1
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Seco A, Pereira AR, Camuenho A, Oliveira J, Dias R, Brás N, Basílio N, Parola AJ, Lima JC, de Freitas V, Pina F. Comparing the Chemistry of Malvidin-3- O-glucoside and Malvidin-3,5- O-diglucoside Networks: A Holistic Approach to the Acidic and Basic Paradigms with Implications in Biological Studies. J Agric Food Chem 2024; 72:7497-7510. [PMID: 38520401 PMCID: PMC10995998 DOI: 10.1021/acs.jafc.4c00552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
The kinetics, thermodynamics, and degradation of malvidin mono- and diglucosides were studied following a holistic approach by extending to the basic medium. In acidic conditions, the reversible kinetics of the flavylium cation toward the equilibrium is controlled by the hydration and cis-trans isomerization steps, while in the basic medium, the OH- nucleophilic addition to the anionic quinoidal bases is the slowest step. There is a pH range (transition pHs), between the acidic and basic paradigms, that includes physiological pH (7.4), where degradation reactions occur faster, preventing the system from reaching the equilibrium. The transition pH of the diglucoside is narrower, and in contrast with the monoglucoside, there is no evidence for the formation of colored oligomers among the degradation products. Noteworthy, OH- addition in position 4 to form B42-, a kinetic product that decreases the overall equilibration rate, was observed only for the diglucoside.
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Affiliation(s)
- André Seco
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Rita Pereira
- LAQV—REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Ambrósio Camuenho
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Joana Oliveira
- LAQV—REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Ricardo Dias
- LAQV—REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Natércia
F. Brás
- LAQV—REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Nuno Basílio
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - A. Jorge Parola
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - João C. Lima
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Victor de Freitas
- LAQV—REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Fernando Pina
- LAQV—REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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2
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Gonzalez L, Chau-Duy Tam Vo S, Faivre B, Pierrel F, Fontecave M, Hamdane D, Lombard M. Activation of Coq6p, a FAD Monooxygenase Involved in Coenzyme Q Biosynthesis, by Adrenodoxin Reductase/Ferredoxin. Chembiochem 2024; 25:e202300738. [PMID: 38141230 DOI: 10.1002/cbic.202300738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/25/2023]
Abstract
Adrenodoxin reductase (AdxR) plays a pivotal role in electron transfer, shuttling electrons between NADPH and iron/sulfur adrenodoxin proteins in mitochondria. This electron transport system is essential for P450 enzymes involved in various endogenous biomolecules biosynthesis. Here, we present an in-depth examination of the kinetics governing the reduction of human AdxR by NADH or NADPH. Our results highlight the efficiency of human AdxR when utilizing NADPH as a flavin reducing agent. Nevertheless, akin to related flavoenzymes such as cytochrome P450 reductase, we observe that low NADPH concentrations hinder flavin reduction due to intricate equilibrium reactions between the enzyme and its substrate/product. Remarkably, the presence of MgCl2 suppresses this complex kinetic behavior by decreasing NADPH binding to oxidized AdxR, effectively transforming AdxR into a classical Michaelis-Menten enzyme. We propose that the addition of MgCl2 may be adapted for studying the reductive half-reactions of other flavoenzymes with NADPH. Furthermore, in vitro experiments provide evidence that the reduction of the yeast flavin monooxygenase Coq6p relies on an electron transfer chain comprising NADPH-AdxR-Yah1p-Coq6p, where Yah1p shuttles electrons between AdxR and Coq6p. This discovery explains the previous in vivo observation that Yah1p and the AdxR homolog, Arh1p, are required for the biosynthesis of coenzyme Q in yeast.
