1
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Bertrand Q, Coquille S, Iorio A, Sterpone F, Madern D. Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases. J Struct Biol 2023; 215:108039. [PMID: 37884067 DOI: 10.1016/j.jsb.2023.108039] [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: 06/22/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023]
Abstract
In this work, we investigated the lactate dehydrogenase (LDH) from Selenomonas ruminantium (S. rum), an enzyme that differs at key amino acid positions from canonical allosteric LDHs. The wild type (Wt) of this enzyme recognises pyuvate as all LDHs. However, introducing a single point mutation in the active site loop (I85R) allows S. Rum LDH to recognize the oxaloacetate substrate as a typical malate dehydrogenase (MalDH), whilst maintaining homotropic activation as an LDH. We report the tertiary structure of the Wt and I85RLDH mutant. The Wt S. rum enzyme structure binds NADH and malonate, whilst also resembling the typical compact R-active state of canonical LDHs. The structure of the mutant with I85R was solved in the Apo State (without ligand), and shows no large conformational reorganization such as that observed with canonical allosteric LDHs in Apo state. This is due to a local structural feature typical of S. rum LDH that prevents large-scale conformational reorganization. The S. rum LDH was also studied using Molecular Dynamics simulations, probing specific local deformations of the active site that allow the S. rum LDH to sample the T-inactive state. We propose that, with respect to the LDH/MalDH superfamily, the S. rum enzyme possesses a specificstructural and dynamical way to ensure homotropic activation.
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Affiliation(s)
- Quentin Bertrand
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France; Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institut, Villigen, Switzerland
| | | | - Antonio Iorio
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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2
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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3
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Robin AY, Brochier-Armanet C, Bertrand Q, Barette C, Girard E, Madern D. Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery. Mol Biol Evol 2023; 40:msad223. [PMID: 37797308 PMCID: PMC10583557 DOI: 10.1093/molbev/msad223] [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: 07/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023] Open
Abstract
Lactate dehydrogenase (LDH, EC.1.1.127) is an important enzyme engaged in the anaerobic metabolism of cells, catalyzing the conversion of pyruvate to lactate and NADH to NAD+. LDH is a relevant enzyme to investigate structure-function relationships. The present work provides the missing link in our understanding of the evolution of LDHs. This allows to explain (i) the various evolutionary origins of LDHs in eukaryotic cells and their further diversification and (ii) subtle phenotypic modifications with respect to their regulation capacity. We identified a group of cyanobacterial LDHs displaying eukaryotic-like LDH sequence features. The biochemical and structural characterization of Cyanobacterium aponinum LDH, taken as representative, unexpectedly revealed that it displays homotropic and heterotropic activation, typical of an allosteric enzyme, whereas it harbors a long N-terminal extension, a structural feature considered responsible for the lack of allosteric capacity in eukaryotic LDHs. Its crystallographic structure was solved in 2 different configurations typical of the R-active and T-inactive states encountered in allosteric LDHs. Structural comparisons coupled with our evolutionary analyses helped to identify 2 amino acid positions that could have had a major role in the attenuation and extinction of the allosteric activation in eukaryotic LDHs rather than the presence of the N-terminal extension. We tested this hypothesis by site-directed mutagenesis. The resulting C. aponinum LDH mutants displayed reduced allosteric capacity mimicking those encountered in plants and human LDHs. This study provides a new evolutionary scenario of LDHs that unifies descriptions of regulatory properties with structural and mutational patterns of these important enzymes.
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Affiliation(s)
- Adeline Y Robin
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS, UMR5558, Villeurbanne F-69622, France
| | - Quentin Bertrand
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
- Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institut, Villigen, Switzerland
| | - Caroline Barette
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE, Grenoble 38000, France
| | - Eric Girard
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Dominique Madern
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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4
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Maschietto F, Morzan UN, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro GW, Nekrasov P, Brooks B, Loria JP, Rivalta I, Batista VS. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nat Commun 2023; 14:2239. [PMID: 37076500 PMCID: PMC10115891 DOI: 10.1038/s41467-023-37956-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.
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Affiliation(s)
- Federica Maschietto
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
| | - Uriel N Morzan
- International Center for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Florentina Tofoleanu
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
- Treeline Biosciences, 500 Arsenal Street, Watertown, MA, 02472, USA
| | - Aria Gheeraert
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Apala Chaudhuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gregory W Kyro
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Peter Nekrasov
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Bernard Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - J Patrick Loria
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Ivan Rivalta
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France.
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy.
