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Yildiz I. Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase. Chemphyschem 2023; 24:e202300431. [PMID: 37540527 DOI: 10.1002/cphc.202300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.
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Affiliation(s)
- Ibrahim Yildiz
- Khalifa University, Chemistry Department and Applied Material Chemistry Center (AMCC), PO Box, 127788, Abu Dhabi, UAE
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2
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Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry 2023; 62:1070-1081. [PMID: 36795942 PMCID: PMC9996824 DOI: 10.1021/acs.biochem.2c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric regulation: residues located far from the active site can exert long-range dynamical effects on the active site residues to modulate catalysis. The structure of Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) shows four loops (L1, L2, L3, and L4) that span the substrate and the FAD-binding domains. Loop L4 comprises residues 329-336, spanning over the flavin cofactor. The I335 residue on loop L4 is ∼10 Å away from the active site and ∼3.8 Å from N(1)-C(2)═O atoms of the flavin. In this study, we used molecular dynamics and biochemical techniques to investigate the effect of the mutation of I335 to histidine on the catalytic function of PaDADH. Molecular dynamics showed that the conformational dynamics of PaDADH are shifted to a more closed conformation in the I335H variant. In agreement with an enzyme that samples more in a closed conformation, the kinetic data of the I335H variant showed a 40-fold decrease in the rate constant of substrate association (k1), a 340-fold reduction in the rate constant of substrate dissociation from the enzyme-substrate complex (k2), and a 24-fold decrease in the rate constant of product release (k5), compared to that of the wild-type. Surprisingly, the kinetic data are consistent with the mutation having a negligible effect on the reactivity of the flavin. Altogether, the data indicate that the residue at position 335 has a long-range dynamical effect on the catalytic function in PaDADH.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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3
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Qu G, Sun Z. In Silico Prediction Methods for Site-Saturation Mutagenesis. Methods Mol Biol 2022; 2397:49-69. [PMID: 34813059 DOI: 10.1007/978-1-0716-1826-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Directed enzyme evolution has proven to be a powerful means to endow biocatalysts with novel catalytic repertoires. Apart from completely random gene mutagenesis, site-directed or site-saturation mutagenesis requires a semi-rational selection of the amino acid positions or the substituted residues, which can dramatically reduce the screening efforts in protein engineering. To this end, in silico prediction methods play a pivotal role in targeting site-saturation mutagenesis. In this chapter, we provide two distinct computational methods, (a) conformational dynamics-guided design and (b) protein-ligand interaction fingerprinting analysis, to identify specific positions for site-saturation mutagenesis toward manipulating substrate specificity/stereoselectivity of an alcohol dehydrogenase, and improving activity of a carboxylic acid reductase, respectively.
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Affiliation(s)
- Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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4
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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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5
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Gao S, Thompson EJ, Barrow SL, Zhang W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis. J Am Chem Soc 2020; 142:19936-19949. [PMID: 33181018 DOI: 10.1021/jacs.0c07866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are intrinsically flexible macromolecules that undergo internal motions with time scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the optimization of reaction barriers for enzyme catalyzed reactions. Time, temperature, and mutation dependent hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has been previously employed to identify spatially resolved, catalysis-linked dynamical regions of enzymes. We now extend this technique to pursue the correlation of protein flexibility and chemical reactivity within the diverse and widespread TIM barrel proteins, targeting murine adenosine deaminase (mADA) that catalyzes the irreversible deamination of adenosine to inosine and ammonia. Following a structure-function analysis of rate and activation energy for a series of mutations at a second sphere phenylalanine positioned in proximity to the bound substrate, the catalytically impaired Phe61Ala with an elevated activation energy (Ea = 7.5 kcal/mol) and the wild type (WT) mADA (Ea = 5.0 kcal/mol) were selected for HDX-MS experiments. The rate constants and activation energies of HDX for peptide segments are quantified and used to assess mutation-dependent changes in local and distal motions. Analyses reveal that approximately 50% of the protein sequence of Phe61Ala displays significant changes in the temperature dependence of HDX behaviors, with the dominant change being an increase in protein flexibility. Utilizing Phe61Ile, which displays the same activation energy for kcat as WT, as a control, we were able to further refine the HDX analysis, highlighting the regions of mADA that are altered in a functionally relevant manner. A map is constructed that illustrates the regions of protein that are proposed to be essential for the thermal optimization of active site configurations that dominate reaction barrier crossings in the native enzyme.