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Affiliation(s)
- Lucie Gonzalez
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Samuel Chau-Duy Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000, Grenoble, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
- Institut de Biologie Paris-Seine, Biology of Aging and Adaptation, UMR 8256, Sorbonne Université, 7 quai Saint-Bernard, 75 252, Paris, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, Sorbonne Université, CNRS UMR8229, PSL Research University, Sorbonne Université, 11 place Marcelin Berthelot, 75 005, Paris, France
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3
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Delavari N, Zhang Z, Stull F. Rapid reaction studies on the chemistry of flavin oxidation in urocanate reductase. J Biol Chem 2024; 300:105689. [PMID: 38280427 PMCID: PMC10882135 DOI: 10.1016/j.jbc.2024.105689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024] Open
Abstract
Urocanate reductase (UrdA) is a bacterial flavin-dependent enzyme that reduces urocanate to imidazole propionate, enabling bacteria to use urocanate as an alternative respiratory electron acceptor. Elevated serum levels of imidazole propionate are associated with the development of type 2 diabetes, and, since UrdA is only present in humans in gut bacteria, this enzyme has emerged as a significant factor linking the health of the gut microbiome and insulin resistance. Here, we investigated the chemistry of flavin oxidation by urocanate in the isolated FAD domain of UrdA (UrdA') using anaerobic stopped-flow experiments. This analysis unveiled the presence of a charge-transfer complex between reduced FAD and urocanate that forms within the dead time of the stopped-flow instrument (∼1 ms), with flavin oxidation subsequently occurring with a rate constant of ∼60 s-1. The pH dependence of the reaction and analysis of an Arg411Ala mutant of UrdA' are consistent with Arg411 playing a crucial role in catalysis by serving as the active site acid that protonates urocanate during hydride transfer from reduced FAD. Mutational analysis of urocanate-binding residues suggests that the twisted conformation of urocanate imposed by the active site of UrdA' facilitates urocanate reduction. Overall, this study provides valuable insight into the mechanism of urocanate reduction by UrdA.
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Affiliation(s)
- Niusha Delavari
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
| | - Zhiyao Zhang
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA.
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4
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Cheng X, Pu Y, Ye S, Xiao X, Zhang X, Chen H. Measuring Solvent Exchange in Silica Nanoparticles with Rotor-Based Fluorophore. Adv Mater 2024; 36:e2305779. [PMID: 37774750 DOI: 10.1002/adma.202305779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/15/2023] [Indexed: 10/01/2023]
Abstract
Measuring the diffusivity of molecules is the first step toward understanding their dependence and controlling diffusion, but the challenge increases with the decrease of molecular size, particularly for non-fluorescent and non-reactive molecules such as solvents. Here, the capability to monitor the solvent exchange process within the micropores of silica with millisecond time resolution is demonstrated, by simply embedding a rotor-based fluorophore (thioflavin T) in colloidal silica nanoparticles. Basically, the silica provides an extreme case of viscous microenvironment, which is affected by the polarity of the solvents. The fluorescence intensity traces can be well fitted to the Fickian diffusion model, allowing analytical solution of the diffusion process, and revealing the diffusion coefficients. The validation experiments, involving the water-to-ethanol and ethanol-to-water solvent exchange, the comparison of different drying conditions, and the variation in the degree of cross-linking in silica, confirmed the effectiveness and sensitivity of this method for characterizing diffusion in silica micropores. This work focuses on the method development of measuring diffusivity and the high temporal resolution in tracking solvent exchange dynamics over a short distance (within 165 nm) opens enormous possibilities for further studies.
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Affiliation(s)
- Xuejun Cheng
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Yingming Pu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Songtao Ye
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Xiao Xiao
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Hongyu Chen
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang, 310024, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
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5
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Davletgildeeva AT, Tyugashev TE, Zhao M, Kuznetsov NA, Ishchenko AA, Saparbaev M, Kuznetsova AA. Individual Contributions of Amido Acid Residues Tyr122, Ile168, and Asp173 to the Activity and Substrate Specificity of Human DNA Dioxygenase ABH2. Cells 2023; 12:1839. [PMID: 37508504 PMCID: PMC10377887 DOI: 10.3390/cells12141839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Human Fe(II)/α-ketoglutarate-dependent dioxygenase ABH2 plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases, e.g., N1-methyladenine (m1A), N3-methylcytosine (m3C), and some etheno derivatives. Moreover, ABH2 is capable of a less efficient oxidation of an epigenetic DNA mark called 5-methylcytosine (m5C), which typically is a specific target of DNA dioxygenases from the TET family. In this study, to elucidate the mechanism of the substrate specificity of ABH2, we investigated the role of several active-site amino acid residues. Functional mapping of the lesion-binding pocket was performed through the analysis of the functions of Tyr122, Ile168, and Asp173 in the damaged base recognition mechanism. Interactions of wild-type ABH2, or its mutants Y122A, I168A, or D173A, with damaged DNA containing the methylated base m1A or m3C or the epigenetic marker m5C were analyzed by molecular dynamics simulations and kinetic assays. Comparative analysis of the enzymes revealed an effect of the substitutions on DNA binding and on catalytic activity. Obtained data clearly demonstrate the effect of the tested amino acid residues on the catalytic activity of the enzymes rather than the DNA-binding ability. Taken together, these data shed light on the molecular and kinetic consequences of the substitution of active-site residues for the mechanism of the substrate recognition.