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
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5
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Allosteric transitions of rabbit skeletal muscle lactate dehydrogenase induced by pH-dependent dissociation of the tetrameric enzyme. Biochimie 2022; 199:23-35. [DOI: 10.1016/j.biochi.2022.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/23/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023]
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6
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Yu L, Liu Q, Luo W, Zhao J, Alzan HF, He L. The Structural Basis of Babesia orientalis Lactate Dehydrogenase. Front Cell Infect Microbiol 2022; 11:790101. [PMID: 35071043 PMCID: PMC8766848 DOI: 10.3389/fcimb.2021.790101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Glycolytic enzymes play a crucial role in the anaerobic glycolysis of apicomplexan parasites for energy generation. Consequently, they are considered as potential targets for new drug development. Previous studies revealed that lactate dehydrogenase (LDH), a glycolytic enzyme, is a potential drug target in different parasites, such as Plasmodium, Toxoplasma, Cryptosporidium, and Piroplasma. Herein, in order to investigate the structural basis of LDH in Babesia spp., we determined the crystal structure of apo Babesia orientalis (Bo) LDH at 2.67-Å resolution in the space group P1. A five-peptide insertion appears in the active pocket loop of BoLDH to create a larger catalytic pocket, like other protozoa (except for Babesia microti LDH) and unlike its mammalian counterparts, and the absence of this extra insertion inactivates BoLDH. Without ligands, the apo BoLDH takes R-state (relaxed) with the active-site loop open. This feature is obviously different from that of allosteric LDHs in T-state (tense) with the active-site loop open. Compared with allosteric LDHs, the extra salt bridges and hydrogen bonds make the subunit interfaces of BoLDH more stable, and that results in the absence of T-state. Interestingly, BoLDH differs significantly from BmLDH, as it exhibits the ability to adapt quickly to the synthetic co-factor APAD+. In addition, the enzymatic activity of BoLDH was inhibited non-competitively by polyphenolic gossypol with a Ki value of 4.25 μM, indicating that BoLDH is sensitive to the inhibition of gossypol and possibly to its new derivative compounds. The current work provides the structural basis of BoLDH for the first time and suggests further investigation on the LDH structure of other Babesia spp. That knowledge would indeed facilitate the screening and designing of new LDH inhibitors to control the intracellular proliferation of Babesia spp.
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Affiliation(s)
- Long Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Qin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Wanxin Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Heba F Alzan
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.,Parasitology and Animal Diseases Department, National Research Center, Giza, Egypt.,Tick and Tick-Borne Disease Research Unit, National Research Center, Giza, Egypt
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China.,Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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7
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Human lactate dehydrogenase A undergoes allosteric transitions under pH conditions inducing the dissociation of the tetrameric enzyme. Biosci Rep 2022; 42:230681. [PMID: 35048959 PMCID: PMC8799922 DOI: 10.1042/bsr20212654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/17/2022] Open
Abstract
The aerobic energetic metabolism of eukaryotic cells relies on the glycolytic generation of pyruvate, which is subsequently channelled to the oxidative phosphorylation taking place in mitochondria. However, under conditions limiting oxidative phosphorylation pyruvate is coupled to alternative energetic pathways, e.g. its reduction to lactate catalysed by lactate dehydrogenases (LDHs). This biochemical process is known to induce a significant decrease of cytosolic pH, and is accordingly denoted lactic acidosis. Nevertheless, the mutual dependence of LDHs action and lactic acidosis is far from being fully understood. Using human LDH-A, here we show that when exposed to acidic pH this enzyme is subjected to homotropic allosteric transitions triggered by pyruvate. Conversely, human LDH-A features Michaelis-Menten kinetics at pH values equal to 7.0 or higher. Further, citrate, isocitrate, and malate were observed to activate human LDH-A, both at pH 5.0 and 6.5, with citrate and isocitrate being responsible for major effects. Dynamic light scattering experiments revealed that the occurrence of allosteric kinetics in human LDH-A is mirrored by a consistent dissociation of the enzyme tetramer, suggesting that pyruvate promotes tetramer association under acidic conditions. Finally, using the human liver cancer cell line HepG2 we isolated cells featuring cytosolic pH equal to 7.3 or 6.5, and we observed a concomitant decrease of cytosolic pH and lactate secretion. Overall, our observations indicate the occurrence of a negative feedback between lactic acidosis and human LDH-A activity, and a complex regulation of this feedback by pyruvate and by some intermediates of the Krebs cycle.