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Affiliation(s)
| | | | | | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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6
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Pagano P, Guo Q, Ranasinghe C, Schroeder E, Robben K, Häse F, Ye H, Wickersham K, Aspuru-Guzik A, Major DT, Gakhar L, Kohen A, Cheatum CM. Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase. ACS Catal 2019; 9:11199-11206. [PMID: 33996196 PMCID: PMC8118594 DOI: 10.1021/acscatal.9b03345] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Thermal motions of enzymes have been invoked to explain the temperature dependence of kinetic isotope effects (KIE) in enzyme-catalyzed hydride transfers. Formate dehydrogenase (FDH) from Candida boidinii exhibits a temperature independent KIE that becomes temperature dependent upon mutation of hydrophobic residues in the active site. Ternary complexes of FDH that mimic the transition state structure allow investigation of how these mutations influence active-site dynamics. A combination of X-ray crystallography, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamic simulations characterize the structure and dynamics of the active site. FDH exhibits oscillatory frequency fluctuations on the picosecond timescale, and the amplitude of these fluctuations correlates with the temperature dependence of the KIE. Both the kinetic and dynamic phenomena can be reproduced computationally. These results provide experimental evidence for a connection between the temperature dependence of KIEs and motions of the active site in an enzyme-catalyzed reaction consistent with activated tunneling models of the hydride transfer reaction.
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Affiliation(s)
- Philip Pagano
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Evan Schroeder
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kevin Robben
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Florian Häse
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Hepeng Ye
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Kyle Wickersham
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
- Senior Fellow, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario M5G 1Z8, Canada
| | - Dan T. Major
- Chemistry Department, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, United States
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7
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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: 10] [Impact Index Per Article: 2.0] [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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8
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Liu B, Qu G, Li J, Fan W, Ma J, Xu Y, Nie Y, Sun Z. Conformational Dynamics‐Guided Loop Engineering of an Alcohol Dehydrogenase: Capture, Turnover and Enantioselective Transformation of Difficult‐to‐Reduce Ketones. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900249] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Beibei Liu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Ge Qu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐Kuan Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Wenchao Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jun‐An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, and Tianjin Collaborative Innovation Center of Chemical Science and EngineeringTianjin University Tianjin 300072 People's Republic of China
| | - Yan Xu
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Yao Nie
- School of Biotechnology, Key laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi 214122 People's Republic of China
| | - Zhoutong Sun
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 West 7th Avenue, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
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9
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Pozzi C, Lopresti L, Tassone G, Mangani S. Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules 2019; 24:molecules24081638. [PMID: 31027295 PMCID: PMC6514825 DOI: 10.3390/molecules24081638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023] Open
Abstract
In cells, thymidylate synthases provide the only de novo source of 2′-deoxythymidine-5′-monophosphate (dTMP), required for DNA synthesis. The activity of these enzymes is pivotal for cell survival and proliferation. Two main families of thymidylate synthases have been identified in bacteria, folate-dependent thymidylate synthase (TS) and flavin-dependent TS (FDTS). TS and FDTS are highly divergent enzymes, characterized by exclusive catalytic mechanisms, involving different sets of cofactors. TS and FDTS mechanisms of action have been recently revised, providing new perspectives for the development of antibacterial drugs targeting these enzymes. Nonetheless, some catalytic details still remain elusive. For bacterial TSs, half-site reactivity is still an open debate and the recent evidences are somehow controversial. Furthermore, different behaviors have been identified among bacterial TSs, compromising the definition of common mechanisms. Moreover, the redox reaction responsible for the regeneration of reduced flavin in FDTSs is not completely clarified. This review describes the recent advances in the structural and functional characterization of bacterial TSs and FDTSs and the current understanding of their mechanisms of action. Furthermore, the recent progresses in the development of inhibitors targeting TS and FDTS in human pathogenic bacteria are summarized.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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10
