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Russell PPS, Maytin AK, Rickard MM, Russell MC, Pogorelov TV, Gruebele M. Metastable States in the Hinge-Bending Landscape of an Enzyme in an Atomistic Cytoplasm Simulation. J Phys Chem Lett 2024; 15:940-946. [PMID: 38252018 PMCID: PMC11180962 DOI: 10.1021/acs.jpclett.3c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Many enzymes undergo major conformational changes to function in cells, particularly when they bind to more than one substrate. We quantify the large-amplitude hinge-bending landscape of human phosphoglycerate kinase (PGK) in a human cytoplasm. Approximately 70 μs of all-atom simulations, upon coarse graining, reveal three metastable states of PGK with different hinge angle distributions and additional substates. The "open" state was more populated than the "semi-open" or "closed" states. In addition to free energies and barriers within the landscape, we characterized the average transition state passage time of ≈0.3 μs and reversible substrate and product binding. Human PGK in a dilute solution simulation shows a transition directly from the open to closed states, in agreement with previous SAXS experiments, suggesting that the cell-like model environment promotes stability of the human PGK semi-open state. Yeast PGK also sampled three metastable states within the cytoplasm model, with the closed state favored in our simulation.
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Affiliation(s)
| | - Andrew K. Maytin
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Meredith M. Rickard
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Matthew C. Russell
- Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
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2
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Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase. Proc Natl Acad Sci U S A 2021; 118:2112986118. [PMID: 34893542 DOI: 10.1073/pnas.2112986118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP]) ratio controls glycolytic flux; however, the regulatory mechanism underlying reactions catalyzed by individual glycolytic enzymes enabling flux adaptation remains incompletely understood. Phosphoglycerate kinase (PGK) catalyzes the reversible phosphotransfer reaction, which directly produces ATP in a near-equilibrium step of glycolysis. Despite extensive studies on the transcriptional regulation of PGK expression, the mechanism in response to changes in the [ATP]/[ADP] ratio remains obscure. Here, we report a protein-level regulation of human PGK (hPGK) by utilizing the switching ligand-binding cooperativities between adenine nucleotides and 3-phosphoglycerate (3PG). This was revealed by nuclear magnetic resonance (NMR) spectroscopy at physiological salt concentrations. MgADP and 3PG bind to hPGK with negative cooperativity, whereas MgAMPPNP (a nonhydrolyzable ATP analog) and 3PG bind to hPGK with positive cooperativity. These opposite cooperativities enable a shift between different ligand-bound states depending on the intracellular [ATP]/[ADP] ratio. Based on these findings, we present an atomic-scale description of the reaction scheme for hPGK under physiological conditions. Our results indicate that hPGK intrinsically modulates its function via ligand-binding cooperativities that are finely tuned to respond to changes in the [ATP]/[ADP] ratio. The alteration of ligand-binding cooperativities could be one of the self-regulatory mechanisms for enzymes in bidirectional pathways, which enables rapid adaptation to changes in the intracellular environment.
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3
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Ciepluch K, Radulescu A, Hoffmann I, Raba A, Allgaier J, Richter D, Biehl R. Influence of PEGylation on Domain Dynamics of Phosphoglycerate Kinase: PEG Acts Like Entropic Spring for the Protein. Bioconjug Chem 2018; 29:1950-1960. [DOI: 10.1021/acs.bioconjchem.8b00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Karol Ciepluch
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, 85748 Garching, Germany
| | - Ingo Hoffmann
- Institute Laue-Langevin (ILL), 71 rue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Andreas Raba
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jürgen Allgaier
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Richter
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
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4
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Franke D, Jeffries CM, Svergun DI. Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra. Nat Methods 2015; 12:419-22. [PMID: 25849637 DOI: 10.1038/nmeth.3358] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 02/18/2015] [Indexed: 01/10/2023]
Abstract
Assessing similarity between data sets with the reduced χ(2) test requires the estimation of experimental errors, which, if incorrect, may render statistical comparisons invalid. We report a goodness-of-fit test, Correlation Map (CorMap), for assessing differences between one-dimensional spectra independently of explicit error estimates, using only data point correlations. Using small-angle X-ray scattering data, we demonstrate that CorMap maintains the power of the reduced χ(2) test; moreover, CorMap is also applicable to other physical experiments.