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8
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Khrapunov S, Waterman A, Persaud R, Chang EP. Structure, Function, and Thermodynamics of Lactate Dehydrogenases from Humans and the Malaria Parasite P. falciparum. Biochemistry 2021; 60:3582-3595. [PMID: 34747601 DOI: 10.1021/acs.biochem.1c00470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Temperature adaptation is ubiquitous among all living organisms, yet the molecular basis for this process remains poorly understood. It can be assumed that for parasite-host systems, the same enzymes found in both organisms respond to the same selection factor (human body temperature) with similar structural changes. Herein, we report the existence of a reversible temperature-dependent structural transition for the glycolytic enzyme lactate dehydrogenase (LDH) from the malaria parasite Plasmodium falciparum (pfLDH) and human heart (hhLDH) occurring in the temperature range of human fever. This transition is observed for LDHs from psychrophiles, mesophiles, and moderate thermophiles in their operating temperature range. Thermodynamic analysis reveals unique thermodynamic signatures of the LDH-substrate complexes defining a specific temperature range to which human LDH is adapted and parasite LDH is not, despite their common mesophilic nature. The results of spectroscopic analysis combined with the available crystallographic data reveal the existence of an active center within pfLDH that imparts psychrophilic structural properties to the enzyme. This center consists of two pockets, one formed by the five amino acids (5AA insert) within the substrate specificity loop and the other by the active site, that mutually regulate one another in response to temperature and induce structural and functional changes in the Michaelis complex. Our findings pave the way toward a new strategy for malaria treatments and drug design using therapeutic agents that inactivate malarial LDH selectively at a specific temperature range of the cyclic malaria paroxysm.
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Affiliation(s)
- Sergei Khrapunov
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Akiba Waterman
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
| | - Rudra Persaud
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
| | - Eric P Chang
- Department of Chemistry and Physical Sciences, Pace University, 1 Pace Plaza, New York, New York 10038, United States
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9
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Iorio A, Roche J, Engilberge S, Coquelle N, Girard E, Sterpone F, Madern D. Biochemical, structural and dynamical studies reveal strong differences in the thermal-dependent allosteric behavior of two extremophilic lactate dehydrogenases. J Struct Biol 2021; 213:107769. [PMID: 34229075 DOI: 10.1016/j.jsb.2021.107769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022]
Abstract
In this work, we combined biochemical and structural investigations with molecular dynamics (MD) simulations to analyze the very different thermal-dependent allosteric behavior of two lactate dehydrogenases (LDH) from thermophilic bacteria. We found that the enzyme from Petrotoga mobilis (P. mob) necessitates an absolute requirement of the allosteric effector (fructose 1, 6-bisphosphate) to ensure functionality. In contrast, even without allosteric effector, the LDH from Thermus thermophilus (T. the) is functional when the temperature is raised. We report the crystal structure of P. mob LDH in the Apo state solved at 1.9 Å resolution. We used this structure and the one from T. the, obtained previously, as a starting point for MD simulations at various temperatures. We found clear differences between the thermal dynamics, which accounts for the behavior of the two enzymes. Our work demonstrates that, within an allosteric enzyme, some areas act as local gatekeepers of signal transmission, allowing the enzyme to populate either the T-inactive or the R-active states with different degrees of stringency.
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Affiliation(s)
- Antonio Iorio
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Jennifer Roche
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sylvain Engilberge
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France; Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Nicolas Coquelle
- Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9 Grenoble, France
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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10
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Halgand F, Houée-Lévin C, Weik M, Madern D. Remote oxidative modifications induced by oxygen free radicals modify T/R allosteric equilibrium of a hyperthermophilic lactate dehydrogenase. J Struct Biol 2020; 210:107478. [PMID: 32087239 DOI: 10.1016/j.jsb.2020.107478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/01/2022]
Abstract
L-Lactate dehydrogenase (LDH) is a model protein allowing to shed light on the fundamental molecular mechanisms that drive the acquisition, evolution and regulation of enzyme properties. In this study, we test the hypothesis of a link between thermal stability of LDHs and their capacity against unfolding induced by reactive oxygen species (ROS) generated by γ-rays irradiation. By using circular dichroism spectroscopy, we analysed that high thermal stability of a thermophilic LDH favours strong resistance against ROS-induced unfolding, in contrast to its psychrophilic and mesophilic counterparts that are less resistant. We suggest that a protein's phenotype linking strong thermal stability and resistance against ROS damages would have been a selective evolutionary advantage. We also find that the enzymatic activity of the thermophilic LDH that is strongly resistant against ROS-unfolding is very sensitive to inactivation by irradiation. To address this counter-intuitive observation, we combined mass spectrometry analyses and enzymatic activity measurements. We demonstrate that the dramatic change on LDH activity was linked to remote chemical modifications away from the active site, that change the equilibrium between low-affinity tense (T-inactive) and high-affinity relaxed (R-active) forms. We found the T-inactive thermophilic enzyme obtained after irradiation can recover its LDH activity by addition of the allosteric effector 1, 6 fructose bis phosphate. We analyse our data within the general framework of allosteric regulation, which requires that an enzyme in solution populates a large diversity of dynamically-interchanging conformations. Our work demonstrates that the radiation-induced inactivation of an enzyme is controlled by its dynamical properties.
