1
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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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2
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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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3
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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4
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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5
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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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6
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Meisner J, Kästner J. Atom Tunneling in Chemistry. Angew Chem Int Ed Engl 2016; 55:5400-13. [DOI: 10.1002/anie.201511028] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/08/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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7
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Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
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8
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Francis K, Sapienza PJ, Lee AL, Kohen A. The Effect of Protein Mass Modulation on Human Dihydrofolate Reductase. Biochemistry 2016; 55:1100-6. [PMID: 26813442 DOI: 10.1021/acs.biochem.5b00945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) from Escherichia coli has long served as a model enzyme with which to elucidate possible links between protein dynamics and the catalyzed reaction. Such physical properties of its human counterpart have not been rigorously studied so far, but recent computer-based simulations suggest that these two DHFRs differ significantly in how closely coupled the protein dynamics and the catalyzed C-H → C hydride transfer step are. To test this prediction, two contemporary probes for studying the effect of protein dynamics on catalysis were combined here: temperature dependence of intrinsic kinetic isotope effects (KIEs), which are sensitive to the physical nature of the chemical step, and protein mass modulation, which slows down fast dynamics (femto- to picosecond time scale) throughout the protein. The intrinsic H/T KIEs of human DHFR, like those of E. coli DHFR, are shown to be temperature-independent in the range from 5 to 45 °C, indicating fast sampling of donor and acceptor distances (DADs) at the reaction's transition state (or tunneling ready state, TRS). Mass modulation of these enzymes through isotopic labeling with (13)C, (15)N, and (2)H at nonexchangeable hydrogens yields an 11% heavier enzyme. The additional mass has no effect on the intrinsic KIEs of the human enzyme. This finding indicates that the mass modulation of the human DHFR affects neither DAD distribution nor the DAD's conformational sampling dynamics. Furthermore, reduction in the enzymatic turnover number and the dissociation rate constant for the product indicate that the isotopic substitution affects kinetic steps that are not the catalyzed C-H → C hydride transfer. The findings are discussed in terms of fast dynamics and their role in catalysis, the comparison of calculations and experiments, and the interpretation of isotopically modulated heavy enzymes in general.
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Affiliation(s)
- Kevin Francis
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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9
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Abstract
Dihydrofolate reductase from
Escherichia coli (ecDHFR) serves as a model system for investigating the role of protein dynamics in enzyme catalysis. We discuss calculations predicting a network of dynamic motions that is coupled to the chemical step catalyzed by this enzyme. Kinetic studies testing these predictions are presented, and their potential use in better understanding the role of these dynamics in enzyme catalysis is considered. The cumulative results implicate motions across the entire protein in catalysis.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA, USA
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10
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Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:70-6. [PMID: 26321598 DOI: 10.1016/j.bbapap.2015.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/07/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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11
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Singh P, Francis K, Kohen A. Network of remote and local protein dynamics in dihydrofolate reductase catalysis. ACS Catal 2015; 5:3067-3073. [PMID: 27182453 DOI: 10.1021/acscatal.5b00331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics calculations and bionformatic studies of dihydrofolate reductase (DHFR) have suggested a network of coupled motions across the whole protein that is correlated to the reaction coordinate. Experimental studies demonstrated that distal residues G121, M42 and F125 in E. coli DHFR participate in that network. The missing link in our understanding of DHFR catalysis is the lack of a mechanism by which such remote residues can affect the catalyzed chemistry at the active site. Here, we present a study of the temperature dependence of intrinsic kinetic isotope effects (KIEs) that indicates synergism between a remote residue in that dynamic network, G121, and the active site's residue I14. The intrinsic KIEs for the I14A-G121V double mutant showed steeper temperature dependence (ΔEa(T-H)) than expected from comparison of the wild type and two single mutants. That effect was non-additive, i.e., ΔEa(T-H)G121V +ΔEa(T-H) I14A < ΔEa(T-H) double mutant, which indicates a synergism between the two residues. This finding links the remote residues in the network under investigation to the enzyme's active site, providing a mechanism by which these residues can be coupled to the catalyzed chemistry. This experimental evidence validates calculations proposing that both remote and active site residues constitute a network of coupled promoting motions correlated to the bond activation step (C-H→C hydride transfer in this case). Additionally, the effect of I14A and G121V mutations on single turnover rates was additive rather than synergistic. Although single turnover rate measurements are more readily available and thus more popular than assessing intrinsic kinetic isotope effects, the current finding demonstrates that for these rates, which in DHFR reflect several microscopic rate constants, can fall short of revealing the nature of the C-H bond activation per se.