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Affiliation(s)
- Daniel Franke
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
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5
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Palmai Z, Seifert C, Gräter F, Balog E. An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis. PLoS Comput Biol 2014; 10:e1003444. [PMID: 24465199 PMCID: PMC3900376 DOI: 10.1371/journal.pcbi.1003444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/03/2013] [Indexed: 11/18/2022] Open
Abstract
3-Phosphogycerate kinase (PGK) is a two domain enzyme, which transfers a phosphate group between its two substrates, 1,3-bisphosphoglycerate bound to the N-domain and ADP bound to the C-domain. Indispensable for the phosphoryl transfer reaction is a large conformational change from an inactive open to an active closed conformation via a hinge motion that should bring substrates into close proximity. The allosteric pathway resulting in the active closed conformation has only been partially uncovered. Using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA), we describe an allosteric pathway, which connects the substrate binding sites to the interdomain hinge region. Glu192 of alpha-helix 7 and Gly394 of loop L14 act as hinge points, at which these two secondary structure elements straighten, thereby moving the substrate-binding domains towards each other. The long-range allosteric pathway regulating hPGK catalytic activity, which is partially validated and can be further tested by mutagenesis, highlights the virtue of monitoring internal forces to reveal signal propagation, even if only minor conformational distortions, such as helix bending, initiate the large functional rearrangement of the macromolecule. 3-Phosphoglycerate kinase (PGK) is an essential enzyme for living organisms. It catalyzes the phospho-transfer reaction between two catabolites during carbohydrate metabolism. In addition to this physiological role, human PGK has been shown to phosphorylate L-nucleoside analogues, potential drugs against viral infection and cancer. PGK is a two domain enzyme, with the two substrates bound to the two separate domains. In order to perform its function the enzyme has to undergo a large conformational change involving a hinge bending to bring the substrates into close proximity. The allosteric pathway from the open non-reactive state of PGK to the closed reactive state as triggered by substrate binding has only been partially uncovered by experimental studies. Here we describe a complete allosteric pathway, which connects the substrate binding sites to the interdomain hinge region using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA). While previously identified key residues involved in PGK domain closure are part of this pathway, we here fill the numerous gaps in the pathway by identifying newly uncovered residues and interesting candidates for future mutational studies.
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Affiliation(s)
- Zoltan Palmai
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Christian Seifert
- Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany
| | - Frauke Gräter
- Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany
- MPG-CAS Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
- * E-mail: (FG); (EB)
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail: (FG); (EB)
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6
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Crystal structure of shrimp arginine kinase in binary complex with arginine—a molecular view of the phosphagen precursor binding to the enzyme. J Bioenerg Biomembr 2013; 45:511-8. [DOI: 10.1007/s10863-013-9521-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/03/2013] [Indexed: 12/20/2022]
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7
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Rivas-Pardo JA, Herrera-Morande A, Castro-Fernandez V, Fernandez FJ, Vega MC, Guixé V. Crystal structure, SAXS and kinetic mechanism of hyperthermophilic ADP-dependent glucokinase from Thermococcus litoralis reveal a conserved mechanism for catalysis. PLoS One 2013; 8:e66687. [PMID: 23818958 PMCID: PMC3688580 DOI: 10.1371/journal.pone.0066687] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Thermococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.
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Affiliation(s)
| | - Alejandra Herrera-Morande
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, España
| | | | | | | | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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8
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Conformational dynamics in phosphoglycerate kinase, an open and shut case? FEBS Lett 2013; 587:1878-83. [DOI: 10.1016/j.febslet.2013.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/06/2013] [Indexed: 01/24/2023]
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9
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Varga A, Palmai Z, Gugolya Z, Gráczer É, Vonderviszt F, Závodszky P, Balog E, Vas M. Importance of aspartate residues in balancing the flexibility and fine-tuning the catalysis of human 3-phosphoglycerate kinase. Biochemistry 2012; 51:10197-207. [PMID: 23231058 DOI: 10.1021/bi301194t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The exact role of the metal ion, usually Mg(2+), in the catalysis of human 3-phosphoglycerate kinase, a well-studied two-domain enzyme, has not been clarified. Here we have prepared single and double alanine mutants of the potential metal-binding residues, D374 and D218. While all mutations weaken the catalytic interactions with Mg(2+), they surprisingly strengthen binding of both MgADP and MgATP, and the effects are even more pronounced for ADP and ATP. Thermodynamic parameters of binding indicate an increase in the binding entropy as a reason for the strengthening. In agreement with the experimental results, computer-simulated annealing calculations for the complexes of these mutants have supported the mobility of the nucleotide phosphates and, as a consequence, formation of their new interaction(s) within the active site. A similar type of mobility is suggested to be a characteristic feature of the nucleotide site of the wild-type enzyme, too, both in its inactive open conformation and in the active closed conformation. This mobility of the nucleotide phosphates that is regulated by the aspartate side chains of D218 and D374 through the complexing Mg(2+) is suggested to be essential in enzyme function.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary.
