1
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Singh G, Austin A, Bai M, Bradshaw J, Hammann BA, Kabotso DEK, Lu Y. Study of the Effects of Remote Heavy Group Vibrations on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD + Model Reactions. ACS OMEGA 2024; 9:20593-20600. [PMID: 38737086 PMCID: PMC11080011 DOI: 10.1021/acsomega.4c02383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 05/14/2024]
Abstract
It has recently been observed that the temperature(T)-dependence of KIEs in H-tunneling reactions, characterized by isotopic activation energy difference (ΔEa = EaD - EaH), is correlated to the rigidity of the tunneling ready states (TRSs) in enzymes. A more rigid system with narrowly distributed H-donor-acceptor distances (DADs) at the TRSs gives rise to a weaker T-dependence of KIEs (i.e., a smaller ΔEa). Theoreticians have attempted to develop new H-tunneling models to explain this, but none has been universally accepted. In order to further understand the observations in enzymes and provide useful data to build new theoretical models, we have studied the electronic and solvent effects on ΔEa's for the hydride-tunneling reactions of NADH/NAD+ analogues. We found that a tighter charge-transfer (CT) complex system gives rises to a smaller ΔEa, consistent with the enzyme observations. In this paper, we use the remote heavy group (R) vibrational effects to mediate the system rigidity to study the rigidity-ΔEa relationship. The specific hypothesis is that slower vibrations of a heavier remote group would broaden the DAD distributions and increase the ΔEa value. Four NADH/NAD+ systems were studied in acetonitrile but most of such heavy group vibrations do not appear to significantly increase the ΔEa. The remote heavy group vibrations in these systems may have not affected the CT complexation rigidity to a degree that can significantly increase the DADs, and further, the ΔEa values.
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Affiliation(s)
- Grishma Singh
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Ava Austin
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Joshua Bradshaw
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | - Blake A. Hammann
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
| | | | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, United States
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2
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Read BJ, Mitchell JBO, da Silva RG. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release. Commun Chem 2024; 7:77. [PMID: 38582930 PMCID: PMC10998830 DOI: 10.1038/s42004-024-01165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.
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Affiliation(s)
- Benjamin J Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - John B O Mitchell
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.
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3
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Bai M, Pratap R, Salarvand S, Lu Y. Correlation of temperature dependence of hydride kinetic isotope effects with donor-acceptor distances in two solvents of different polarities. Org Biomol Chem 2023; 21:5090-5097. [PMID: 37278324 PMCID: PMC10339711 DOI: 10.1039/d3ob00718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recently observed nearly temperature (T)-independent kinetic isotope effects (KIEs) in wild-type enzymes and T-dependent KIEs in variants were used to suggest that H-tunneling in enzymes is assisted by the fast protein vibrations that help sample short donor-acceptor distances (DADs). This supports the recently proposed role of protein vibrations in DAD sampling catalysis. However, use of T-dependence of KIEs to suggest DAD sampling associated with protein vibrations is debated. We have formulated a hypothesis regarding the correlation and designed experiments in solution to investigate it. The hypothesis is, a more rigid system with shorter DADTRS's at the tunneling ready states (TRSs) gives rise to a weaker T-dependence of KIEs, i.e., a smaller ΔEa (= EaD - EaH). In a former work, the solvent effects of acetonitrile versus chloroform on the ΔEa of NADH/NAD+ model reactions were determined, and the DADPRC's of the productive reactant complexes (PRCs) were computed to substitute the DADTRS for the DADTRS-ΔEa correlation study. A smaller ΔEa was found in the more polar acetonitrile where the positively charged PRC is better solvated and has a shorter DADPRC, indirectly supporting the hypothesis. In this work, the TRS structures of different DADTRS's for the hydride tunneling reaction from 1,3-dimethyl-2-phenylimidazoline to 10-methylacridinium were computed. The N-CH3/CD3 secondary KIEs on both reactants were calculated and fitted to the observed values to find the DADTRS order in both solutions. It was found that the equilibrium DADTRS is shorter in acetonitrile than in chloroform. Results directly support the DADTRS-ΔEa correlation hypothesis as well as the explanation that links T-dependence of KIEs to DAD sampling catalysis in enzymes.
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Affiliation(s)
- Mingxuan Bai
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Rijal Pratap
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Sanaz Salarvand
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
| | - Yun Lu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA.