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Affiliation(s)
- Priyanka Singh
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Kevin Francis
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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12
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Abstract
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The role of the enzyme’s dynamic motions
in catalysis is at the center of heated contemporary debates among
both theoreticians and experimentalists. Resolving these apparent
disputes is of both intellectual and practical importance: incorporation
of enzyme dynamics could be critical for any calculation of enzymatic
function and may have profound implications for structure-based drug
design and the design of biomimetic catalysts. Analysis of the
literature suggests that while part of the dispute may reflect substantial
differences between theoretical approaches, much of the debate is
semantic. For example, the term “protein dynamics” is
often used by some researchers when addressing motions that are in
thermal equilibrium with their environment, while other researchers
only use this term for nonequilibrium events. The last cases are those
in which thermal energy is “stored” in a specific protein
mode and “used” for catalysis before it can dissipate
to its environment (i.e., “nonstatistical dynamics”).
This terminology issue aside, a debate has arisen among theoreticians
around the roles of nonstatistical vs statistical dynamics in catalysis.
However, the author knows of no experimental findings available today
that examined this question in enzyme catalyzed reactions. Another
source of perhaps nonsubstantial argument might stem from the varying
time scales of enzymatic motions, which range from seconds to femtoseconds.
Motions at different time scales play different roles in the many
events along the catalytic cascade (reactant binding, reprotonation
of reactants, structural rearrangement toward the transition state,
product release, etc.). In several cases, when various experimental
tools have been used to probe catalytic events at differing time scales,
illusory contradictions seem to have emerged. In this Account, recent
attempts to sort the merits of those questions are discussed along
with possible future directions. A possible summary of current
studies could be that enzyme, substrate, and solvent dynamics contribute
to enzyme catalyzed reactions in several ways: first via mutual “induced-fit”
shifting of their conformational ensemble upon binding; then via thermal
search of the conformational space toward the reaction’s transition-state
(TS) and the rare event of the barrier crossing toward products, which
is likely to be on faster time scales then the first and following
events; and finally via the dynamics associated with products release,
which are rate-limiting for many enzymatic reactions. From a chemical
perspective, close to the TS, enzymatic systems seem to stiffen, restricting
motions orthogonal to the chemical coordinate and enabling dynamics
along the reaction coordinate to occur selectively. Studies of how
enzymes evolved to support those efficient dynamics at various time
scales are still in their infancy, and further experiments and calculations
are needed to reveal these phenomena in both enzymes and uncatalyzed
reactions.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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13
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Liu CT, Francis K, Layfield JP, Huang X, Hammes-Schiffer S, Kohen A, Benkovic SJ. Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: temporal order and the roles of Asp27 and Tyr100. Proc Natl Acad Sci U S A 2014; 111:18231-6. [PMID: 25453098 PMCID: PMC4280594 DOI: 10.1073/pnas.1415940111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) has become a model for understanding enzyme catalysis, and yet several details of its mechanism are still unresolved. Specifically, the mechanism of the chemical step, the hydride transfer reaction, is not fully resolved. We found, unexpectedly, the presence of two reactive ternary complexes [enzyme:NADPH:7,8-dihydrofolate (E:NADPH:DHF)] separated by one ionization event. Furthermore, multiple kinetic isotope effect (KIE) studies revealed a stepwise mechanism in which protonation of the DHF precedes the hydride transfer from the nicotinamide cofactor (NADPH) for both reactive ternary complexes of the WT enzyme. This mechanism was supported by the pH- and temperature-independent intrinsic KIEs for the C-H→C hydride transfer between NADPH and the preprotonated DHF. Moreover, we showed that active site residues D27 and Y100 play a synergistic role in facilitating both the proton transfer and subsequent hydride transfer steps. Although D27 appears to have a greater effect on the overall rate of conversion of DHF to tetrahydrofolate, Y100 plays an important electrostatic role in modulating the pKa of the N5 of DHF to enable the preprotonation of DHF by an active site water molecule.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Xinyi Huang
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801-3364
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242; and
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802;
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14
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Francis K, Kohen A. Protein motions and the activation of the CH bond catalyzed by dihydrofolate reductase. Curr Opin Chem Biol 2014; 21:19-24. [PMID: 24742825 PMCID: PMC4149937 DOI: 10.1016/j.cbpa.2014.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/03/2014] [Accepted: 03/05/2014] [Indexed: 11/28/2022]
Abstract
The role of protein motions in enzymatic CH→C transfer is an area of great contemporary debate. An effective tool in probing such a role is the temperature dependence of the intrinsic kinetic isotope effects for the enzyme-catalyzed reaction. The outcome of those experiments is interpreted within the context of phenomenological Marcus-like models of hydrogen tunneling. The current review focuses on recent studies of dihydrofolate reductase (DHFR) and how the role of protein motions in the catalyzed reaction has been demonstrated. The motions in DHFR are controlled by local effects of active site residues, global effects involving remote residues across the enzyme and appear to be preserved during the evolution of the enzyme from bacteria to human.