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10
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Varga A, Gráczer E, Chaloin L, Liliom K, Závodszky P, Lionne C, Vas M. Selectivity of kinases on the activation of tenofovir, an anti-HIV agent. Eur J Pharm Sci 2012. [PMID: 23201309 DOI: 10.1016/j.ejps.2012.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nucleoside analogues, used in HIV-therapy, need to be phosphorylated by cellular enzymes in order to become potential substrates for HIV reverse transcriptase. After incorporation into the viral DNA chain, because of lacking of their 3'-hydroxyl groups, they stop the elongation process and lead to the death of the virus. Phosphorylation of the HIV-drug derivative, tenofovir monophosphate was tested with the recombinant mammalian nucleoside diphosphate kinase (NDPK), 3-phosphoglycerate kinase (PGK), creatine kinase (CK) and pyruvate kinase (PK). Among them, only CK was found to phosphorylate tenofovir monophosphate with a reasonable rate (about 45-fold lower than with its natural substrate, ADP), while PK exhibits even lower, but still detectable activity (about 1000-fold lower compared to the value with ADP). On the other hand, neither NDPK nor PGK has any detectable activity on tenofovir monophosphate. The absence of activity with PGK is surprising, since the drug tenofovir competitively inhibits both CK and PGK towards their nucleotide substrates, with similar inhibitory constants, K(I) of 2.9 and 4.8mM, respectively. Computer modelling (docking) of tenofovir mono- or diphosphate forms to these four kinases suggests that the requirement of large-scale domain closure for functioning (as for PGK) may largely restrict their applicability for phosphorylation/activation of pro-drugs having a structure similar to tenofovir monophosphate.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary.
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11
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Schofield J, Inder P, Kapral R. Modeling of solvent flow effects in enzyme catalysis under physiological conditions. J Chem Phys 2012; 136:205101. [PMID: 22667589 DOI: 10.1063/1.4719539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.
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Affiliation(s)
- Jeremy Schofield
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
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12
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Roychowdhury A, Mukherjee S, Das AK. Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate kinase from methicillin-resistant Staphylococcus aureus MRSA252. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:668-71. [PMID: 21636907 PMCID: PMC3107138 DOI: 10.1107/s1744309111007391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 02/26/2011] [Indexed: 11/10/2022]
Abstract
Phosphoglycerate kinase (PGK) from methicillin-resistant Staphylococcus aureus MRSA252 has been cloned in pQE30 expression vector, overexpressed in Escherichia coli SG13009 (pREP4) cells and purified to homogeneity. The protein was crystallized from 0.15 M CaCl(2), 0.1 M HEPES-NaOH pH 6.8, 20%(w/v) polyethylene glycol 2000 at 298 K by the hanging-drop vapour-diffusion method. The crystals belonged to space group P2(1), with unit-cell parameters a = 45.14, b = 74.75, c = 58.67 Å, β = 95.72°. X-ray diffraction data have been collected and processed to a maximum resolution of 2.3 Å. The presence of one molecule in the asymmetric unit gives a Matthews coefficient (V(M)) of 2.26 Å(3) Da(-1) with a solvent content of 46%. The structure has been solved by molecular replacement and structure refinement is now in progress.
