Modulating Enzyme Activity by Altering Protein Dynamics with Solvent
- Michael R. Duff Jr
Michael R. Duff, JrBiochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, United StatesMore by Michael R. Duff, Jr
- ,
- Jose M. Borreguero
Jose M. BorregueroNeutron Data Analysis and Visualization Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Jose M. Borreguero
- ,
- Matthew J. Cuneo
Matthew J. CuneoBiology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Matthew J. Cuneo
- ,
- Arvind Ramanathan
Arvind RamanathanComputer Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Arvind Ramanathan
- ,
- Junhong He
Junhong HeNeutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Junhong He
- ,
- Ganesh Kamath
Ganesh KamathComputer Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Ganesh Kamath
- ,
- S. Chakra Chennubhotla
S. Chakra ChennubhotlaDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United StatesMore by S. Chakra Chennubhotla
- ,
- Flora Meilleur
Flora MeilleurBiology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMolecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina, United StatesMore by Flora Meilleur
- ,
- Elizabeth E. Howell
Elizabeth E. HowellBiochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, United StatesMore by Elizabeth E. Howell
- ,
- Kenneth W. Herwig
Kenneth W. HerwigNeutron Technologies Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Kenneth W. Herwig
- ,
- Dean A. A. Myles
Dean A. A. MylesBiology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Dean A. A. Myles
- , and
- Pratul K. Agarwal*
Pratul K. Agarwal*E-mail: [email protected]. Phone: (865) 765-7750.Biochemistry & Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, United StatesComputer Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United StatesMore by Pratul K. Agarwal
Abstract
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent khydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzymeʼs ability to access its functionally relevant conformational substates, explaining the decreased khydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.
Cited By
This article is cited by 23 publications.
- Rodrigo Noriega. Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces. The Journal of Physical Chemistry B 2021, 125 (22) , 5667-5675. https://doi.org/10.1021/acs.jpcb.1c01546
- Scott D. Gorman, Dennis S. Winston, Debashish Sahu, David D. Boehr. Different Solvent and Conformational Entropy Contributions to the Allosteric Activation and Inhibition Mechanisms of Yeast Chorismate Mutase. Biochemistry 2020, 59 (27) , 2528-2540. https://doi.org/10.1021/acs.biochem.0c00277
- Anddre Osmar Valdivia, Pratul K. Agarwal, Sanjoy K. Bhattacharya. Myelin Basic Protein Phospholipid Complexation Likely Competes with Deimination in Experimental Autoimmune Encephalomyelitis Mouse Model. ACS Omega 2020, 5 (25) , 15454-15467. https://doi.org/10.1021/acsomega.0c01590
- Christian Beck, Marco Grimaldo, Felix Roosen-Runge, Ralph Maier, Olga Matsarskaia, Michal Braun, Benedikt Sohmen, Orsolya Czakkel, Ralf Schweins, Fajun Zhang, Tilo Seydel, Frank Schreiber. Following Protein Dynamics in Real Time during Crystallization. Crystal Growth & Design 2019, 19 (12) , 7036-7045. https://doi.org/10.1021/acs.cgd.9b00858
- Yun Lu, Samantha Wilhelm, Mingxuan Bai, Peter Maness, Li Ma. Replication of the Enzymatic Temperature Dependency of the Primary Hydride Kinetic Isotope Effects in Solution: Caused by the Protein-Controlled Rigidity of the Donor–Acceptor Centers?. Biochemistry 2019, 58 (39) , 4035-4046. https://doi.org/10.1021/acs.biochem.9b00574
- Jiayue Li, Gabriel Fortunato, Jennifer Lin, Pratul K. Agarwal, Amnon Kohen, Priyanka Singh, Christopher M. Cheatum. Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase. Biochemistry 2019, 58 (37) , 3861-3868. https://doi.org/10.1021/acs.biochem.9b00460
