1
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McDonald AG, Tipton KF. Parameter Reliability and Understanding Enzyme Function. Molecules 2022; 27:263. [PMID: 35011495 PMCID: PMC8746786 DOI: 10.3390/molecules27010263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge of the Michaelis-Menten parameters and their meaning in different circumstances is an essential prerequisite to understanding enzyme function and behaviour. The published literature contains an abundance of values reported for many enzymes. The problem concerns assessing the appropriateness and validity of such material for the purpose to which it is to be applied. This review considers the evaluation of such data with particular emphasis on the assessment of its fitness for purpose.
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Affiliation(s)
- Andrew G. McDonald
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland;
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2
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Raich L, Meier K, Günther J, Christ CD, Noé F, Olsson S. Discovery of a hidden transient state in all bromodomain families. Proc Natl Acad Sci U S A 2021; 118:e2017427118. [PMID: 33468647 PMCID: PMC7848705 DOI: 10.1073/pnas.2017427118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These posttranslational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov state modeling, and available structural data to reveal a transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated to histone binding. By analyzing more than 1,900 experimental structures, we unveil just two adopting the hidden state, explaining why it has been previously unnoticed and providing direct structural evidence for its existence. Our results suggest that this state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA-binding mode.
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Affiliation(s)
- Lluís Raich
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Katharina Meier
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 42096 Wuppertal, Germany
| | - Judith Günther
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Clara D Christ
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
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3
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Allomorphy as a mechanism of post-translational control of enzyme activity. Nat Commun 2020; 11:5538. [PMID: 33139716 PMCID: PMC7608592 DOI: 10.1038/s41467-020-19215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Enzyme regulation is vital for metabolic adaptability in living systems. Fine control of enzyme activity is often delivered through post-translational mechanisms, such as allostery or allokairy. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for complete catabolism of trehalose and maltose, through the isomerisation of β-glucose 1-phosphate to glucose 6-phosphate via β-glucose 1,6-bisphosphate. Surprisingly for a gatekeeper of glycolysis, no fine control mechanism of βPGM has yet been reported. Herein, we describe allomorphy, a post-translational control mechanism of enzyme activity. In βPGM, isomerisation of the K145-P146 peptide bond results in the population of two conformers that have different activities owing to repositioning of the K145 sidechain. In vivo phosphorylating agents, such as fructose 1,6-bisphosphate, generate phosphorylated forms of both conformers, leading to a lag phase in activity until the more active phosphorylated conformer dominates. In contrast, the reaction intermediate β-glucose 1,6-bisphosphate, whose concentration depends on the β-glucose 1-phosphate concentration, couples the conformational switch and the phosphorylation step, resulting in the rapid generation of the more active phosphorylated conformer. In enabling different behaviours for different allomorphic activators, allomorphy allows an organism to maximise its responsiveness to environmental changes while minimising the diversion of valuable metabolites. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for catabolism of trehalose and maltose. Coupled analyses of multiple βPGM structures and enzymatic activity lead to the proposal of allomorphy — a post-translational mechanism controlling enzyme activity.
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4
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Abstract
NMR spectroscopy and other solution methods are increasingly being used to obtain novel insights into the mechanisms by which MAPK regulatory proteins bind and direct the activity of MAPKs. Here, we describe how interactions between the MAPK p38α and its regulatory proteins are studied using NMR spectroscopy, isothermal titration calorimetry, and small angle X-ray scattering (SAXS).
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Affiliation(s)
- Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02912, USA. .,Department of Chemistry, Brown University, Providence, RI, 02912, USA.