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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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11
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Gurevic I, Islam Z, Świderek K, Trepka K, Ghosh AK, Moliner V, Kohen A. Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase. ACS Catal 2018; 8:10241-10253. [PMID: 31275729 DOI: 10.1021/acscatal.8b02554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TSase), an enzyme responsible for the de novo biosynthesis of 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) necessary for DNA synthesis, has been a drug target for decades. TSase is a highly conserved enzyme across species ranging from very primitive organisms to mammals. Among the many conserved active site residues, an asparagine (N177, using Escherichia coli residues numbering) appears to make direct hydrogen bonds with both the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate and its pyrimidine ring's N3. Recent studies have reassessed the TSase catalytic mechanism, focusing on the degree of negative charge accumulation at the O4 carbonyl of the substrate during two critical H-transfers - a proton abstraction and a hydride transfer. To obtain insights into the role of this conserved N177 on the hydride transfer, we examined its aspartic acid (D) and serine (S) mutants - each of which is expected to alter hydrogen bonding and charge stabilization around the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate. Steady-state kinetics, substrate binding order studies and temperature-dependency analysis of intrinsic KIEs for the hydride transfer step of the TSase catalytic cycle suggest the active site of N177D is not precisely organized for that step. A smaller disruption was observed for N177S, which could be rationalized by partial compensation by water molecules and rearrangement of other residues toward preparation of the system for the hydride transfer under study. These experimental findings are qualitatively mirrored by QM/MM computational simulations, thereby shedding light on the sequence and synchronicity of steps in the TSase-catalyzed reaction. This information could potentially inform the design of mechanism-based drugs targeting this enzyme.
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Affiliation(s)
- Ilya Gurevic
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Zahidul Islam
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Kai Trepka
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Ananda K. Ghosh
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
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12
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Finer-Moore JS, Lee TT, Stroud RM. A Single Mutation Traps a Half-Sites Reactive Enzyme in Midstream, Explaining Asymmetry in Hydride Transfer. Biochemistry 2018; 57:2786-2795. [PMID: 29717875 DOI: 10.1021/acs.biochem.8b00176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In Escherichia coli thymidylate synthase (EcTS), rate-determining hydride transfer from the cofactor 5,10-methylene-5,6,7,8-tetrahydrofolate to the intermediate 5-methylene-2'-deoxyuridine 5'-monophosphate occurs by hydrogen tunneling, requiring precise alignment of reactants and a closed binding cavity, sealed by the C-terminal carboxyl group. Mutations that destabilize the closed conformation of the binding cavity allow small molecules such as β-mercaptoethanol (β-ME) to enter the active site and compete with hydride for addition to the 5-methylene group of the intermediate. The C-terminal deletion mutant of EcTS produced the β-ME adduct in proportions that varied dramatically with cofactor concentration, from 50% at low cofactor concentrations to 0% at saturating cofactor conditions, suggesting communication between active sites. We report the 2.4 Å X-ray structure of the C-terminal deletion mutant of E. coli TS in complex with a substrate and a cofactor analogue, CB3717. The structure is asymmetric, with reactants aligned in a manner consistent with hydride transfer in only one active site. In the second site, CB3717 has shifted to a site where the normal cofactor would be unlikely to form 5-methylene-2'-deoxyuridine 5'-monophosphate, consistent with no formation of the β-ME adduct. The structure shows how the binding of the cofactor at one site triggers hydride transfer and borrows needed stabilization from substrate binding at the second site. It indicates pathways through the dimer interface that contribute to allostery relevant to half-sites reactivity.