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Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Somnath Mukherjee
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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Zerrad L, Merli A, Schröder GF, Varga A, Gráczer É, Pernot P, Round A, Vas M, Bowler MW. A spring-loaded release mechanism regulates domain movement and catalysis in phosphoglycerate kinase. J Biol Chem 2011; 286:14040-8. [PMID: 21349853 PMCID: PMC3077604 DOI: 10.1074/jbc.m110.206813] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 02/22/2011] [Indexed: 11/06/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is the enzyme responsible for the first ATP-generating step of glycolysis and has been implicated extensively in oncogenesis and its development. Solution small angle x-ray scattering (SAXS) data, in combination with crystal structures of the enzyme in complex with substrate and product analogues, reveal a new conformation for the resting state of the enzyme and demonstrate the role of substrate binding in the preparation of the enzyme for domain closure. Comparison of the x-ray scattering curves of the enzyme in different states with crystal structures has allowed the complete reaction cycle to be resolved both structurally and temporally. The enzyme appears to spend most of its time in a fully open conformation with short periods of closure and catalysis, thereby allowing the rapid diffusion of substrates and products in and out of the binding sites. Analysis of the open apoenzyme structure, defined through deformable elastic network refinement against the SAXS data, suggests that interactions in a mostly buried hydrophobic region may favor the open conformation. This patch is exposed on domain closure, making the open conformation more thermodynamically stable. Ionic interactions act to maintain the closed conformation to allow catalysis. The short time PGK spends in the closed conformation and its strong tendency to rest in an open conformation imply a spring-loaded release mechanism to regulate domain movement, catalysis, and efficient product release.
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Affiliation(s)
- Louiza Zerrad
- From the Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble, France
| | - Angelo Merli
- the Department of Biochemistry and Molecular Biology, University of Parma, Parco Area delle Scienze, 23/A 43100, Parma, Italy
| | - Gunnar F. Schröder
- the Institute of Structural Biology and Biophysics, Structural Biochemistry, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Andrea Varga
- the Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary, and
| | - Éva Gráczer
- the Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary, and
| | - Petra Pernot
- From the Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble, France
| | - Adam Round
- the European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Mária Vas
- the Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary, and
| | - Matthew W. Bowler
- From the Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble, France
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14
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Varga A, Chaloin L, Sági G, Sendula R, Gráczer E, Liliom K, Závodszky P, Lionne C, Vas M. Nucleotide promiscuity of 3-phosphoglycerate kinase is in focus: implications for the design of better anti-HIV analogues. MOLECULAR BIOSYSTEMS 2011; 7:1863-73. [PMID: 21505655 DOI: 10.1039/c1mb05051f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The wide specificity of 3-phosphoglycerate kinase (PGK) towards its nucleotide substrate is a property that allows contribution of this enzyme to the effective phosphorylation (i.e. activation) of nucleotide-based pro-drugs against HIV. Here, the structural basis of the nucleotide-PGK interaction is characterised in comparison to other kinases, namely pyruvate kinase (PK) and creatine kinase (CK), by enzyme kinetic analysis and structural modelling (docking) studies. The results provided evidence for favouring the purine vs. pyrimidine base containing nucleotides for PGK rather than for PK or CK. This is due to the exceptional ability of PGK in forming the hydrophobic contacts of the nucleotide rings that assures the appropriate positioning of the connected phosphate-chain for catalysis. As for the D-/L-configurations of the nucleotides, the L-forms (both purine and pyrimidine) are well accepted by PGK rather than either by PK or CK. Here again the dominance of the hydrophobic interactions of the L-form of pyrimidines with PGK is underlined in comparison with those of PK or CK. Furthermore, for the l-forms, the absence of the ribose OH-groups with PGK is better tolerated for the purine than for the pyrimidine containing compounds. On the other hand, the positioning of the phosphate-chain is an even more important term for PGK in the case of both purines and pyrimidines with an L-configuration, as deduced from the present kinetic studies with various nucleotide-site mutants of PGK. These characteristics of the kinase-nucleotide interactions can provide a guideline for designing new drugs.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P O Box 7, H-1518 Budapest, Hungary.
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Abstract
Abstract
Small-angle scattering (SAS) of X-rays and neutrons reveals low-resolution structures of biological macromolecules in solution. With the recent experimental and methodological advances, SAS became a unique tool for characterising biological systems. The method covers an extremely broad range of molecule sizes (from a few kDa to hundreds of MDa) and experimental conditions (temperature, pH, salinity, ligand addition, etc.), which is of primary importance for a systemic approach in structural biology. The method provides unique information about the overall structure and conformational changes of native individual proteins, functional complexes, flexible macromolecules and hierarchical systems. New developments in small-angle X-ray and neutron scattering studies of biological macromolecules in solution are briefly reviewed, with a special emphasis on technical and methodological approaches useful for structural systems biology. Possibilities of synergistic use of the method with other techniques are considered.