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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5
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Konermann L. Addressing a Common Misconception: Ammonium Acetate as Neutral pH "Buffer" for Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1827-1835. [PMID: 28710594 DOI: 10.1007/s13361-017-1739-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 05/12/2023]
Abstract
Native ESI-MS involves the transfer of intact proteins and biomolecular complexes from solution into the gas phase. One potential pitfall is the occurrence of pH-induced changes that can affect the analyte while it is still surrounded by solvent. Most native ESI-MS studies employ neutral aqueous ammonium acetate solutions. It is a widely perpetuated misconception that ammonium acetate buffers the analyte solution at neutral pH. By definition, a buffer consists of a weak acid and its conjugate weak base. The buffering range covers the weak acid pKa ± 1 pH unit. NH4+ and CH3-COO- are not a conjugate acid/base pair, which means that they do not constitute a buffer at pH 7. Dissolution of ammonium acetate salt in water results in pH 7, but this pH is highly labile. Ammonium acetate does provide buffering around pH 4.75 (the pKa of acetic acid) and around pH 9.25 (the pKa of ammonium). This implies that neutral ammonium acetate solutions electrosprayed in positive ion mode will likely undergo acidification down to pH 4.75 ± 1 in the ESI plume. Ammonium acetate nonetheless remains a useful additive for native ESI-MS. It is a volatile electrolyte that can mimic the solvation properties experienced by proteins under physiological conditions. Also, a drop from pH 7 to around pH 4.75 is less dramatic than the acidification that would take place in pure water. It is hoped that the habit of referring to pH 7 solutions as ammonium acetate "buffer" will disappear from the literature. Ammonium acetate "solution" should be used instead. Graphical Abstract ᅟ.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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6
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Hüttner S, Klaubauf S, de Vries RP, Olsson L. Characterisation of three fungal glucuronoyl esterases on glucuronic acid ester model compounds. Appl Microbiol Biotechnol 2017; 101:5301-5311. [PMID: 28429057 PMCID: PMC5486812 DOI: 10.1007/s00253-017-8266-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/12/2017] [Accepted: 03/27/2017] [Indexed: 01/07/2023]
Abstract
The glucuronoyl esterases (GEs) that have been identified so far belong to family 15 of the carbohydrate esterases in the CAZy classification system and are presumed to target ester bonds between lignin alcohols and (4-O-methyl-)d-glucuronic acid residues of xylan. Few GEs have been cloned, expressed and characterised to date. Characterisation has been done on a variety of synthetic substrates; however, the number of commercially available substrates is very limited. We identified novel putative GEs from a wide taxonomic range of fungi and expressed the enzymes originating from Acremonium alcalophilum and Wolfiporia cocos as well as the previously described PcGE1 from Phanerochaete chrysosporium. All three fungal GEs were active on the commercially available compounds benzyl glucuronic acid (BnGlcA), allyl glucuronic acid (allylGlcA) and to a lower degree on methyl glucuronic acid (MeGlcA). The enzymes showed pH stability over a wide pH range and tolerated 6-h incubations of up to 50 °C. Kinetic parameters were determined for BnGlcA. This study shows the suitability of the commercially available model compounds BnGlcA, MeGlcA and allylGlcA in GE activity screening and characterisation experiments. We enriched the spectrum of characterised GEs with two new members of a relatively young enzyme family. Due to its biotechnological significance, this family deserves to be more extensively studied. The presented enzymes are promising candidates as auxiliary enzymes to improve saccharification of plant biomass.
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Affiliation(s)
- Silvia Hüttner
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Sylvia Klaubauf
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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7
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Olsson S, Noé F. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR. J Am Chem Soc 2016; 139:200-210. [DOI: 10.1021/jacs.6b09460] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Simon Olsson
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
| | - Frank Noé
- Computational Molecular
Biology,
FB Mathematik und Informatik, Freie Universität Berlin, Berlin 14195, Germany
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8
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Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg 2+ Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B 2016; 120:12420-12431. [PMID: 27973819 DOI: 10.1021/acs.jpcb.6b08323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article communicates our study to elucidate the molecular determinants of weak Mg2+ interaction with the ribonuclease H (RNH) domain of HIV-1 reverse transcriptase in solution. As the interaction is weak (a ligand-dissociation constant >1 mM), nonspecific Mg2+ interaction with the protein or interaction of the protein with other solutes that are present in the buffer solution can confound the observed Mg2+-titration data. To investigate these indirect effects, we monitored changes in the chemical shifts of backbone amides of RNH by recording NMR 1H-15N heteronuclear single-quantum coherence spectra upon titration of Mg2+ into an RNH solution. We performed the titration under three different conditions: (1) in the absence of NaCl, (2) in the presence of 50 mM NaCl, and (3) at a constant 160 mM Cl- concentration. Careful analysis of these three sets of titration data, along with molecular dynamics simulation data of RNH with Na+ and Cl- ions, demonstrates two characteristic phenomena distinct from the specific Mg2+ interaction with the active site: (1) weak interaction of Mg2+, as a salt, with the substrate-handle region of the protein and (2) overall apparent lower Mg2+ affinity in the absence of NaCl compared to that in the presence of 50 mM NaCl. A possible explanation may be that the titrated MgCl2 is consumed as a salt and interacts with RNH in the absence of NaCl. In addition, our data suggest that Na+ increases the kinetic rate of the specific Mg2+ interaction at the active site of RNH. Taken together, our study provides biophysical insight into the mechanism of weak metal interaction on a protein.