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Affiliation(s)
- Anastasiia T Davletgildeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Timofey E Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Mingxing Zhao
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexander A Ishchenko
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Murat Saparbaev
- Groupe Mechanisms of DNA Repair and Carcinogenesis, CNRS UMR9019, Gustave Roussy Cancer Campus, Université Paris-Saclay, CEDEX, F-94805 Villejuif, France
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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6
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Gérard E, Mokkawes T, Johannissen LO, Warwicker J, Spiess RR, Blanford CF, Hay S, Heyes DJ, de Visser SP. How Is Substrate Halogenation Triggered by the Vanadium Haloperoxidase from Curvularia inaequalis? ACS Catal 2023; 13:8247-8261. [PMID: 37342830 PMCID: PMC10278073 DOI: 10.1021/acscatal.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/05/2023] [Indexed: 06/23/2023]
Abstract
Vanadium haloperoxidases (VHPOs) are unique enzymes in biology that catalyze a challenging halogen transfer reaction and convert a strong aromatic C-H bond into C-X (X = Cl, Br, I) with the use of a vanadium cofactor and H2O2. The VHPO catalytic cycle starts with the conversion of hydrogen peroxide and halide (X = Cl, Br, I) into hypohalide on the vanadate cofactor, and the hypohalide subsequently reacts with a substrate. However, it is unclear whether the hypohalide is released from the enzyme or otherwise trapped within the enzyme structure for the halogenation of organic substrates. A substrate-binding pocket has never been identified for the VHPO enzyme, which questions the role of the protein in the overall reaction mechanism. Probing its role in the halogenation of small molecules will enable further engineering of the enzyme and expand its substrate scope and selectivity further for use in biotechnological applications as an environmentally benign alternative to current organic chemistry synthesis. Using a combined experimental and computational approach, we elucidate the role of the vanadium haloperoxidase protein in substrate halogenation. Activity studies show that binding of the substrate to the enzyme is essential for the reaction of the hypohalide with substrate. Stopped-flow measurements demonstrate that the rate-determining step is not dependent on substrate binding but partially on hypohalide formation. Using a combination of molecular mechanics (MM) and molecular dynamics (MD) simulations, the substrate binding area in the protein is identified and even though the selected substrates (methylphenylindole and 2-phenylindole) have limited hydrogen-bonding abilities, they are found to bind relatively strongly and remain stable in a binding tunnel. A subsequent analysis of the MD snapshots characterizes two small tunnels leading from the vanadate active site to the surface that could fit small molecules such as hypohalide, halide, and hydrogen peroxide. Density functional theory studies using electric field effects show that a polarized environment in a specific direction can substantially lower barriers for halogen transfer. A further analysis of the protein structure indeed shows a large dipole orientation in the substrate-binding pocket that could enable halogen transfer through an applied local electric field. These findings highlight the importance of the enzyme in catalyzing substrate halogenation by providing an optimal environment to lower the energy barrier for this challenging aromatic halide insertion reaction.
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Affiliation(s)
- Emilie
F. Gérard
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
| | - Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jim Warwicker
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- School
of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester 13 9PL, United
Kingdom
| | - Reynard R. Spiess
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Christopher F. Blanford
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, United Kingdom
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7
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Henke W, Peng Y, Meier A, Fujita E, Grills D, Polyansky D, Blakemore J. Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes. Proc Natl Acad Sci U S A 2023; 120:e2217189120. [PMID: 37186841 PMCID: PMC10214172 DOI: 10.1073/pnas.2217189120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/17/2023] [Indexed: 05/17/2023] Open
Abstract
Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η5-pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η4-pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2'-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)]+, an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)]+. Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.