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16
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Cliff MJ, Bowler MW, Varga A, Marston JP, Szabó J, Hounslow AM, Baxter NJ, Blackburn GM, Vas M, Waltho JP. Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis. J Am Chem Soc 2010; 132:6507-16. [PMID: 20397725 DOI: 10.1021/ja100974t] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition state analogue (TSA) complexes formed by phosphoglycerate kinase (PGK) have been used to test the hypothesis that balancing of charge within the transition state dominates enzyme-catalyzed phosphoryl transfer. High-resolution structures of trifluoromagnesate (MgF(3)(-)) and tetrafluoroaluminate (AlF(4)(-)) complexes of PGK have been determined using X-ray crystallography and (19)F-based NMR methods, revealing the nature of the catalytically relevant state of this archetypal metabolic kinase. Importantly, the side chain of K219, which coordinates the alpha-phosphate group in previous ground state structures, is sequestered into coordinating the metal fluoride, thereby creating a charge environment complementary to the transferring phosphoryl group. In line with the dominance of charge balance in transition state organization, the substitution K219A induces a corresponding reduction in charge in the bound aluminum fluoride species, which changes to a trifluoroaluminate (AlF(3)(0)) complex. The AlF(3)(0) moiety retains the octahedral geometry observed within AlF(4)(-) TSA complexes, which endorses the proposal that some of the widely reported trigonal AlF(3)(0) complexes of phosphoryl transfer enzymes may have been misassigned and in reality contain MgF(3)(-).
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Affiliation(s)
- Matthew J Cliff
- The Krebs Institute & The Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Marston JP, Cliff MJ, Reed MAC, Blackburn GM, Hounslow AM, Craven CJ, Waltho JP. Structural tightening and interdomain communication in the catalytic cycle of phosphoglycerate kinase. J Mol Biol 2010; 396:345-60. [PMID: 19944703 DOI: 10.1016/j.jmb.2009.11.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 11/25/2022]
Abstract
Changes in amide-NH chemical shift and hydrogen exchange rates as phosphoglycerate kinase progresses through its catalytic cycle have been measured to assess whether they correlate with changes in hydrogen bonding within the protein. Four representative states were compared: the free enzyme, a product complex containing 3-phosphoglyceric acid (3PG), a substrate complex containing ADP and a transition-state analogue (TSA) complex containing a 3PG-AlF(4)(-)-ADP moiety. There are an overall increases in amide protection from hydrogen exchange when the protein binds the substrate and product ligands and an additional increase when the TSA complex is formed. This is consistent with stabilisation of the protein structure by ligand binding. However, there is no correlation between the chemical shift changes and the protection factor changes, indicating that the protection factor changes are not associated with an overall shortening of hydrogen bonds in the protected ground state, but rather can be ascribed to the properties of the high-energy, exchange-competent state. Therefore, an overall structural tightening mechanism is not supported by the data. Instead, we observed that some cooperativity is exhibited in the N-domain, such that within this domain the changes induced upon forming the TSA complex are an intensification of those induced by binding 3PG. Furthermore, chemical shift changes induced by 3PG binding extend through the interdomain region to the C-domain beta-sheet, highlighting a network of hydrogen bonds between the domains that suggests interdomain communication. Interdomain communication is also indicated by amide protection in one domain being significantly altered by binding of substrate to the other, even where no associated change in the structure of the substrate-free domain is indicated by chemical shifts. Hence, the communication between domains is also manifested in the accessibility of higher-energy, exchange-competent states. Overall, the data that are consistent with structural tightening relate to defined regions and are close to the 3PG binding site and in the hinge regions of 3-phosphoglycerate kinase.