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Affiliation(s)
- Janet S Finer-Moore
- Department of Biochemistry and Biophysics , University of California , San Francisco , California 94143-2240 , United States
| | - Tom T Lee
- Department of Biochemistry and Biophysics , University of California , San Francisco , California 94143-2240 , United States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics , University of California , San Francisco , California 94143-2240 , United States
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13
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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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14
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Boehr DD, D'Amico RN, O'Rourke KF. Engineered control of enzyme structural dynamics and function. Protein Sci 2018; 27:825-838. [PMID: 29380452 DOI: 10.1002/pro.3379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/20/2022]
Abstract
Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions. Post-translational covalent modification can provide an additional level of enzyme control. These studies have not only provided insights into the functional role of protein motions, but they offer opportunities to create stimulus-responsive enzymes. These enzymes can be engineered to respond to a number of external stimuli, including light, pH, and the presence of novel allosteric modulators. Altogether, the ability to engineer and control enzyme structural dynamics can provide new tools for biotechnology and medicine.
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Affiliation(s)
- David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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15
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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16
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Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1470-1478. [PMID: 28843728 DOI: 10.1016/j.bbapap.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/20/2022]
Abstract
The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[2H4]-choline as a substrate. The limiting rate constants klim1 and klim2 at saturating substrate were well separated (klim1/klim2>9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that klim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that klim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the klim1 and klim2 values increased with increasing temperature, allowing for the analyses of H+ and H- transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the klim1 value (H2Oklim1/D2Oklim1) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the klim2 value gave lines with the slope(choline)>slope(D-choline), suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed.
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17
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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18
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Catalano A, Luciani R, Carocci A, Cortesi D, Pozzi C, Borsari C, Ferrari S, Mangani S. X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors. Eur J Med Chem 2016; 123:649-664. [PMID: 27517810 DOI: 10.1016/j.ejmech.2016.07.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022]
Abstract
Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design.
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Affiliation(s)
- Alessia Catalano
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Rosaria Luciani
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Alessia Carocci
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy
| | - Debora Cortesi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Chiara Borsari
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefania Ferrari
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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19
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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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20
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Kholodar SA, Kohen A. Noncovalent Intermediate of Thymidylate Synthase: Fact or Fiction? J Am Chem Soc 2016; 138:8056-9. [PMID: 27327197 DOI: 10.1021/jacs.6b03826] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase is an attractive target for antibiotic and anticancer drugs due to its essential role in the de novo biosynthesis of the DNA nucleotide thymine. The enzymatic reaction is initiated by a nucleophilic activation of the substrate via formation of a covalent bond to an active site cysteine. The traditionally accepted mechanism is then followed by a series of covalently bound intermediates, where that bond is only cleaved upon product release. Recent computational and experimental studies suggest that the covalent bond between the protein and substrate is actually quite labile. Importantly, these findings predict the existence of a noncovalently bound bisubstrate intermediate, not previously anticipated, which could be the target of a novel class of drugs inhibiting DNA biosynthesis. Here we report the synthesis of the proposed intermediate and findings supporting its chemical and kinetic competence. These findings substantiate the predicted nontraditional mechanism and the potential of this intermediate as a new drug lead.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
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21
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Guo Q, Gakhar L, Wickersham K, Francis K, Vardi-Kilshtain A, Major DT, Cheatum CM, Kohen A. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry 2016; 55:2760-71. [PMID: 27100912 DOI: 10.1021/acs.biochem.6b00181] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.
