Journal article
Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase
ACS catalysis, Vol.9(12), pp.11199-11206
12/06/2019
DOI: 10.1021/acscatal.9b03345
PMCID: PMC8118594
PMID: 33996196
Abstract
Thermal motions of enzymes have been invoked to explain the temperature dependence of kinetic isotope effects (KIE) in enzyme-catalyzed hydride transfers. Formate dehydrogenase (FDH) from
Candida boidinii
exhibits a temperature independent KIE that becomes temperature dependent upon mutation of hydrophobic residues in the active site. Ternary complexes of FDH that mimic the transition state structure allow investigation of how these mutations influence active-site dynamics. A combination of X-ray crystallography, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamic simulations characterize the structure and dynamics of the active site. FDH exhibits oscillatory frequency fluctuations on the picosecond timescale, and the amplitude of these fluctuations correlates with the temperature dependence of the KIE. Both the kinetic and dynamic phenomena can be reproduced computationally. These results provide experimental evidence for a connection between the temperature dependence of KIEs and motions of the active site in an enzyme-catalyzed reaction consistent with activated tunneling models of the hydride transfer reaction.
Details
- Title: Subtitle
- Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase
- Creators
- Philip Pagano - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesQi Guo - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesChethya Ranasinghe - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesEvan Schroeder - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesKevin Robben - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesFlorian Häse - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesHepeng Ye - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesKyle Wickersham - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesAlán Aspuru-Guzik - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesDan T Major - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesLokesh Gakhar - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesAmnon Kohen - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United StatesChristopher M Cheatum - Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
- Resource Type
- Journal article
- Publication Details
- ACS catalysis, Vol.9(12), pp.11199-11206
- DOI
- 10.1021/acscatal.9b03345
- PMID
- 33996196
- PMCID
- PMC8118594
- NLM abbreviation
- ACS Catal
- ISSN
- 2155-5435
- eISSN
- 2155-5435
- Grant note
- DOI: 10.13039/100000165, name: Division of Chemistry, award: 1707598; DOI: 10.13039/501100001742, name: United States-Israel Binational Science Foundation, award: 2012340; DOI: 10.13039/100007229, name: Harvard University; DOI: 10.13039/100006151, name: Basic Energy Sciences, award: DE-SC0001088; DOI: 10.13039/100000057, name: National Institute of General Medical Sciences, award: GM079368
- Language
- English
- Date published
- 12/06/2019
- Academic Unit
- Liberal Arts and Science Admin; Chemistry; Medicine Administration
- Record Identifier
- 9984216700602771
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