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Affiliation(s)
- Kevin Francis
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, United States.
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15
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Wang Z, Singh P, Czekster CM, Kohen A, Schramm VL. Protein mass-modulated effects in the catalytic mechanism of dihydrofolate reductase: beyond promoting vibrations. J Am Chem Soc 2014; 136:8333-41. [PMID: 24820793 PMCID: PMC4063187 DOI: 10.1021/ja501936d] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The role of fast protein dynamics
in enzyme catalysis has been
of great interest in the past decade. Recent “heavy enzyme”
studies demonstrate that protein mass-modulated vibrations are linked
to the energy barrier for the chemical step of catalyzed reactions.
However, the role of fast dynamics in the overall catalytic mechanism
of an enzyme has not been addressed. Protein mass-modulated effects
in the catalytic mechanism of Escherichia coli dihydrofolate
reductase (ecDHFR) are explored by isotopic substitution (13C, 15N, and non-exchangeable 2H) of the wild-type
ecDHFR (l-DHFR) to generate a vibrationally perturbed
“heavy ecDHFR” (h-DHFR). Steady-state,
pre-steady-state, and ligand binding kinetics, intrinsic kinetic isotope
effects (KIEint) on the chemical step, and thermal unfolding
experiments of both l- and h-DHFR
show that the altered protein mass affects the conformational ensembles
and protein–ligand interactions, but does not affect the hydride
transfer at physiological temperatures (25–45 °C). Below
25 °C, h-DHFR shows altered transition state
(TS) structure and increased barrier-crossing probability of the chemical
step compared with l-DHFR, indicating temperature-dependent
protein vibrational coupling to the chemical step. Protein mass-modulated
vibrations in ecDHFR are involved in TS interactions at cold temperatures
and are linked to dynamic motions involved in ligand binding at physiological
temperatures. Thus, mass effects can affect enzymatic catalysis beyond
alterations in promoting vibrations linked to chemistry.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
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16
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Francis K, Kohen A. Standards for the reporting of kinetic isotope effects in enzymology. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Roston D, Islam Z, Kohen A. Kinetic isotope effects as a probe of hydrogen transfers to and from common enzymatic cofactors. Arch Biochem Biophys 2014; 544:96-104. [PMID: 24161942 PMCID: PMC3946509 DOI: 10.1016/j.abb.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Enzymes use a number of common cofactors as sources of hydrogen to drive biological processes, but the physics of the hydrogen transfers to and from these cofactors is not fully understood. Researchers study the mechanistically important contributions from quantum tunneling and enzyme dynamics and connect those processes to the catalytic power of enzymes that use these cofactors. Here we describe some progress that has been made in studying these reactions, particularly through the use of kinetic isotope effects (KIEs). We first discuss the general theoretical framework necessary to interpret experimental KIEs, and then describe practical uses for KIEs in the context of two case studies. The first example is alcohol dehydrogenase, which uses a nicotinamide cofactor to catalyze a hydride transfer, and the second example is thymidylate synthase, which uses a folate cofactor to catalyze both a hydride and a proton transfer.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Zahidul Islam
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA.