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4
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Andrews BA, Dyer RB. Comparison of the Role of Protein Dynamics in Catalysis by Dihydrofolate Reductase from E. coli and H. sapiens. J Phys Chem B 2022; 126:7126-7134. [PMID: 36069763 DOI: 10.1021/acs.jpcb.2c05112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydrofolate reductase (DHFR) is a well-studied, clinically relevant enzyme known for being highly dynamic over the course of its catalytic cycle. However, the role dynamic motions play in the explicit hydride transfer from the nicotinamide cofactor to the dihydrofolate substrate remains unclear because reaction initiation and direct spectroscopic examination on the appropriate time scale for such femtosecond to picosecond motions is challenging. Here, we employ pre-steady-state kinetics to observe the hydride transfer as directly as possible in two different species of DHFR: Escherichia coli and Homo sapiens. While the hydride transfer has been well-characterized in DHFR from E. coli, improvements in time resolution now allow for sub-millisecond dead times for stopped-flow spectroscopy, which reveals that the maximum rate is indeed faster than previously recorded. The rate in the human enzyme, previously only estimated, is also able to be directly observed using cutting-edge stopped-flow instrumentation. In addition to the pH dependence of the hydride transfer rates for both enzymes, we examine the primary H/D kinetic isotope effect to reveal a temperature dependence in the human enzyme that is absent from the E. coli counterpart. This dependence, which appears above a temperature of 15 °C is a shared feature among other hydride transfer enzymes and is also consistent with computational work suggesting the presence of a fast promoting-vibration that provides donor-acceptor compression on the time scale of catalysis to facilitate the chemistry step.
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Affiliation(s)
- Brooke A Andrews
- Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Chemistry Department, Emory University, Atlanta, Georgia 30322, United States
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5
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Li J, Lin J, Kohen A, Singh P, Francis K, Cheatum CM. Evolution of Optimized Hydride Transfer Reaction and Overall Enzyme Turnover in Human Dihydrofolate Reductase. Biochemistry 2021; 60:3822-3828. [PMID: 34875176 PMCID: PMC8697555 DOI: 10.1021/acs.biochem.1c00558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Evolution of dihydrofolate
reductase (DHFR) has been studied using
the enzyme from Escherichia coli DHFR
(ecDHFR) as a model, but less studies have used the enzyme from Homo sapiens DHFR (hsDHFR). Each enzyme maintains
a short and narrow distribution of hydride donor-acceptor distances
(DAD) at the tunneling ready state (TRS). Evolution of the enzyme
was previously studied in ecDHFR where three key sites were identified
as important to the catalyzed reaction. The corresponding sites in
hsDHFR are F28, 62-PEKN, and 26-PPLR. Each of these sites was studied
here through the creation of mutant variants of the enzyme and measurements
of the temperature dependence of the intrinsic kinetic isotope effects
(KIEs) on the reaction. F28 is mutated first to M (F28M) and then
to the L of the bacterial enzyme (F28L). The KIEs of the F28M variant
are larger and more temperature-dependent than wild-type (WT), suggesting
a broader and longer average DAD at the TRS. To more fully mimic ecDHFR,
we also study a triple mutant of the human enzyme (F32L-PP26N-PEKN62G).
Remarkably, the intrinsic KIEs, while larger in magnitude, are temperature-independent
like the WT enzymes. We also construct deletion mutations of hsDHFR
removing both the 62-PEKN and 26-PPLR sequences. The results mirror
those described previously for insertion mutants of ecDHFR. Taken
together, these results suggest a balancing act during DHFR evolution
between achieving an optimal TRS for hydride transfer and preventing
product inhibition arising from the different intercellular pools
of NADPH and NADP+ in prokaryotic and eukaryotic cells.
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Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- Texas A&M University-Kingsville, Kingsville, Texas 78363, United States
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6
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Adesina AS, Luk LYP, Allemann RK. Cryo-kinetics Reveal Dynamic Effects on the Chemistry of Human Dihydrofolate Reductase. Chembiochem 2021; 22:2410-2414. [PMID: 33876533 PMCID: PMC8360168 DOI: 10.1002/cbic.202100017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/16/2021] [Indexed: 12/03/2022]
Abstract
Effects of isotopic substitution on the rate constants of human dihydrofolate reductase (HsDHFR), an important target for anti-cancer drugs, have not previously been characterized due to its complex fast kinetics. Here, we report the results of cryo-measurements of the kinetics of the HsDHFR catalyzed reaction and the effects of protein motion on catalysis. Isotopic enzyme labeling revealed an enzyme KIE (kHLE /kHHE ) close to unity above 0 °C; however, the enzyme KIE was increased to 1.72±0.15 at -20 °C, indicating that the coupling of protein motions to the chemical step is minimized under optimal conditions but enhanced at non-physiological temperatures. The presented cryogenic approach provides an opportunity to probe the kinetics of mammalian DHFRs, thereby laying the foundation for characterizing their transition state structure.
