad. Sci. USA, 2001, 98, 848-851.

9. Protein flexibility correlates with degree of hydrogen tunneling in thermophilic and mesophilic alcohol dehydrogenases, Kohen, A.; J. P. Klinman J. Am. Chem. Soc., 2000, 122, 10738-10739.

8. Hydrogen Tunneling in Biology, Kohen, A.; Klinman, J. P. Chemistry and Biology 1999, 6, R191-198. [review]

7. Enzyme Dynamics and Hydrogen Tunneling in a Thermophilic Alcohol Dehydrogenase, Kohen, A.; Cannio, R.; Bartolucci, S.; Klinman, J. P. Nature 1999, 399, 496-499.

6. Enzyme Catalysis: Beyond Classical Paradigms, Kohen, A.; Klinman, P. J. Acc. Chem. Res. 1998, 31, 397-404. [review]

5. Catalytic Mechanism of KDO8P Synthase: Transient Kinetic Studies and Evaluation of a Putative Reaction Intermediate., Liang, P. H.; Lewis, J.; Anderson, K. S.; Kohen, A.; D'Souza, F. W.; Benenson, Y.; Baasov, T. Biochemistry 1998, 37, 16390-16399.

4. Effect of Protein Glycosylation on Catalysis: Changes in Hydrogen Tunneling and Enthalpy of Activation in the Glucose Oxidase Reaction., Kohen, A.; Jonsson, T.; Klinman, P. J. Biochemistry 1997, 36, 2603-2611.

3. Effect of Enzyme Glycosylation on the Chemical Step of Catalysis, as Probed by Hydrogen Tunneling and Enthalpy of Activation, Kohen, A.; Jonsson, T.; Klinman, J. P. Tech. Prot. Chem 1997, VIII, 311-319.

2. Catalytic Mechanism of KDO8P Synthase. Pre-Steady-State Kinetic Analysis Using Rapid Chemical Quench Flow Methods, Liang, P. H.; Kohen, A.; Baasov, T.; Anderson, K. S. Bioorganic & Medical Chem. Lett. 1997, 7, 2463-2468.

1. Synthesis, Inhibition and Acid-Catalyzed Hydrolysis Studies of Model Compounds of the Proposed Intermediate in the KDO8P Synthase Catalyzed Reaction, Baasov, T.; Kohen, A. J. Am. Chem. Soc. 1995, 117, 6165-6174.