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Affiliation(s)
- Frédéric Halgand
- Université Paris Sud-CNRS, UMR 8000, bâtiments 201 P2 and 350, 91405 Orsay, France
| | - Chantal Houée-Lévin
- Université Paris Sud-CNRS, UMR 8000, bâtiments 201 P2 and 350, 91405 Orsay, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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11
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Katava M, Marchi M, Madern D, Sztucki M, Maccarini M, Sterpone F. Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse. J Phys Chem B 2020; 124:1001-1008. [DOI: 10.1021/acs.jpcb.9b10776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. Katava
- UPR9080, Laboratoire de Biochimie Théorique, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - M. Marchi
- Centre d’Etudes de Saclay, Commissariat à l’Energie Atomique DRF/Joliot/SB2SM, 91191 Gif sur Yvette Cedex, France
| | - D. Madern
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - M. Sztucki
- ESRF - The European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - M. Maccarini
- Laboratoire TIMC/IMAG UMR CNRS 5525, Université Grenoble Alpes, 38000 Grenoble, France
| | - F. Sterpone
- UPR9080, Laboratoire de Biochimie Théorique, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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12
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Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Phys Chem Chem Phys 2020; 22:18361-18373. [DOI: 10.1039/d0cp02738c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The thermal resistance of two homolog enzymes is investigated, with an emphasis on their local stability and flexibility, and on the possible implications regarding their reactivity.
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Affiliation(s)
- Irene Maffucci
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Damien Laage
- PASTEUR
- Département de chimie
- École Normale Supérieure
- PSL University
- Sorbonne Université
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique
- Institut de Biologie Physico-Chimique
- PSL University
- Paris
- France
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13
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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Roche J, Girard E, Mas C, Madern D. The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization. J Struct Biol 2019; 208:7-17. [PMID: 31301348 DOI: 10.1016/j.jsb.2019.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/19/2022]
Abstract
The NAD(P)-dependent malate dehydrogenases (MalDHs) and NAD-dependent lactate dehydrogenases (LDHs) are homologous enzymes involved in central metabolism. They display a common protein fold and the same catalytic mechanism, yet have a stringent capacity to discriminate between their respective substrates. The MalDH/LDH superfamily is divided into several phylogenetically related groups. It has been shown that the canonical LDHs and LDH-like group of MalDHs are primarily tetrameric enzymes that diverged from a common ancestor. In order to gain understanding of the evolutionary history of the LDHs and MalDHs, the biochemical properties and crystallographic structure of the LDH-like MalDH from the hyperthermophilic archaeon Ignicoccus islandicus (I. isl) were determined. I. isl MalDH recognizes oxaloacetate as main substrate, but it is also able to use pyruvate. Surprisingly, with pyruvate, the enzymatic activity profile looks like that of allosteric LDHs, suggesting a hidden allosteric capacity in a MalDH. The I. isl MalDH tetrameric structure in the apo state is considerably different from those of canonical LDH-like MalDHs and LDHs, representing an alternative oligomeric organization. A comparison with MalDH and LDH counterparts provides strong evidence that the divergence between allosteric and non-allosteric members of the superfamily involves homologs with intermediate, atypical properties.