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Affiliation(s)
- James P Marston
- Department of Molecular Biology and Biotechnology, Firth Court, The University of Sheffield, Western Bank, Sheffield, UK
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18
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Palmai Z, Chaloin L, Lionne C, Fidy J, Perahia D, Balog E. Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study. Proteins 2009; 77:319-29. [DOI: 10.1002/prot.22437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Varga A, Szabó J, Flachner B, Gugolya Z, Vonderviszt F, Závodszky P, Vas M. Thermodynamic analysis of substrate induced domain closure of 3-phosphoglycerate kinase. FEBS Lett 2009; 583:3660-4. [PMID: 19854185 DOI: 10.1016/j.febslet.2009.10.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 10/15/2009] [Accepted: 10/16/2009] [Indexed: 11/26/2022]
Abstract
The energetic changes accompanying domain closure of 3-phosphoglycerate kinase, a typical hinge-bending enzyme, were assessed. Calorimetric titrations of the enzyme with each substrate, both in the absence and presence of the other one, provide information not only about the energetics of substrate binding, but of the associated conformational changes, including domain closure. Our results suggest that conformational rearrangements in the hinge generated by binding of both substrates provide the main driving force for domain closure overcoming the slightly unfavourable contact interactions between the domains.
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Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, PO Box 7, H-1518 Budapest, Hungary
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20
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Varga A, Lionne C, Lallemand P, Szabó J, Adamek N, Valentin C, Vas M, Barman T, Chaloin L. Direct Kinetic Evidence That Lysine 215 Is Involved in the Phospho-Transfer Step of Human 3-Phosphoglycerate Kinase. Biochemistry 2009; 48:6998-7008. [DOI: 10.1021/bi900396h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Varga
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Corinne Lionne
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Perrine Lallemand
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Judit Szabó
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Nancy Adamek
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Christian Valentin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Mária Vas
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Út 29, H-1113 Budapest, Hungary
| | - Tom Barman
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
| | - Laurent Chaloin
- Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS, Université Montpellier 1, Université Montpellier 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier Cedex 2, France
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21
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Communication between the nucleotide site and the main molecular hinge of 3-phosphoglycerate kinase. Biochemistry 2008; 47:6735-44. [PMID: 18540639 DOI: 10.1021/bi800411w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
3-Phosphoglycerate kinase is a hinge-bending enzyme with substrate-assisted domain closure. However, the closure mechanism has not been described in terms of structural details. Here we present experimental evidence of the participation of individual substrate binding side chains in the operation of the main hinge which is distant from the substrate binding sites. The combined mutational, kinetic, and structural (DSC and SAXS) data for human 3-phosphoglycerate kinase have shown that catalytic residue R38, which also binds the substrate 3-phosphoglycerate, is essential in inducing domain closure. Similarly, residues K219, N336, and E343 which interact with the nucleotide substrates are involved in the process of domain closure. The other catalytic residue, K215, covers a large distance during catalysis but has no direct role in domain closure. The transmission path of the nucleotide effect toward the main hinge of PGK is described for the first time at the level of interactions existing in the tertiary structure.
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22
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Szabó J, Varga A, Flachner B, Konarev PV, Svergun DI, Závodszky P, Vas M. Role of side-chains in the operation of the main molecular hinge of 3-phosphoglycerate kinase. FEBS Lett 2008; 582:1335-40. [DOI: 10.1016/j.febslet.2008.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 02/14/2008] [Accepted: 03/12/2008] [Indexed: 11/16/2022]
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23
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Gondeau C, Chaloin L, Varga A, Roy B, Lallemand P, Périgaud C, Barman T, Vas M, Lionne C. Differences in the transient kinetics of the binding of D-ADP and its mirror image L-ADP to human 3-phosphoglycerate kinase revealed by the presence of 3-phosphoglycerate. Biochemistry 2008; 47:3462-73. [PMID: 18288812 DOI: 10.1021/bi7023145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
L-Nucleosides comprise a new class of antiviral and anticancer agents that are converted in vivo by a cascade of kinases to pharmacologically active nucleoside triphosphates. The last step of the cascade may be catalyzed by 3-phosphoglycerate kinase (PGK), an enzyme that has low specificity for nucleoside diphosphate (NDP): NDP + 1,3-bisphosphoglycerate <--> NTP + 3-phosphoglycerate. Here we compared the kinetics of the formation of the complexes of human PGK with d- and its mirror image l-ADP and the effect of 3-phosphoglycerate (PG) on these by exploiting the fluorescence signal of PGK that occurs upon its interaction with nucleotide substrate. Two types of experiment were carried out: equilibrium (estimation of dissociation constants) and stopped-flow (transient kinetics of the interactions). We show that under our experimental conditions (buffer containing 30% methanol, 4 degrees C) PGK binds d- and l-ADP with similar kinetics. However, whereas PG increased the dissociation rate constant for d-ADP by a factor of 8-which is a kinetic explanation for "substrate antagonism"-PG had little effect on this constant for l-ADP. We explain this difference by a molecular modeling study that showed that the beta-phosphates of d- and l-ADP have different orientations when bound to the active site of human PGK. The difference is unexpected because l-ADP is almost as catalytically competent as d-ADP [ Varga, A. et al. (2008) Biochem. Biophys. Res. Commun. 366, 994-1000].