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Affiliation(s)
- Wade C. Henke
- Department of Chemistry, University of Kansas, Lawrence, KS66045
| | - Yun Peng
- Department of Chemistry, University of Kansas, Lawrence, KS66045
| | - Alex A. Meier
- Department of Chemistry, University of Kansas, Lawrence, KS66045
| | - Etsuko Fujita
- Chemistry Division, Brookhaven National Laboratory, Upton, NY11973-5000
| | - David C. Grills
- Chemistry Division, Brookhaven National Laboratory, Upton, NY11973-5000
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8
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Golten O, Ayuso-Fernández I, Hall KR, Stepnov AA, Sørlie M, Røhr ÅK, Eijsink VGH. Reductants fuel lytic polysaccharide monooxygenase activity in a pH-dependent manner. FEBS Lett 2023; 597:1363-1374. [PMID: 37081294 DOI: 10.1002/1873-3468.14629] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023]
Abstract
Polysaccharide-degrading mono-copper lytic polysaccharide monooxygenases (LPMOs) are efficient peroxygenases that require electron donors (reductants) to remain in the active Cu(I) form and to generate the H2 O2 co-substrate from molecular oxygen. Here, we show how commonly used reductants affect LPMO catalysis in a pH-dependent manner. Between pH 6.0 and 8.0, reactions with ascorbic acid show little pH-dependency, whereas reactions with gallic acid become much faster at increased pH. These dependencies correlate with the reductant ionization state, which affects its ability to react with molecular oxygen and generate H2 O2 . The correlation does not apply to L-cysteine because, as shown by stopped-flow kinetics, increased H2 O2 production at higher pH is counteracted by increased binding of L-cysteine to the copper active site. The findings highlight the importance of the choice of reductant and pH in LPMO reactions.
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Affiliation(s)
- Ole Golten
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Iván Ayuso-Fernández
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Kelsi R Hall
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Åsmund Kjendseth Røhr
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU- Norwegian University of Life Sciences, Ås, Norway
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9
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Zaniewski TM, Hancock WO. Positive charge in the K-loop of the kinesin-3 motor KIF1A regulates superprocessivity by enhancing microtubule affinity in the one-head-bound state. J Biol Chem 2023; 299:102818. [PMID: 36549649 PMCID: PMC9871336 DOI: 10.1016/j.jbc.2022.102818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
KIF1A is an essential neuronal transport motor protein in the kinesin-3 family, known for its superprocessive motility. However, structural features underlying this function are unclear. Here, we determined that superprocessivity of KIF1A dimers originates from a unique structural domain, the lysine-rich insertion in loop-12 termed the 'K-loop', which enhances electrostatic interactions between the motor and the microtubule. In 80 mM PIPES buffer, replacing the native KIF1A loop-12 with that of kinesin-1 resulted in a 6-fold decrease in run length, whereas adding additional positive charge to loop-12 enhanced the run length. Interestingly, swapping the KIF1A loop-12 into kinesin-1 did not enhance its run length, consistent with the two motor families using different mechanochemical tuning to achieve persistent transport. To investigate the mechanism by which the KIF1A K-loop enhances processivity, we used microtubule pelleting and single-molecule dwell time assays in ATP and ADP. First, the microtubule affinity was similar in ATP and in ADP, consistent with the motor spending the majority of its cycle in a weakly bound state. Second, the microtubule affinity and single-molecule dwell time in ADP were 6-fold lower in the loop-swap mutant than WT. Thus, the positive charge in loop-12 of KIF1A enhances the run length by stabilizing binding of the motor in its vulnerable one-head-bound state. Finally, through a series of mutants with varying positive charge in the K-loop, we found that KIF1A processivity is linearly dependent on the charge of loop-12, further highlighting how loop-12 contributes to the function of this key motor protein.
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Affiliation(s)
- Taylor M Zaniewski
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - William O Hancock
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA.