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Affiliation(s)
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
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7
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Singh P, Vandemeulebroucke A, Li J, Schulenburg C, Fortunato G, Kohen A, Hilvert D, Cheatum CM. Evolution of the Chemical Step in Enzyme Catalysis. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | | | - Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Cindy Schulenburg
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Gabriel Fortunato
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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8
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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9
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Ranasinghe C, Pagano P, Sapienza PJ, Lee AL, Kohen A, Cheatum CM. Isotopic Labeling of Formate Dehydrogenase Perturbs the Protein Dynamics. J Phys Chem B 2019; 123:10403-10409. [PMID: 31696711 DOI: 10.1021/acs.jpcb.9b08426] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isotope substitution of enzymes has become a means of addressing the participation of protein motions in enzyme-catalyzed reactions. The idea is that only the enzyme mass will be altered and not the electrostatics, so that the protein dynamics are essentially the same but at lower frequencies because of the mass change. In this study, we variably label all carbon atoms in formate dehydrogenase (FDH) with 13C, all nitrogen atoms with 15N, and all nonexchangeable hydrogen atoms with deuterium and investigate the impact that isotopic substitution has on the dynamics at the active site by two-dimensional infrared spectroscopy and compare with the measurements of the temperature dependence of the intrinsic kinetic isotope effects (KIEs). We show that 15N labeling of FDH has the largest effect and makes the active site more heterogeneous, whereas the addition of nonexchangeable deuterium appears to have the opposite effect of 15N on active-site dynamics, resulting in a behavior similar to that of native FDH. Nevertheless, the temperature dependence of the KIEs shows a monotonic trend with protein mass that does not correspond with the changes in dynamics. These results suggest that isotope labeling has more than just a mass effect on enzyme dynamics and may influence electrostatics in ways that complicate the interpretation of the protein isotope effect.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Philip Pagano
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Amnon Kohen
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
| | - Christopher M Cheatum
- Department of Chemistry , University of Iowa , Iowa City , Iowa 52242-1727 , United States
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10
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Li J, Fortunato G, Lin J, Agarwal PK, Kohen A, Singh P, Cheatum CM. Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase. Biochemistry 2019; 58:3861-3868. [PMID: 31423766 PMCID: PMC7296831 DOI: 10.1021/acs.biochem.9b00460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Understanding protein motions and their role in enzymatic reactions is an important and timely topic in enzymology. Protein motions that are involved in the chemical step of catalysis are particularly intriguing but difficult to identify. A global network of coupled residues in Escherichia coli dihydrofolate reductase (E. coli DHFR), which assists in catalyzing the chemical step, has previously been demonstrated through quantum mechanical/molecular mechanical and molecular dynamics simulations as well as bioinformatic analyses. A few specific residues (M42, G121, F125, and I14) were shown to function synergistically with measurements of single-turnover rates and the temperature dependence of intrinsic kinetic isotope effects (KIEsint) of site-directed mutants. This study hypothesizes that the global network of residues involved in the chemical step is evolutionarily conserved and probes homologous residues of the potential global network in human DHFR through measurements of the temperature dependence of KIEsint and computer simulations based on the empirical valence bond method. We study mutants M53W and S145V. Both of these remote residues are homologous to network residues in E. coli DHFR. Non-additive isotope effects on activation energy are observed between M53 and S145, indicating their synergistic effect on the chemical step in human DHFR, which suggests that both of these residues are part of a network affecting the chemical step in enzyme catalysis. This finding supports the hypothesis that human and E. coli DHFR share similar networks, consistent with evolutionary preservation of such networks.