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Affiliation(s)
- Ichhuk Karki
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Martin T Christen
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Justin Spiriti
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Ryan L Slack
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Masayuki Oda
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Kenji Kanaori
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Daniel M Zuckerman
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
| | - Rieko Ishima
- Department of Structural Biology and ‡Department of Computational and Systems Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University and ⊥Department of Biomolecular Engineering, Kyoto Institute of Technology , Kyoto 606, Japan
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9
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Kozak S, Lercher L, Karanth MN, Meijers R, Carlomagno T, Boivin S. Optimization of protein samples for NMR using thermal shift assays. JOURNAL OF BIOMOLECULAR NMR 2016; 64:281-9. [PMID: 26984476 PMCID: PMC4869703 DOI: 10.1007/s10858-016-0027-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/08/2016] [Indexed: 05/09/2023]
Abstract
Maintaining a stable fold for recombinant proteins is challenging, especially when working with highly purified and concentrated samples at temperatures >20 °C. Therefore, it is worthwhile to screen for different buffer components that can stabilize protein samples. Thermal shift assays or ThermoFluor(®) provide a high-throughput screening method to assess the thermal stability of a sample under several conditions simultaneously. Here, we describe a thermal shift assay that is designed to optimize conditions for nuclear magnetic resonance studies, which typically require stable samples at high concentration and ambient (or higher) temperature. We demonstrate that for two challenging proteins, the multicomponent screen helped to identify ingredients that increased protein stability, leading to clear improvements in the quality of the spectra. Thermal shift assays provide an economic and time-efficient method to find optimal conditions for NMR structural studies.
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Affiliation(s)
- Sandra Kozak
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lukas Lercher
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Megha N Karanth
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Rob Meijers
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany
| | - Teresa Carlomagno
- SCB Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.
- Research Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Brunswick, Germany.
| | - Stephane Boivin
- SPC Facility, European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607, Hamburg, Germany.
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10
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Abstract
Nucleic acid crystallization buffers contain a large variety of chemicals fitting specific needs. Among them, anions are often solely considered for pH-regulating purposes and as cationic co-salts while their ability to directly bind to nucleic acid structures is rarely taken into account. Here we review current knowledge related to the use of anions in crystallization buffers along with data on their biological prevalence. Chloride ions are frequently identified in crystal structures but display low cytosolic concentrations. Hence, they are thought to be distant from nucleic acid structures in the cell. Sulfate ions are also frequently identified in crystal structures but their localization in the cell remains elusive. Nevertheless, the characterization of the binding properties of these ions is essential for better interpreting the solvent structure in crystals and consequently, avoiding mislabeling of electron densities. Furthermore, understanding the binding properties of these anions should help to get clues related to their potential effects in crowded cellular environments.
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Affiliation(s)
- Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, UPR 9002 CNRS/Université de Strasbourg, 15, rue René Descartes, Strasbourg Cedex, 67084, France
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11
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Oyen D, Fenwick RB, Stanfield RL, Dyson HJ, Wright PE. Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway. J Am Chem Soc 2015; 137:9459-68. [PMID: 26147643 PMCID: PMC4521799 DOI: 10.1021/jacs.5b05707] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/29/2022]
Abstract
The enzyme dihydrofolate reductase (DHFR, E) from Escherichia coli is a paradigm for the role of protein dynamics in enzyme catalysis. Previous studies have shown that the enzyme progresses through the kinetic cycle by modulating the dynamic conformational landscape in the presence of substrate dihydrofolate (DHF), product tetrahydrofolate (THF), and cofactor (NADPH or NADP(+)). This study focuses on the quantitative description of the relationship between protein fluctuations and product release, the rate-limiting step of DHFR catalysis. NMR relaxation dispersion measurements of millisecond time scale motions for the E:THF:NADP(+) and E:THF:NADPH complexes of wild-type and the Leu28Phe (L28F) point mutant reveal conformational exchange between an occluded ground state and a low population of a closed state. The backbone structures of the occluded ground states of the wild-type and mutant proteins are very similar, but the rates of exchange with the closed excited states are very different. Integrated analysis of relaxation dispersion data and THF dissociation rates measured by stopped-flow spectroscopy shows that product release can occur by two pathways. The intrinsic pathway consists of spontaneous product dissociation and occurs for all THF-bound complexes of DHFR. The allosteric pathway features cofactor-assisted product release from the closed excited state and is utilized only in the E:THF:NADPH complexes. The L28F mutation alters the partitioning between the pathways and results in increased flux through the intrinsic pathway relative to the wild-type enzyme. This repartitioning could represent a general mechanism to explain changes in product release rates in other E. coli DHFR mutants.