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10
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Zakharova MY, Kuznetsova AA, Uvarova VI, Fomina AD, Kozlovskaya LI, Kaliberda EN, Kurbatskaia IN, Smirnov IV, Bulygin AA, Knorre VD, Fedorova OS, Varnek A, Osolodkin DI, Ishmukhametov AA, Egorov AM, Gabibov AG, Kuznetsov NA. Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Front Pharmacol 2021; 12:773198. [PMID: 34938188 PMCID: PMC8686763 DOI: 10.3389/fphar.2021.773198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
The design of effective target-specific drugs for COVID-19 treatment has become an intriguing challenge for modern science. The SARS-CoV-2 main protease, Mpro, responsible for the processing of SARS-CoV-2 polyproteins and production of individual components of viral replication machinery, is an attractive candidate target for drug discovery. Specific Mpro inhibitors have turned out to be promising anticoronaviral agents. Thus, an effective platform for quantitative screening of Mpro-targeting molecules is urgently needed. Here, we propose a pre-steady-state kinetic analysis of the interaction of Mpro with inhibitors as a basis for such a platform. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type Mpro and by its catalytically inactive mutant C145A. The enzyme induces conformational changes of the peptide during the reaction. The inhibition of Mpro by boceprevir, telaprevir, GC-376, PF-00835231, or thimerosal was investigated. Detailed pre-steady-state kinetics of the interaction of the wild-type enzyme with the most potent inhibitor, PF-00835231, revealed a two-step binding mechanism, followed by covalent complex formation. The C145A Mpro mutant interacts with PF-00835231 approximately 100-fold less effectively. Nevertheless, the binding constant of PF-00835231 toward C145A Mpro is still good enough to inhibit the enzyme. Therefore, our results suggest that even noncovalent inhibitor binding due to a fine conformational fit into the active site is sufficient for efficient inhibition. A structure-based virtual screening and a subsequent detailed assessment of inhibition efficacy allowed us to select two compounds as promising noncovalent inhibitor leads of SARS-CoV-2 Mpro.
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Affiliation(s)
- Maria Yu Zakharova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Victoria I Uvarova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Anastasiia D Fomina
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Liubov I Kozlovskaya
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Elena N Kaliberda
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Inna N Kurbatskaia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Anatoly A Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Vera D Knorre
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia
| | - Alexandre Varnek
- Laboratoire de Chémoinformatique, UMR 7140 CNRS, Université de Strasbourg, Strasbourg, France
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia
| | - Alexander G Gabibov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia.,Lomonosov Moscow State University, Moscow, Russia.,Department of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch (SB) of RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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11
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Pagano L, Malagrinò F, Nardella C, Gianni S, Toto A. Experimental Characterization of the Interaction between the N-Terminal SH3 Domain of Crkl and C3G. Int J Mol Sci 2021; 22:13174. [PMID: 34947971 DOI: 10.3390/ijms222413174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Crkl is a protein involved in the onset of several cancer pathologies that exerts its function only through its protein-protein interaction domains, a SH2 domain and two SH3 domains. SH3 domains are small protein interaction modules that mediate the binding and recognition of proline-rich sequences. One of the main physiological interactors of Crkl is C3G (also known as RAPGEF1), an interaction with key implications in regulating cellular growth and differentiation, cell morphogenesis and adhesion processes. Thus, understanding the interaction between Crkl and C3G is fundamental to gaining information about the molecular determinants of the several cancer pathologies in which these proteins are involved. In this paper, through a combination of fast kinetics at different experimental conditions and site-directed mutagenesis, we characterize the binding reaction between the N-SH3 domain of Crkl and a peptide mimicking a specific portion of C3G. Our results show a clear effect of pH on the stability of the complex, due to the protonation of negatively charged residues in the binding pocket of N-SH3. Our results are discussed under the light of previous work on SH3 domains.
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12
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Liu NN, Song ZY, Guo HL, Yin H, Chen WF, Dai YX, Xin BG, Ai X, Ji L, Wang QM, Hou XM, Dou SX, Rety S, Xi XG. Endogenous Bos taurus RECQL is predominantly monomeric and more active than oligomers. Cell Rep 2021; 36:109688. [PMID: 34496242 DOI: 10.1016/j.celrep.2021.109688] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/11/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
There is broad consensus that RecQ family helicase is a high-order oligomer that dissociates into a dimer upon ATP binding. This conclusion is based mainly on studies of highly purified recombinant proteins, and the oligomeric states of RecQ helicases in living cells remain unknown. We show here that, in contrast to current models, monomeric RECQL helicase is more abundant than oligomer/dimer forms in living cells. Further characterization of endogenous BtRECQL and isolated monomeric BtRECQL using various approaches demonstrates that both endogenous and recombinant monomeric BtRECQL effectively function as monomers, displaying higher helicase and ATPase activities than dimers and oligomers. Furthermore, monomeric BtRECQL unfolds intramolecular G-quadruplex DNA as efficiently as human RECQL and BLM helicases. These discoveries have implications for understanding endogenous RECQL oligomeric structures and their regulation. It is worth revisiting oligomeric states of the other members of the RecQ family helicases in living cells.