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Affiliation(s)
- Qi Guo
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Kyle Wickersham
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Kevin Francis
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Alexandra Vardi-Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Dan T Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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22
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Abeysinghe T, Hong B, Wang Z, Kohen A. Preserved hydride transfer mechanism in evolutionarily divergent thymidylate synthases. CURRENT TOPICS IN BIOCHEMICAL RESEARCH 2016; 17:19-30. [PMID: 28018055 PMCID: PMC5172458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Thymidylate synthase (TSase) catalyzes a hydride transfer in the last step of the de novo biosynthesis of the DNA nucleotide thymine. We compared two isozymes, namely, TSase from Escherichia coli (ecTSase) and TSase from Bacillus subtilis (bsTSase) that represent a case of divergent evolution. Interestingly, a highly conserved histidine (H147 of ecTSase) was proposed to serve a critical role in catalysis, but in bsTSase it is naturally substituted by valine (Val). Yet, bsTSase is more active than ecTSase, and the intrinsic kinetic isotope effects (KIEs) of both are temperature-independent, suggesting a similarly well-organized transition state (TS) for the catalyzed hydride transfer. To examine the role of that histidine (His) in TSase catalysis, we examined the kinetics of H147V ecTSase, which "bridges" between these two TSases. In contrast to both wild-type TSases, the single mutation results in deficient catalysis. The mutation leads to intrinsic KIEs that are temperature-dependent, indicating a substantial imperfection in its TS. The findings reveal two important features: a direct role of H147 in the hydride transfer step catalyzed by the ecTSase and the evolutionary compensation for its deficiency in bsTSase via extensive polymorphism across the protein. Very different active site residues are observed for these evolutionarily divergent isozymes, which result in a well-organized TS for both. It is suggested that evolutionary pressure compensated for the H to V substitution at the active site of bsTSase by polymorphism leading to a well-organized TS in both enzymes.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Baoyu Hong
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Genentech, South San Francisco, CA 94080, USA
| | - Zhen Wang
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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23
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Islam Z, Strutzenberg TS, Ghosh AK, Kohen A. Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction. ACS Catal 2015; 5:6061-6068. [PMID: 26576323 PMCID: PMC4643671 DOI: 10.1021/acscatal.5b01332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2'-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry2013, 52, 2348-2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc.2011, 133, 6692-6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design.
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Affiliation(s)
- Zahidul Islam
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | | | - Ananda K. Ghosh
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
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24
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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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25
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Thomas K, Cameron SA, Almo SC, Burgos ES, Gulab SA, Schramm VL. Active site and remote contributions to catalysis in methylthioadenosine nucleosidases. Biochemistry 2015; 54:2520-9. [PMID: 25806409 PMCID: PMC4485437 DOI: 10.1021/bi501487w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5'-Methylthioadenosine/S-adenosyl-l-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5'-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. We mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation of altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. The overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences.
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Affiliation(s)
- Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Scott A. Cameron
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Emmanuel S. Burgos
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Shivali A. Gulab
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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26
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Abeysinghe T, Kohen A. Role of long-range protein dynamics in different thymidylate synthase catalyzed reactions. Int J Mol Sci 2015; 16:7304-19. [PMID: 25837629 PMCID: PMC4425018 DOI: 10.3390/ijms16047304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 02/01/2023] Open
Abstract
Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function.
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Affiliation(s)
- Thelma Abeysinghe
- 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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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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28
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Singh P, Abeysinghe T, Kohen A. Linking protein motion to enzyme catalysis. Molecules 2015; 20:1192-209. [PMID: 25591120 PMCID: PMC4341894 DOI: 10.3390/molecules20011192] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/07/2015] [Indexed: 12/01/2022] Open
Abstract
Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes—dihydrofolate reductase (DHFR) and thymidylate synthase (TSase)—and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs) and their temperature dependence as tools in probing such phenomena.
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Affiliation(s)
- Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA.
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29
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Meadows C, Tsang JE, Klinman JP. Picosecond-resolved fluorescence studies of substrate and cofactor-binding domain mutants in a thermophilic alcohol dehydrogenase uncover an extended network of communication. J Am Chem Soc 2014; 136:14821-33. [PMID: 25314615 PMCID: PMC4210157 DOI: 10.1021/ja506667k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 01/18/2023]
Abstract
Time-resolved fluorescence dynamics are investigated in two mutants of a thermophilic alcohol dehydrogenase (ht-ADH): Y25A (at the dimer interface) and V260A (at the cofactor-binding domain). These residues, ca. 32 Å apart, are shown to exhibit opposing low-temperature effects on the hydride tunneling step. Using single-tryptophan constructs at the active site (Trp87) and a remote, surface-exposed site (Trp167), time-dependent Stokes shifts and collisional quenching data allow an analysis of intra-protein dynamical communication. A double mutant, Y25A:V260A, was also inserted into each single-Trp construct and analyzed accordingly. None of the mutations affect fluorescence lifetimes, Stokes shift relaxation rates, and quenching data for the surface-exposed Trp167 to an appreciable extent. By contrast, fluorescent probes of the active-site tryptophan 87 reveal distinctive forms of dynamical communication. Stokes shifts show that the distal Y25A increases active-site flexibility, V260A introduces a temperature-dependent equilibration process not previously reported by such measurements, and the double mutant (Y25A:V260A) eliminates the temperature-dependent transition sensed by the active-site tryptophan in the presence of V260A. Collisional quenching data at Trp87 further show a structural change in the active-site environment/solvation for V260A. In the aggregate, the temperature dependencies of the fluorescence data are distinct from the breaks in behavior previously reported for catalysis and hydrogen/deuterium exchange, attributed to time scales for the interconversion of protein conformational substates that are slower and more global than the local motions monitored within. An extended network of dynamical communication between the protein dimer surface and substrate- and cofactor-binding domains emerges from the flourescent data.
