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Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

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Department of Biochemistry, Box 3711, Duke University, Durham, North Carolina 27710, United States
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
Phone: (814) 865-6442. Fax: (814) 865-2927. E-mail: [email protected]
Cite this: Biochemistry 2011, 50, 48, 10422–10430
Publication Date (Web):October 26, 2011
https://doi.org/10.1021/bi201486f
Copyright © 2011 American Chemical Society

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    Abstract

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    This brief review discusses our current understanding of the molecular basis of enzyme catalysis. A historical development is presented, beginning with steady state kinetics and progressing through modern fast reaction methods, nuclear magnetic resonance, and single-molecule fluorescence techniques. Experimental results are summarized for ribonuclease, aspartate aminotransferase, and especially dihydrofolate reductase (DHFR). Multiple intermediates, multiple conformations, and cooperative conformational changes are shown to be an essential part of virtually all enzyme mechanisms. In the case of DHFR, theoretical investigations have provided detailed information about the movement of atoms within the enzyme–substrate complex as the reaction proceeds along the collective reaction coordinate for hydride transfer. A general mechanism is presented for enzyme catalysis that includes multiple intermediates and a complex, multidimensional standard free energy surface. Protein flexibility, diverse protein conformations, and cooperative conformational changes are important features of this model.

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    52. C. Tony Liu, Lin Wang, Nina M. Goodey, Philip Hanoian, and Stephen J. Benkovic . Temporally Overlapped but Uncoupled Motions in Dihydrofolate Reductase Catalysis. Biochemistry 2013, 52 (32) , 5332-5334. https://doi.org/10.1021/bi400858m
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    56. Zhen Wang, Thelma Abeysinghe, Janet S. Finer-Moore, Robert M. Stroud, and Amnon Kohen . A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase. Journal of the American Chemical Society 2012, 134 (42) , 17722-17730. https://doi.org/10.1021/ja307859m
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    58. Megha Anand and Raghavan B. Sunoj . Mechanism of Cooperative Catalysis in a Lewis Acid Promoted Nickel-Catalyzed Dual C–H Activation Reaction. Organic Letters 2012, 14 (17) , 4584-4587. https://doi.org/10.1021/ol302047c
    59. Bryce V. Plapp and S. Ramaswamy . Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD+ and Fluoroalcohols Define Strained Michaelis Complexes. Biochemistry 2012, 51 (19) , 4035-4048. https://doi.org/10.1021/bi300378n
    60. J. W. Peng . Exposing the Moving Parts of Proteins with NMR Spectroscopy. The Journal of Physical Chemistry Letters 2012, 3 (8) , 1039-1051. https://doi.org/10.1021/jz3002103
    61. Stephen Lo, Chloe Z.‐J. Ren, Pablo Solís‐Muñana, Jack L.‐Y. Chen. Dynamic Self‐assembled Supramolecular Catalysts. 2023, 469-493. https://doi.org/10.1002/9783527834044.ch17
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    67. Qianru Wang, Jianping Guo, Ping Chen. Complex transition metal hydrides for heterogeneous catalysis. Chem Catalysis 2023, 3 (3) , 100524. https://doi.org/10.1016/j.checat.2023.100524
    68. Annika J. E. Borg, Oriol Esquivias, Joan Coines, Carme Rovira, Bernd Nidetzky. Enzymatische C4‐Epimerisierung von UDP‐Glucuronsäure: präzise gesteuerte Rotation eines transienten 4‐Ketointermediats für eine invertierende Reaktion ohne Decarboxylierung. Angewandte Chemie 2023, 135 (4) https://doi.org/10.1002/ange.202211937
    69. Annika J. E. Borg, Oriol Esquivias, Joan Coines, Carme Rovira, Bernd Nidetzky. Enzymatic C4‐Epimerization of UDP‐Glucuronic Acid: Precisely Steered Rotation of a Transient 4‐Keto Intermediate for an Inverted Reaction without Decarboxylation. Angewandte Chemie International Edition 2023, 62 (4) https://doi.org/10.1002/anie.202211937
    70. Himani Sharma, Baddipadige Raju, Gera Narendra, Mohit Motiwale, Bhavna Sharma, Himanshu Verma, Om Silakari. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023, 8 (1) https://doi.org/10.1002/slct.202203319
    71. Chung Eun Ha, N.V. Bhagavan. Energetics of biological systems, enzymes, and enzyme regulation. 2023, 83-112. https://doi.org/10.1016/B978-0-323-88541-6.00013-2
    72. Kevin J. Naidoo, Tomás Bruce-Chwatt, Tharindu Senapathi. Enzyme Reaction Dynamics From Adaptive Reaction Coordinate Forces. 2023https://doi.org/10.1016/B978-0-12-821978-2.00124-0
    73. Siyuan Du, Stephanie A. Wankowicz, Filip Yabukarski, Tzanko Doukov, Daniel Herschlag, James S. Fraser. Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data. 2023, 223-254. https://doi.org/10.1016/bs.mie.2023.06.009