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Affiliation(s)
- Na-Nv Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ze-Yu Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hai-Lei Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hu Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei-Fei Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang-Xue Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ben-Ge Xin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xia Ai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qing-Man Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Stephane Rety
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, Gif-sur-Yvette, France.
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13
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Nakasone Y, Terazima M. A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules. Front Genet 2021; 12:691010. [PMID: 34276791 PMCID: PMC8278059 DOI: 10.3389/fgene.2021.691010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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14
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Phintha A, Prakinee K, Jaruwat A, Lawan N, Visitsatthawong S, Kantiwiriyawanitch C, Songsungthong W, Trisrivirat D, Chenprakhon P, Mulholland A, van Pée KH, Chitnumsub P, Chaiyen P. Dissecting the low catalytic capability of flavin-dependent halogenases. J Biol Chem 2021; 296:100068. [PMID: 33465708 PMCID: PMC7948982 DOI: 10.1074/jbc.ra120.016004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
Although flavin-dependent halogenases (FDHs) are attractive biocatalysts, their practical applications are limited because of their low catalytic efficiency. Here, we investigated the reaction mechanisms and structures of tryptophan 6-halogenase (Thal) from Streptomyces albogriseolus using stopped-flow, rapid-quench flow, quantum/mechanics molecular mechanics calculations, crystallography, and detection of intermediate (hypohalous acid [HOX]) liberation. We found that the key flavin intermediate, C4a-hydroperoxyflavin (C4aOOH-FAD), formed by Thal and other FDHs (tryptophan 7-halogenase [PrnA] and tryptophan 5-halogenase [PyrH]), can react with I-, Br-, and Cl- but not F- to form C4a-hydroxyflavin and HOX. Our experiments revealed that I- reacts with C4aOOH-FAD the fastest with the lowest energy barrier and have shown for the first time that a significant amount of the HOX formed leaks out as free HOX. This leakage is probably a major cause of low product coupling ratios in all FDHs. Site-saturation mutagenesis of Lys79 showed that changing Lys79 to any other amino acid resulted in an inactive enzyme. However, the levels of liberated HOX of these variants are all similar, implying that Lys79 probably does not form a chloramine or bromamine intermediate as previously proposed. Computational calculations revealed that Lys79 has an abnormally lower pKa compared with other Lys residues, implying that the catalytic Lys may act as a proton donor in catalysis. Analysis of new X-ray structures of Thal also explains why premixing of FDHs with reduced flavin adenine dinucleotide generally results in abolishment of C4aOOH-FAD formation. These findings reveal the hidden factors restricting FDHs capability which should be useful for future development of FDHs applications.
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Affiliation(s)
- Aisaraphon Phintha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Aritsara Jaruwat
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Kantiwiriyawanitch
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Warangkhana Songsungthong
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand
| | - Adrian Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Karl-Heinz van Pée
- General Biochemistry, Faculty of Chemistry and Food Chemistry, Technical University of Dresden, Dresden, Germany
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand.
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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15
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Porter CJ, Werber JR, Zhong M, Wilson CJ, Elimelech M. Pathways and Challenges for Biomimetic Desalination Membranes with Sub-Nanometer Channels. ACS Nano 2020; 14:10894-10916. [PMID: 32886487 DOI: 10.1021/acsnano.0c05753] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Transmembrane protein channels, including ion channels and aquaporins that are responsible for fast and selective transport of water, have inspired membrane scientists to exploit and mimic their performance in membrane technologies. These biomimetic membranes comprise discrete nanochannels aligned within amphiphilic matrices on a robust support. While biological components have been used directly, extensive work has also been conducted to produce stable synthetic mimics of protein channels and lipid bilayers. However, the experimental performance of biomimetic membranes remains far below that of biological membranes. In this review, we critically assess the status and potential of biomimetic desalination membranes. We first review channel chemistries and their transport behavior, identifying key characteristics to optimize water permeability and salt rejection. We compare various channel types within an industrial context, considering transport performance, processability, and stability. Through a re-examination of previous vesicular stopped-flow studies, we demonstrate that incorrect permeability equations result in an overestimation of the water permeability of nanochannels. We find in particular that the most optimized aquaporin-bearing bilayer had a pure water permeability of 2.1 L m-2 h-1 bar-1, which is comparable to that of current state-of-the-art polymeric desalination membranes. Through a quantitative assessment of biomimetic membrane formats, we analytically show that formats incorporating intact vesicles offer minimal benefit, whereas planar biomimetic selective layers could allow for dramatically improved salt rejections. We then show that the persistence of nanoscale defects explains observed subpar performance. We conclude with a discussion on optimal strategies for minimizing these defects, which could enable breakthrough performance.