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Affiliation(s)
- Jiayue Li
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | | | - Jennifer Lin
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
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11
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Deng H, Dyer RB, Callender R. Active-Site Glu165 Activation in Triosephosphate Isomerase and Its Deprotonation Kinetics. J Phys Chem B 2019; 123:4230-4241. [PMID: 31013084 DOI: 10.1021/acs.jpcb.9b02981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP) via an enediol(ate) intermediate. The active-site residue Glu165 serves as the catalytic base during catalysis. It abstracts a proton from C1 carbon of DHAP to form the reaction intermediate and donates a proton to C2 carbon of the intermediate to form product GAP. Our difference Fourier transform infrared spectroscopy studies on the yeast TIM (YeTIM)/phosphate complex revealed a C═O stretch band at 1706 cm-1 from the protonated Glu165 carboxyl group at pH 7.5, indicating that the p Ka of the catalytic base is increased by >3.0 pH units upon phosphate binding, and that the Glu165 carboxyl environment in the complex is still hydrophilic in spite of the increased p Ka. Hence, the results show that the binding of the phosphodianion group is part of the activation mechanism which involves the p Ka elevation of the catalytic base Glu165. The deprotonation kinetics of Glu165 in the μs to ms time range were determined via infrared (IR) T-jump studies on the YeTIM/phosphate and ("heavy enzyme") [U-13C,-15N]YeTIM/phosphate complexes. The slower deprotonation kinetics in the ms time scale is due to phosphate dissociation modulated by the loop motion, which slows down by enzyme mass increase to show a normal heavy enzyme kinetic isotope effect (KIE) ∼1.2 (i.e., slower rate in the heavy enzyme). The faster deprotonation kinetics in the tens of μs time scale is assigned to temperature-induced p Ka decrease, while phosphate is still bound, and it shows an inverse heavy enzyme KIE ∼0.89 (faster rate in the heavy enzyme). The IR static and T-jump spectroscopy provides atomic-level resolution of the catalytic mechanism because of its ability to directly observe the bond breaking/forming process.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx, New York 10461 , United States
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Robert Callender
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx, New York 10461 , United States
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12
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Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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13
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
![]()
Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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14
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Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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15
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Bacterial versus human thymidylate synthase: Kinetics and functionality. PLoS One 2018; 13:e0196506. [PMID: 29715278 PMCID: PMC5929524 DOI: 10.1371/journal.pone.0196506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Thymidylate Synthase (TSase) is a highly conserved enzyme that catalyzes the production of the DNA building block thymidylate. Structurally, functionally and mechanistically, bacterial and mammalian TSases share remarkable similarities. Because of this closeness, bacterial enzymes have long been used as model systems for human TSase. Furthermore, while TSase inhibitors have long served as chemotherapeutic drugs, no TSase inhibitor serves as an antibiotic. Despite their high resemblance, the mammalian TSases are distinct in a few known aspects, such as having a N-terminal tail and two insertions in the primary sequence and active/inactive conformations. Here, we aim to comprehensively characterize human (hs) TSase and delineate its contrasts and the similarities to the well-studied Escherichia coli (ec) TSase. We found that, in contrast to ecTSase, Mg2+ does not enhance reaction rates for hsTSase. The temperature dependence of intrinsic kinetic isotope effects (KIEs), on the other hand, suggests that Mg2+ has little or no impact on the transition state of hydride transfer in either enzyme, and that the transition state for the hydride transfer in hsTSase is looser than in ecTSase. Additionally, the substrates’ binding order is strictly ordered for ecTSase but slightly less ordered for hsTSase. The observed kinetic and functional differences between bacterial and human enzymes may aid in the development of antibiotic drugs with reduced toxicity.
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16
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Jones HBL, Crean RM, Matthews C, Troya AB, Danson MJ, Bull SD, Arcus VL, van der Kamp MW, Pudney CR. Uncovering the Relationship between the Change in Heat Capacity for Enzyme Catalysis and Vibrational Frequency through Isotope Effect Studies. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Vickery L. Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton 3240, New Zealand
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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17
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Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017; 139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotopically labeled enzymes (denoted as "heavy" or "Born-Oppenheimer" enzymes) have been used to test the role of protein dynamics in catalysis. The original idea was that the protein's higher mass would reduce the frequency of its normal-modes without altering its electrostatics. Heavy enzymes have been used to test if the vibrations in the native enzyme are coupled to the chemistry it catalyzes, and different studies have resulted in ambiguous findings. Here the temperature-dependence of intrinsic kinetic isotope effects of the enzyme formate dehydrogenase is used to examine the distribution of H-donor to H-acceptor distance as a function of the protein's mass. The protein dynamics are altered in the heavy enzyme to diminish motions that determine the transition state sampling in the native enzyme, in accordance with a Born-Oppenheimer-like effect on bond activation. Findings of this work suggest components related to fast frequencies that can be explained by Born-Oppenheimer enzyme hypothesis (vibrational) and also slower time scale events that are non-Born-Oppenheimer in nature (electrostatic), based on evaluations of protein mass dependence of donor-acceptor distance and forward commitment to catalysis along with steady state and single turnover measurements. Together, the findings suggest that the mass modulation affected both local, fast, protein vibrations associated with the catalyzed chemistry and the protein's macromolecular electrostatics at slower time scales; that is, both Born-Oppenheimer and non-Born-Oppenheimer effects are observed. Comparison to previous studies leads to the conclusion that isotopic labeling of the protein may have different effects on different systems, however, making heavy enzyme studies a very exciting technique for exploring the dynamics link to catalysis in proteins.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel M. Quinn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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18
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Zinovjev K, Tuñón I. Quantifying the limits of transition state theory in enzymatic catalysis. Proc Natl Acad Sci U S A 2017; 114:12390-12395. [PMID: 29101125 PMCID: PMC5703300 DOI: 10.1073/pnas.1710820114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis.