    74. Gemma Fisher, Marina Corbella, Magnus S. Alphey, John Nicholson, Benjamin J. Read, Shina C. L. Kamerlin, Rafael G. da Silva. Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. Nature Communications 2022, 13 (1) https://doi.org/10.1038/s41467-022-34960-9
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    77. Guillem Casadevall, Cristina Duran, Miquel Estévez‐Gay, Sílvia Osuna. Estimating conformational heterogeneity of tryptophan synthase with a template‐based Alphafold2 approach. Protein Science 2022, 31 (10) https://doi.org/10.1002/pro.4426
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    80. Ross L. Stein. Mechanisms of macromolecular reactions. History and Philosophy of the Life Sciences 2022, 44 (2) https://doi.org/10.1007/s40656-022-00492-0
    81. Sedigheh Abedanzadeh, Zainab Moosavi-Movahedi, Nader Sheibani, Ali A. Moosavi-Movahedi. Nanozymes: Supramolecular perspective. Biochemical Engineering Journal 2022, 183 , 108463. https://doi.org/10.1016/j.bej.2022.108463
    82. Jonathan Trouvé, Rafael Gramage‐Doria. Chemical Reactions Controlled By Remote Zn ⋯ N Interactions Between Substrates and Catalysts. 2022, 201-209. https://doi.org/10.1002/9783527832033.ch14
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    86. Wei Li, Benjamen Nforneh, Katie L. Whitcomb, Kurt Warncke. Resolution and characterization of confinement- and temperature-dependent dynamics in solvent phases that surround proteins in frozen aqueous solution by using spin-probe EPR spectroscopy. 2022, 25-57. https://doi.org/10.1016/bs.mie.2022.02.009
    87. Michelle Redhair, William M. Atkins. Analytical and functional aspects of protein-ligand interactions: Beyond induced fit and conformational selection. Archives of Biochemistry and Biophysics 2021, 714 , 109064. https://doi.org/10.1016/j.abb.2021.109064
    88. D.A. Mokhtari, M.J. Appel, P.M. Fordyce, D. Herschlag. High throughput and quantitative enzymology in the genomic era. Current Opinion in Structural Biology 2021, 71 , 259-273. https://doi.org/10.1016/j.sbi.2021.07.010
    89. Bengt Mannervik, Aram Ismail, Helena Lindström, Birgitta Sjödin, Nancy H. Ing. Glutathione Transferases as Efficient Ketosteroid Isomerases. Frontiers in Molecular Biosciences 2021, 8 https://doi.org/10.3389/fmolb.2021.765970
    90. Guoqing Zhang, Xueni Ren, Xiuhong Liang, Yaqun Wang, Dexin Feng, Yujun Zhang, Mo Xian, Huibin Zou. Improving the Microbial Production of Amino Acids: From Conventional Approaches to Recent Trends. Biotechnology and Bioprocess Engineering 2021, 26 (5) , 708-727. https://doi.org/10.1007/s12257-020-0390-1
    91. Jonathan Trouvé, Paolo Zardi, Shaymaa Al‐Shehimy, Thierry Roisnel, Rafael Gramage‐Doria. Enzyme‐like Supramolecular Iridium Catalysis Enabling C−H Bond Borylation of Pyridines with meta ‐Selectivity. Angewandte Chemie 2021, 133 (33) , 18154-18161. https://doi.org/10.1002/ange.202101997
    92. Jonathan Trouvé, Paolo Zardi, Shaymaa Al‐Shehimy, Thierry Roisnel, Rafael Gramage‐Doria. Enzyme‐like Supramolecular Iridium Catalysis Enabling C−H Bond Borylation of Pyridines with meta ‐Selectivity. Angewandte Chemie International Edition 2021, 60 (33) , 18006-18013. https://doi.org/10.1002/anie.202101997
    93. Alfonso García-Márquez, Antonio Frontera, Thierry Roisnel, Rafael Gramage-Doria. Ultrashort H δ+ ⋯H δ− intermolecular distance in a supramolecular system in the solid state. Chemical Communications 2021, 57 (58) , 7112-7115. https://doi.org/10.1039/D1CC02143E
    94. Chaminda P. Samaranayake, Sudhir K. Sastry. Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity. Physical Chemistry Chemical Physics 2021, 23 (26) , 14422-14432. https://doi.org/10.1039/D0CP05950A
    95. Todd P. Silverstein. Enzyme free energy profiles: Can substrate binding be nonspontaneous? Can ground state interactions enhance catalysis?. Biophysical Chemistry 2021, 274 , 106606. https://doi.org/10.1016/j.bpc.2021.106606
    96. Stephen J. Benkovic. From Bioorganic Models to Cells. Annual Review of Biochemistry 2021, 90 (1) , 57-76. https://doi.org/10.1146/annurev-biochem-062320-062929
    97. Sílvia Osuna. The challenge of predicting distal active site mutations in computational enzyme design. WIREs Computational Molecular Science 2021, 11 (3) https://doi.org/10.1002/wcms.1502
    98. Ryan W. Penhallurick, Alliyah Harold, Maya D. Durnal, Toshiko Ichiye. How adding a single methylene to dihydrofolate reductase can change its conformational dynamics. The Journal of Chemical Physics 2021, 154 (16) https://doi.org/10.1063/5.0047942
    99. Monu, Binod Kumar Oram, Biman Bandyopadhyay. Simultaneous exhibition of positive and negative cooperativity by purely CH⋯O H‐bonded (1,3‐cyclohexanedione) n ( n = 2–6) clusters: A density functional theoretical investigation. International Journal of Quantum Chemistry 2021, 121 (8) https://doi.org/10.1002/qua.26581
    100. Jonathan Trouvé, Rafael Gramage-Doria. Beyond hydrogen bonding: recent trends of outer sphere interactions in transition metal catalysis. Chemical Society Reviews 2021, 50 (5) , 3565-3584. https://doi.org/10.1039/D0CS01339K
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