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Affiliation(s)
- Corey
W. Meadows
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Jonathan E. Tsang
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
| | - Judith P. Klinman
- Department of Chemistry, Department of Molecular and Cell
Biology, and the California
Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States
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30
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Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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31
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Gobeil SMC, Clouthier CM, Park J, Gagné D, Berghuis AM, Doucet N, Pelletier JN. Maintenance of native-like protein dynamics may not be required for engineering functional proteins. ACTA ACUST UNITED AC 2014; 21:1330-1340. [PMID: 25200606 DOI: 10.1016/j.chembiol.2014.07.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 06/27/2014] [Accepted: 07/09/2014] [Indexed: 12/16/2022]
Abstract
Proteins are dynamic systems, and understanding dynamics is critical for fully understanding protein function. Therefore, the question of whether laboratory engineering has an impact on protein dynamics is of general interest. Here, we demonstrate that two homologous, naturally evolved enzymes with high degrees of structural and functional conservation also exhibit conserved dynamics. Their similar set of slow timescale dynamics is highly restricted, consistent with evolutionary conservation of a functionally important feature. However, we also show that dynamics of a laboratory-engineered chimeric enzyme obtained by recombination of the two homologs exhibits striking difference on the millisecond timescale, despite function and high-resolution crystal structure (1.05 Å) being conserved. The laboratory-engineered chimera is thus functionally tolerant to modified dynamics on the timescale of catalytic turnover. Tolerance to dynamic variation implies that maintenance of native-like protein dynamics may not be required when engineering functional proteins.
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Affiliation(s)
- Sophie M C Gobeil
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Biochimie, Université de Montréal, Montréal QC H3T 1J4, Canada
| | - Christopher M Clouthier
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Chimie, Université de Montréal, Montréal QC H3T 1J4, Canada
| | - Jaeok Park
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Department of Biochemistry and Department of Microbiology and Immunology, McGill University, Montreal QC H3G 1Y6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada
| | - Donald Gagné
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada; INRS-Institut Armand-Frappier, Université du Québec, Laval QC H7V 1B7, Canada
| | - Albert M Berghuis
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Department of Biochemistry and Department of Microbiology and Immunology, McGill University, Montreal QC H3G 1Y6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada
| | - Nicolas Doucet
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada; INRS-Institut Armand-Frappier, Université du Québec, Laval QC H7V 1B7, Canada
| | - Joelle N Pelletier
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Biochimie, Université de Montréal, Montréal QC H3T 1J4, Canada; Département de Chimie, Université de Montréal, Montréal QC H3T 1J4, Canada; Center for Green Chemistry and Catalysis (CCVC), Montréal QC H3A 0B8, Canada.