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Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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19
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Abstract
Heavy isotope labeling of enzymes slows protein motions without disturbing the electrostatics and can therefore be used to probe the role of dynamics in enzyme catalysis. To identify the structural elements responsible for dynamic effects, individual segments of an enzyme can be labeled and the resulting effect on the kinetics of the reaction can be measured. Such hybrid isotopomers can be constructed by expressed protein ligation, in which complementary labeled and unlabeled peptide segments are prepared by recombinant gene expression and linked by means of chemical ligation. The construction of such hybrid isotopomers is exemplified here with the paradigmatic enzyme dihydrofolate reductase (DHFR) from Escherichia coli.
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20
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Abstract
Enzyme isotope effects, or the kinetic effects of "heavy" enzymes, refer to the effect of isotopically labeled protein residues on the enzyme's activity or physical properties. These effects are increasingly employed in the examination of the possible contributions of protein dynamics to enzyme catalysis. One hypothesis assumed that isotopic substitution of all 12C, 14N, and nonexchangeable 1H by 13C, 15N, and 2H, would slow down protein picosecond to femtosecond dynamics without any effect on the system's electrostatics following the Born-Oppenheimer approximation. It was suggested that reduced reaction rates reported for several "heavy" enzymes accords with that hypothesis. However, numerous deviations from the predictions of that hypothesis were also reported. Current studies also attempt to test the role of individual residues by site-specific labeling or by labeling a pattern of residues on activity. It appears that in several systems the protein's fast dynamics are indeed reduced in "heavy" enzymes in a way that reduces the probability of barrier crossing of its chemical step. Other observations, however, indicated that slower protein dynamics are electrostatically altered in isotopically labeled enzymes. Interestingly, these effects appear to be system dependent, thus it might be premature to suggest a general role of "heavy" enzymes' effect on catalysis.
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21
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Longbotham JE, Hardman SJO, Görlich S, Scrutton NS, Hay S. Untangling Heavy Protein and Cofactor Isotope Effects on Enzyme-Catalyzed Hydride Transfer. J Am Chem Soc 2016; 138:13693-13699. [PMID: 27676389 DOI: 10.1021/jacs.6b07852] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
"Heavy" (isotopically labeled) enzyme isotope effects offer a direct experimental probe of the role of protein vibrations on enzyme-catalyzed reactions. Here we have developed a strategy to generate isotopologues of the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) where the protein and/or intrinsic flavin mononucleotide (FMN) cofactor are isotopically labeled with 2H, 15N, and 13C. Both the protein and cofactor contribute to the enzyme isotope effect on the reductive hydride transfer reaction, but their contributions are not additive and may partially cancel each other out. However, the isotope effect specifically arising from the FMN suggests that vibrations local to the active site play a role in the hydride transfer chemistry, while the protein-only "heavy enzyme" effect demonstrates that protein vibrations contribute to catalysis in PETNR. In all cases, enthalpy-entropy compensation plays a major role in minimizing the magnitude of "heavy enzyme" isotope effects. Fluorescence lifetime measurements of the intrinsic flavin mononucleotide show marked differences between "light" and "heavy" enzymes on the nanosecond-picosecond time scale, suggesting relevant time scale(s) for those vibrations implicated in the "heavy enzyme" isotope effect on the PETNR reaction.
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Affiliation(s)
- James E Longbotham
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Samantha J O Hardman
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Stefan Görlich
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S Scrutton
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- BBSRC/EPSRC Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester , 131 Princess Street, Manchester, M1 7DN, United Kingdom
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22
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Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
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