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18
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Singh P, Sen A, Francis K, Kohen A. Extension and limits of the network of coupled motions correlated to hydride transfer in dihydrofolate reductase. J Am Chem Soc 2014; 136:2575-82. [PMID: 24450297 PMCID: PMC3985941 DOI: 10.1021/ja411998h] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Enzyme catalysis
has been studied extensively, but the role of
enzyme dynamics in the catalyzed chemical conversion is still an enigma.
The enzyme dihydrofolate reductase (DHFR) is often used as a model
system to assess a network of coupled motions across the protein that
may affect the catalyzed chemical transformation. Molecular dynamics
simulations, quantum mechanical/molecular mechanical studies, and
bioinformatics studies have suggested the presence of a “global
dynamic network” of residues in DHFR. Earlier studies of two
DHFR distal mutants, G121V and M42W, indicated that these residues
affect the chemical step synergistically. While this finding was in
accordance with the concept of a network of functional motions across
the protein, two residues do not constitute a network. To better define
the extent and limits of the proposed network, the current work studied
two remote residues predicted to be part of the same network: W133
and F125. The effect of mutations in these residues on the nature
of the chemical step was examined via measurements of the temperature-dependence
of the intrinsic kinetic isotope effects (KIEs) and other kinetic
parameters, and double mutants were used to tie the findings to G121
and M42. The findings indicate that residue F125, which was implicated
by both calculations and bioinformatic methods, is a part of the same
global dynamic network as G121 and M42, while W133, implicated only
by bioinformatics, is not. These findings extend our understanding
of the proposed network and the relations between functional and genomic
couplings. Delineating that network illuminates the need to consider
remote residues and protein structural dynamics in the rational design
of drugs and of biomimetic catalysts.
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Affiliation(s)
- Priyanka Singh
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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19
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Francis K, Stojković V, Kohen A. Preservation of protein dynamics in dihydrofolate reductase evolution. J Biol Chem 2013; 288:35961-8. [PMID: 24158440 PMCID: PMC3861645 DOI: 10.1074/jbc.m113.507632] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/09/2013] [Indexed: 11/06/2022] Open
Abstract
The hydride transfer reaction catalyzed by dihydrofolate reductase (DHFR) is a model for examining how protein dynamics contribute to enzymatic function. The relationship between functional motions and enzyme evolution has attracted significant attention. Recent studies on N23PP Escherichia coli DHFR (ecDHFR) mutant, designed to resemble parts of the human enzyme, indicated a reduced single turnover rate. NMR relaxation dispersion experiments with that enzyme showed rigidification of millisecond Met-20 loop motions (Bhabha, G., Lee, J., Ekiert, D. C., Gam, J., Wilson, I. A., Dyson, H. J., Benkovic, S. J., and Wright, P. E. (2011) Science 332, 234-238). A more recent study of this mutant, however, indicated that fast motions along the reaction coordinate are actually more dispersed than for wild-type ecDHFR (WT). Furthermore, a double mutant (N23PP/G51PEKN) that better mimics the human enzyme seems to restore both the single turnover rates and narrow distribution of fast dynamics (Liu, C. T., Hanoian, P., French, T. H., Hammes-Schiffer, S., and Benkovic, S. J. (2013) Proc. Natl. Acad. Sci. U.S.A. 110, 10159-11064). Here, we measured intrinsic kinetic isotope effects for both N23PP and N23PP/G51PEKN double mutant DHFRs over a temperature range. The findings indicate that although the C-H→C transfer and dynamics along the reaction coordinate are impaired in the altered N23PP mutant, both seem to be restored in the N23PP/G51PEKN double mutant. This indicates that the evolution of G51PEKN, although remote from the Met-20 loop, alleviated the loop rigidification that would have been caused by N23PP, enabling WT-like H-tunneling. The correlation between the calculated dynamics, the nature of C-H→C transfer, and a phylogenetic analysis of DHFR sequences are consistent with evolutionary preservation of the protein dynamics to enable H-tunneling from well reorganized active sites.