- J. T. Gerig. Examination of Trifluoroethanol Interactions with Trp-Cage in Trifluoroethanol–Water at 298 K through Molecular Dynamics Simulations and Intermolecular Nuclear Overhauser Effects. The Journal of Physical Chemistry B 2019, 123 (15) , 3248-3258. https://doi.org/10.1021/acs.jpcb.9b01171
- Pratul K. Agarwal. A Biophysical Perspective on Enzyme Catalysis. Biochemistry 2019, 58 (6) , 438-449. https://doi.org/10.1021/acs.biochem.8b01004
- G. Vitola, R. Mazzei, L. Giorno. Biohybrid membranes for organophosphate pesticides degradation: Hyperactivation of immobilized phosphotriesterase by surfactants. Environmental Technology & Innovation 2023, 30 , 103053. https://doi.org/10.1016/j.eti.2023.103053
- Griffin A. Welfer, Veniamin A. Borin, Luis M. Cortez, Patricia L. Opresko, Pratul K. Agarwal, Bret D. Freudenthal. Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants. Genes 2023, 14 (2) , 281. https://doi.org/10.3390/genes14020281
- Tyler M. Weaver, Timothy H. Click, Thu H. Khoang, M. Todd Washington, Pratul K. Agarwal, Bret D. Freudenthal. Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1. Nature Communications 2022, 13 (1) https://doi.org/10.1038/s41467-022-30577-0
- Gabriela C. Schröder, William B. O'Dell, Simon P. Webb, Pratul K. Agarwal, Flora Meilleur. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chemical Science 2022, 13 (45) , 13303-13320. https://doi.org/10.1039/D2SC05031E
- Hossein Heidari, Mahdi Rezaei Karamati, Hossein Motavalli. Tumor growth modeling via Fokker–Planck equation. Physica A: Statistical Mechanics and its Applications 2022, 596 , 127168. https://doi.org/10.1016/j.physa.2022.127168
- C. Satheesan Babu, Carmay Lim. Influence of solution ionic strength on the stabilities of M20 loop conformations in apo E. coli dihydrofolate reductase. The Journal of Chemical Physics 2021, 154 (19) https://doi.org/10.1063/5.0048968
- Jasmina S. Redzic, Michael R. Duff, Ashley Blue, Todd M. Pitts, Pratul Agarwal, Elan Zohar Eisenmesser. Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B. Frontiers in Molecular Biosciences 2021, 8 https://doi.org/10.3389/fmolb.2021.691208
- Nicole M. Hoitsma, Timothy H. Click, Pratul K. Agarwal, Bret D. Freudenthal. Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Computational and Structural Biotechnology Journal 2021, 19 , 3293-3302. https://doi.org/10.1016/j.csbj.2021.05.035
- Yaohui Li, Rongzhen Zhang, Yan Xu. Structure-based mechanisms: On the way to apply alcohol dehydrogenases/reductases to organic-aqueous systems. International Journal of Biological Macromolecules 2021, 168 , 412-427. https://doi.org/10.1016/j.ijbiomac.2020.12.068
- Lorea Alejaldre, Claudèle Lemay-St-Denis, Carles Perez Lopez, Ferran Sancho Jodar, Victor Guallar, Joelle N. Pelletier. Known Evolutionary Paths Are Accessible to Engineered ß-Lactamases Having Altered Protein Motions at the Timescale of Catalytic Turnover. Frontiers in Molecular Biosciences 2020, 7 https://doi.org/10.3389/fmolb.2020.599298
- Pratul K. Agarwal, David N. Bernard, Khushboo Bafna, Nicolas Doucet. Enzyme Dynamics: Looking Beyond a Single Structure. ChemCatChem 2020, 12 (19) , 4704-4720. https://doi.org/10.1002/cctc.202000665
- Michael R Duff, Jasmina S Redzic, Lucas P Ryan, Natasia Paukovich, Rui Zhao, Jay C Nix, Todd M Pitts, Pratul Agarwal, Elan Zohar Eisenmesser. Structure, dynamics and function of the evolutionarily changing biliverdin reductase B family. The Journal of Biochemistry 2020, 168 (2) , 191-202. https://doi.org/10.1093/jb/mvaa039
- David P. Hoogerheide, V. Trevor Forsyth, Katherine A. Brown. Neutron scattering for structural biology. Physics Today 2020, 73 (6) , 36-42. https://doi.org/10.1063/PT.3.4498
- José G. Sampedro, Miguel A. Rivera-Moran, Salvador Uribe-Carvajal. Kramers’ Theory and the Dependence of Enzyme Dynamics on Trehalose-Mediated Viscosity. Catalysts 2020, 10 (6) , 659. https://doi.org/10.3390/catal10060659
- Khushboo Bafna, Chitra Narayanan, S. Chakra Chennubhotla, Nicolas Doucet, Pratul K. Agarwal, . Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. PLOS ONE 2019, 14 (8) , e0220037. https://doi.org/10.1371/journal.pone.0220037