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Affiliation(s)
- Claire Gondeau
- Centre d'tudes d'agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS-Université Montpellier 1-Université Montpellier 2, Montpellier cedex 2, France
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24
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Koch MHJ, Bras W. Synchrotron radiation studies of non-crystalline systems. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b703892p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Interaction of human 3-phosphoglycerate kinase with L-ADP, the mirror image of D-ADP. Biochem Biophys Res Commun 2007; 366:994-1000. [PMID: 18096512 DOI: 10.1016/j.bbrc.2007.12.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 12/10/2007] [Indexed: 11/21/2022]
Abstract
l-Nucleoside-analogues, mirror images of the natural d-nucleosides, are a new class of antiviral and anticancer agents. In the cell they have to be phosphorylated to pharmacologically active triphosphate forms, the last step seems to involve human 3-phosphoglycerate kinase (hPGK). Here we present a steady state kinetic and biophysical study of the interaction of the model compound l-MgADP with hPGK. l-MgADP is a good substrate with k(cat) and K(m) values of 685s(-1) and 0.27mM, respectively. Double inhibition studies suggest that l-MgADP binds to the specific adenosine-binding site and protects the conformation of hPGK molecule against heat denaturation, as detected by microcalorimetry. Structural details of the interaction in the enzyme active site are different for the d- and l-enantiomers (e.g. the effect of Mg(2+)), but these differences do not prevent the occurrence of the catalytic cycle, which is accompanied by the hinge-bending domain closure, as indicated by SAXS measurements.
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26
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White EM, Holland AR, MacDonald G. Infrared studies reveal unique vibrations associated with the PGK-ATP-3-PG ternary complex. Biochemistry 2007; 47:84-91. [PMID: 18078348 DOI: 10.1021/bi701723c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoglycerate kinase (PGK) catalyzes a reversible phospho-transfer reaction between ATP and 3-phosphoglycerate (3-PG) that is thought to require a hinge-bending motion in the protein that brings two separate substrate-binding domains together. We have used difference infrared spectroscopy to better understand the conformational changes that are unique to the PGK-ATP-3-PG complex. Caged nucleotides (caged-ADP and caged-ATP) were used to initiate nucleotide binding to PGK or PGK-3-PG complexes. The difference spectra include those of PGK-ATP minus PGK, PGK-3-PG-ATP minus PGK-3-PG, PGK-3-PG-ADP minus PGK-3-PG, and PGK-ADP minus PGK. The resulting spectra were compared in attempts to identify bands associated with each PGK complex. In addition, complementary activity assays were performed in the presence of caged-nucleotides. While PGK activity decreased in the presence of caged-ADP, the activity was not influenced by the addition of caged-ATP. The activity assay results suggest that the caged-ADP may interact with PGK substrate binding site(s) and inhibit phospho-transfer. Therefore, additional difference infrared nucleotide exchange experiments were used to isolate the differences between ADP and ATP binding to PGK. Difference FTIR spectra obtained on PGK-nucleotide-3-PG complexes show distinct bands that may result from amino acid side chains as well as structural changes in the hinge region and/or increased interactions such as salt bridges forming between the two domains. The infrared data obtained on the active ternary complexes show evidence of changes in alpha-helix and beta-structures as well as signals consistent with Arg, Asn, His, Lys, Asp, Glu, and additional side chains that are uniquely perturbed in the active ternary complex as compared to other PGK complexes.
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Affiliation(s)
- Ellen M White
- Department of Chemistry, James Madison University, Harrisonburg, Virginia 22807, USA
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