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Affiliation(s)
- Kevin Francis
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Vanja Stojković
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Amnon Kohen
- From the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
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Advances in kinetic isotope effect measurement techniques for enzyme mechanism study. Molecules 2013; 18:9278-92. [PMID: 23917115 PMCID: PMC6270257 DOI: 10.3390/molecules18089278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
Kinetic isotope effects (KIEs) are a very powerful tool for investigating enzyme mechanisms. Precision of measurement is the most important factor for KIE determinations, especially for small heavy atom KIEs. Internal competition is commonly used to measure small KIEs on V/K. Several methods, including such as liquid scintillation counting, mass spectrometry, nuclear magnetic resonance spectroscopy and polarimetry have been used to determine KIEs. In this paper, which does not aspire to be an exhaustive review, we briefly review different experimental approaches for the measurement of KIEs on enzymatic reaction with an emphasis on newer techniques employing mass spectrometry and nuclear magnetic resonance spectrometry as well as some corresponding examples.
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21
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Roston D, Islam Z, Kohen A. Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions. Molecules 2013; 18:5543-67. [PMID: 23673528 PMCID: PMC4342783 DOI: 10.3390/molecules18055543] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/16/2022] Open
Abstract
Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers.
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Affiliation(s)
| | | | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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22
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Cheatum CM, Kohen A. Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer. Top Curr Chem (Cham) 2013; 337:1-39. [PMID: 23539379 PMCID: PMC4699684 DOI: 10.1007/128_2012_407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H → C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes.
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Experimental and theoretical studies of enzyme-catalyzed hydrogen-transfer reactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [PMID: 22607755 DOI: 10.1016/b978-0-12-398312-1.00006-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The mechanisms of enzyme-catalyzed reactions are medicinally important and present a fascinating intellectual challenge. Many experimental and theoretical techniques can shed light on these mechanisms, and here, we shall focus on the utility of kinetic isotope effects (KIEs) to study enzymatic reactions that involve hydrogen transfers. We will provide a short background on the prevailing models to interpret KIEs and then present more detailed reviews of two model enzymes: alcohol dehydrogenase and thymidylate synthase. These two examples provide a context to describe the types of experiments and theoretical calculations that drive this field forward and the kind of information each can furnish. We emphasize the importance of cooperation between experimentalists and theoreticians to continue the progress toward a comprehensive theory of enzyme catalysis.
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Sen A, Stojković V, Kohen A. Synthesis of radiolabeled nicotinamide cofactors from labeled pyridines: versatile probes for enzyme kinetics. Anal Biochem 2012; 430:123-9. [PMID: 22922383 DOI: 10.1016/j.ab.2012.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/07/2012] [Accepted: 08/14/2012] [Indexed: 11/30/2022]
Abstract
(14)C-labeled nicotinamide cofactors are widely employed in biomedical investigations, for example, to delineate metabolic pathways, to elucidate enzymatic mechanisms, and as substrates in kinetic isotope effect (KIE) experiments. The (14)C label has generally been located remote from the reactive position, frequently at the adenine ring. Rising costs of commercial precursors and disruptions in the availability of enzymes required for established syntheses have recently made the preparation of labeled nicotinamides such as [Ad-(14)C]NADPH unviable. Here, we report the syntheses and characterization of several alternatives: [carbonyl-(14)C]NADPH, 4R-[carbonyl-(14)C, 4-(2)H]NADPH, and [carbonyl-(14)C, 4-(2)H(2)]NADPH. The new procedures use [carbonyl-(14)C]nicotinamide as starting material, because it is significantly cheaper than other commercial (14)C precursors of NADPH, and require only one commercially available enzyme to prepare NAD(P)(+) and NAD(P)H. The proximity of carbonyl-(14)C to the reactive center raises the risk of an inopportune (14)C isotope effect. This concern has been alleviated via competitive KIE measurements with Escherichia coli dihydrofolate reductase (EcDHFR) that use this specific carbonyl-(14)C NADPH. A combination of binding isotope effect and KIE measurements yielded no significant (12)C/(14)C isotope effect at the amide carbonyl (KIE=1.003±0.004). The reported procedure provides a high-yield, high-purity, and cost-effective alternative to labeled nicotinamide cofactors synthesized by previously published routes.
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Affiliation(s)
- Arundhuti Sen
- Department of Chemistry, University of Iowa, Iowa City, IA 52245, USA
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