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32
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Islam Z, Strutzenberg TS, Gurevic I, Kohen A. Concerted versus stepwise mechanism in thymidylate synthase. J Am Chem Soc 2014; 136:9850-3. [PMID: 24949852 PMCID: PMC4105062 DOI: 10.1021/ja504341g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) catalyzes the intracellular de novo formation of thymidylate (a DNA building block) in most living organisms, making it a common target for chemotherapeutic and antibiotic drugs. Two mechanisms have been proposed for the rate-limiting hydride transfer step in TSase catalysis: a stepwise mechanism in which the hydride transfer precedes the cleavage of the covalent bond between the enzymatic cysteine and the product and a mechanism where both happen concertedly. Striking similarities between the enzyme-bound enolate intermediates formed in the initial and final step of the reaction supported the first mechanism, while QM/MM calculations favored the concerted mechanism. Here, we experimentally test these two possibilities using secondary kinetic isotope effect (KIE), mutagenesis study, and primary KIEs. The findings support the concerted mechanism and demonstrate the critical role of an active site arginine in substrate binding, activation of enzymatic nucleophile, and the hydride transfer studied here. The elucidation of this reduction/substitution sheds light on the critical catalytic step in TSase and may aid future drug or biomimetic catalyst design.
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Affiliation(s)
- Zahidul Islam
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
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33
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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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34
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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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35
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Liu CT, Wang L, Goodey NM, Hanoian P, Benkovic SJ. Temporally overlapped but uncoupled motions in dihydrofolate reductase catalysis. Biochemistry 2013; 52:5332-4. [PMID: 23883151 DOI: 10.1021/bi400858m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Temporal correlations between protein motions and enzymatic reactions are often interpreted as evidence for catalytically important motions. Using dihydrofolate reductase as a model system, we show that there are many protein motions that temporally overlapped with the chemical reaction, and yet they do not exhibit the same kinetic behaviors (KIE and pH dependence) as the catalyzed chemical reaction. Thus, despite the temporal correlation, these motions are not directly coupled to the chemical transformation, and they might represent a different part of the catalytic cycle or simply be the product of the intrinsic flexibility of the protein.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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36
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Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A. Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J Am Chem Soc 2013; 135:7583-92. [PMID: 23611499 PMCID: PMC3674108 DOI: 10.1021/ja400761x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thelma Abeysinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Calvin Luzum
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Janet S. Finer-Moore
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M. Stroud
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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37
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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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38
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Abstract
There is a wide gap between the generation of large-scale biological data sets and more-detailed, structural and mechanistic studies. However, recent studies that explicitly combine data from systems and structural biological approaches are having a profound effect on our ability to predict how mutations and small molecules affect atomic-level mechanisms, disrupt systems-level networks, and ultimately lead to changes in organismal fitness. In fact, we argue that a shared framework for analysis of nonadditive genetic and thermodynamic responses to perturbations will accelerate the integration of reductionist and global approaches. A stronger bridge between these two areas will allow for a deeper and more-complete understanding of complex biological phenomenon and ultimately provide needed breakthroughs in biomedical research.
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Affiliation(s)
- James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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39
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Wang Z, Ferrer S, Moliner V, Kohen A. QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase. Biochemistry 2013; 52:2348-58. [PMID: 23464672 DOI: 10.1021/bi400267q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cleavage of covalent C-H bonds is one of the most energetically demanding, yet biologically essential, chemical transformations. Two C-H bond cleavages are involved in the reaction catalyzed by thymidylate synthase (TSase), which provides the sole de novo source of thymidylate (i.e., the DNA base T) for most organisms. Our QM/MM free energy calculations show that the C-H → O proton transfer has three transition states that are energetically similar but structurally diverse. These characteristics are different from our previous calculation results on the C-H → C hydride transfer, providing an explanation for differences in temperature dependences of KIEs on these two C-H bond activation steps. The calculations also suggest that the traditionally proposed covalent bond between the protein and substrate (the C6-S bond) is very labile during the multistep catalytic reaction. Collective protein motions not only assist cleavage of the C6-S bond to stabilize the transition state of the proton transfer step but also rearrange the H-bond network at the end of this step to prepare the active site for subsequent chemical steps. These computational results illustrate functionalities of specific protein residues that reconcile many previous experimental observations and provide guidance for future experiments to examine the proposed mechanisms. The synchronized conformational changes in the protein and ligands observed in our simulations demonstrate participation of protein motions in the reaction coordinate of enzymatic reactions. Our computational findings suggest the existence of new reaction intermediates not covalently bound to TSase, which may lead to a new class of drugs targeting DNA biosynthesis.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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