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Affiliation(s)
- Jennifer Roche
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Eric Girard
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Caroline Mas
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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15
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Nicholl ID, Matsui T, Weiss TM, Stanley CB, Heller WT, Martel A, Farago B, Callaway DJE, Bu Z. α-Catenin Structure and Nanoscale Dynamics in Solution and in Complex with F-Actin. Biophys J 2018; 115:642-654. [PMID: 30037495 DOI: 10.1016/j.bpj.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/17/2018] [Accepted: 07/05/2018] [Indexed: 12/26/2022] Open
Abstract
As a core component of the adherens junction, α-catenin stabilizes the cadherin/catenin complexes to the actin cytoskeleton for the mechanical coupling of cell-cell adhesion. α-catenin also modulates actin dynamics, cell polarity, and cell-migration functions that are independent of the adherens junction. We have determined the solution structures of the α-catenin monomer and dimer using in-line size-exclusion chromatography small-angle X-ray scattering, as well as the structure of α-catenin dimer in complex to F-actin filament using selective deuteration and contrast-matching small angle neutron scattering. We further present the first observation, to our knowledge, of the nanoscale dynamics of α-catenin by neutron spin-echo spectroscopy, which explicitly reveals the mobile regions of α-catenin that are crucial for binding to F-actin. In solution, the α-catenin monomer is more expanded than either protomer shown in the crystal structure dimer, with the vinculin-binding M fragment and the actin-binding domain being able to adopt different configurations. The α-catenin dimer in solution is also significantly more expanded than the dimer crystal structure, with fewer interdomain and intersubunit contacts than the crystal structure. When in complex to F-actin, the α-catenin dimer has an even more open and extended conformation than in solution, with the actin-binding domain further separated from the main body of the dimer. The α-catenin-assembled F-actin bundle develops into an ordered filament packing arrangement at increasing α-catenin/F-actin molar ratios. Together, the structural and dynamic studies reveal that α-catenin possesses dynamic molecular conformations that prime this protein to function as a mechanosensor protein.
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Affiliation(s)
- Iain D Nicholl
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, Menlo Park, California
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Light Source, Menlo Park, California
| | | | - William T Heller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | | | - David J E Callaway
- Department of Chemistry and Biochemistry, City College of New York, City University of New York, New York, New York.
| | - Zimei Bu
- Department of Chemistry and Biochemistry, City College of New York, City University of New York, New York, New York.
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16
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Hernández-Meza JM, Sampedro JG. Trehalose Mediated Inhibition of Lactate Dehydrogenase from Rabbit Muscle. The Application of Kramers' Theory in Enzyme Catalysis. J Phys Chem B 2018; 122:4309-4317. [PMID: 29595977 DOI: 10.1021/acs.jpcb.8b01656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactate dehydrogenase (LDH) catalyzes the reduction of pyruvate to lactate by using NADH. LDH kinetics has been proposed to be dependent on the dynamics of a loop over the active site. Kramers' theory has been useful in the study of enzyme catalysis dependent on large structural dynamics. In this work, LDH kinetics was studied in the presence of trehalose and at different temperatures. In the absence of trehalose, temperature increase raised exponentially the LDH Vmax and revealed a sigmoid transition of Km toward a low-affinity state similar to protein unfolding. Notably, LDH Vmax diminished when in the presence of trehalose, while pyruvate affinity increased and the temperature-mediated binding site transition was hindered. The effect of trehalose on kcat was viscosity dependent as described by Kramers' theory since Vmax correlated inversely with the viscosity of the medium. As a result, activation energy ( Ea) for pyruvate reduction was dramatically increased by trehalose presence. This work provides experimental evidence that the dynamics of a structural component in LDH is essential for catalysis, i.e., the closing of the loop on the active site. While the trehalose mediated-increased of pyruvate affinity is proposed to be due to the compaction and/or increase of structural order at the binding site.
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Affiliation(s)
- Juan M Hernández-Meza
- Instituto de Física, Universidad Autónoma de San Luis Potosí , Manuel Nava 6, Zona Universitaria , C.P. 78290 San Luis Potosí , SLP , México
| | - José G Sampedro
- Instituto de Física, Universidad Autónoma de San Luis Potosí , Manuel Nava 6, Zona Universitaria , C.P. 78290 San Luis Potosí , SLP , México
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17
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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18
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Abstract
Inspired by Somero's corresponding state principle that relates protein enhanced thermal stability with mechanical rigidity, we deployed state of the art computational techniques (based on atomistic steered molecular dynamics and Hamiltonian-replica exchange simulations) to study the in silico realization of mechanical and thermal unfolding of two homologous Csp proteins that have evolved to thrive in different thermal environments. By complementing recent single-molecule experiments, we unambiguously show that, for these homologues whose structures are very similar, the increased thermal resistance of the thermophilic variant is not associated with an increased mechanical stability. Our approach provides microscopic insights that are otherwise inaccessible to experimental techniques, and explains why the protein weak spots for thermal and mechanical denaturation are distinct.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Fabio Sterpone
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University , 13 rue Pierre et Marie Curie, 75005, Paris, France
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