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Affiliation(s)
- David Oyen
- Department of Integrative
Structural and Computational Biology and Skaggs Institute for Chemical
Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - R. Bryn Fenwick
- Department of Integrative
Structural and Computational Biology and Skaggs Institute for Chemical
Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Robyn L. Stanfield
- Department of Integrative
Structural and Computational Biology and Skaggs Institute for Chemical
Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H. Jane Dyson
- Department of Integrative
Structural and Computational Biology and Skaggs Institute for Chemical
Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E. Wright
- Department of Integrative
Structural and Computational Biology and Skaggs Institute for Chemical
Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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12
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Tonelli M, Eller CH, Singarapu KK, Lee W, Bahrami A, Westler WM, Raines RT, Markley JL. Assignments of RNase A by ADAPT-NMR and enhancer. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:81-8. [PMID: 24619609 PMCID: PMC4162851 DOI: 10.1007/s12104-014-9549-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 02/28/2014] [Indexed: 05/23/2023]
Abstract
We report here backbone (1)H and (15)N assignments for ribonuclease A obtained by using ADAPT-NMR, a fully-automated approach for combined data collection, spectral analysis and resonance assignment. ADAPT-NMR was able to assign 98% of the resonances with 93% agreement with traditional data collection and assignment. Further refinement of the automated results with ADAPT-NMR enhancer led to complete (100%) assignments with 96% agreement with assignments by the traditional approach.
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Affiliation(s)
- Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI, 53706, USA,
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13
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Khirich G, Loria JP. Complexity of protein energy landscapes studied by solution NMR relaxation dispersion experiments. J Phys Chem B 2015; 119:3743-54. [PMID: 25680027 DOI: 10.1021/acs.jpcb.5b00212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The millisecond time scale motions in ribonuclease A (RNase A) were studied by solution NMR CPMG and off-resonance R1ρ relaxation dispersion experiments over a wide pH and temperature range. These experiments identify three separate protein regions termed Cluster 1, Cluster 2, and R33, whose motions are governed by distinct thermodynamic parameters. Moreover, each of these regions has motions with different pH dependencies. Cluster 1 shows an increase in activation enthalpy and activation entropy as the pH is lowered, whereas Cluster 2 exhibits the opposite behavior. In contrast, the activation enthalpy and entropy of R33 show no pH dependence. Compounding the differences, Δω values for Cluster 2 are characteristic of two-site conformational exchange, yet similar analysis for Cluster 1 indicates that this region of the enzyme exhibits conformational fluctuations between a major conformer and a pH-dependent average of protonated and deprotonated minor conformers.
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Affiliation(s)
- Gennady Khirich
- Department of Chemistry, Yale University , 225 Prospect Street, New Haven, Connecticut 06520, United States
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14
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Abstract
Solution-state NMR has been widely applied to determine the three-dimensional structure, dynamics, and molecular interactions of proteins. The designs of experiments used in protein NMR differ from those used for small-molecule NMR, primarily because the information available prior to an experiment, such as molecular mass and knowledge of the primary structure, is unique for proteins compared to small molecules. In this review article, protein NMR for structural biology is introduced with comparisons to small-molecule NMR, such as descriptions of labeling strategies and the effects of molecular dynamics on relaxation. Next, applications for protein NMR are reviewed, especially practical aspects for protein-observed ligand-protein interaction studies. Overall, the following topics are described: (1) characteristics of protein NMR, (2) methods to detect protein-ligand interactions by NMR, and (3) practical aspects of carrying out protein-observed inhibitor-protein interaction studies.
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Affiliation(s)
- Rieko Ishima
- Address correspondence to Rieko Ishima: Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Tel: 412-648-9056; Fax: 412-648-9008;
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15
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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