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Affiliation(s)
- Cassandra J Porter
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Jay R Werber
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mingjiang Zhong
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Corey J Wilson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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16
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Bednářová K, Vorlíčková M, Renčiuk D. Diversity of Parallel Guanine Quadruplexes Induced by Guanine Substitutions. Int J Mol Sci 2020; 21:E6123. [PMID: 32854410 PMCID: PMC7503932 DOI: 10.3390/ijms21176123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 01/17/2023] Open
Abstract
Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.
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Affiliation(s)
| | | | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; (K.B.); (M.V.)
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17
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Alevridis A, Tsiasioti A, Zacharis CK, Tzanavaras PD. Fluorimetric Method for the Determination of Histidine in Random Human Urine Based on Zone Fluidics. Molecules 2020; 25:E1665. [PMID: 32260350 DOI: 10.3390/molecules25071665] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
In the present study, the determination of histidine (HIS) by an on-line flow method based on the concept of zone fluidics is reported. HIS reacts fast with o-phthalaldehyde at a mildly basic medium (pH 7.5) and in the absence of additional nucleophilic compounds to yield a highly fluorescent derivative (λex/λem = 360/440 nm). The flow procedure was optimized and validated, paying special attention to its selectivity and sensitivity. The LOD was 31 nmol·L−1, while the within-day and day-to-day precisions were better than 1.0% and 5.0%, respectively (n = 6). Random urine samples from adult volunteers (n = 7) were successfully analyzed without matrix effect (<1%). Endogenous HIS content ranged between 116 and 1527 μmol·L−1 with percentage recoveries in the range of 87.6%–95.4%.
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18
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Tzanavaras PD, Papadimitriou S, Zacharis CK. Automated Stopped-Flow Fluorimetric Sensor for Biologically Active Adamantane Derivatives Based on Zone Fluidics. Molecules 2019; 24:molecules24213975. [PMID: 31684129 PMCID: PMC6864522 DOI: 10.3390/molecules24213975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 11/16/2022] Open
Abstract
A zone-fluidics (ZF) based automated fluorimetric sensor for the determination of pharmaceutically active adamantine derivatives, i.e., amantadine (AMA), memantine (MEM) and rimantadine (RIM) is reported. Discrete zones of the analytes and reagents (o-phthalaldehyde and N-acetylcysteine) mix and react under stopped-flow conditions to yield fluorescent iso-indole derivatives (λex/ λem = 340/455 nm). The proposed ZF sensor was developed and validated to prove suitable for quality control tests (assay and content uniformity) of commercially available formulations purchased from the Greek market (EU licensed) and from non-EU web-pharmacies at a sampling rate of 16 h-1. Interestingly, a formulation obtained through the internet and produced in a third-non-EU-country (AMA capsules, 100 mg per cap), was found to be out of specifications (mean assay of 85.3%); a validated HPLC method was also applied for confirmatory purposes.
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Affiliation(s)
- Paraskevas D Tzanavaras
- Laboratory of Analytical Chemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece.
| | - Sofia Papadimitriou
- Laboratory of Analytical Chemistry, School of Chemistry, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece.
| | - Constantinos K Zacharis
- Laboratory of Pharmaceutical Analysis, Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki GR-54124, Greece.
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19
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Wu G, Berka V, Derry PJ, Mendoza K, Kakadiaris E, Roy T, Kent TA, Tour JM, Tsai AL. Critical Comparison of the Superoxide Dismutase-like Activity of Carbon Antioxidant Nanozymes by Direct Superoxide Consumption Kinetic Measurements. ACS Nano 2019; 13:11203-11213. [PMID: 31509380 PMCID: PMC6832779 DOI: 10.1021/acsnano.9b04229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The superoxide dismutase-like activity of poly(ethylene glycolated) hydrophilic carbon clusters (PEG-HCCs), anthracite and bituminous graphene quantum dots (PEG-aGQDs and PEG-bGQDs, respectively), and two fullerene carbon nanozymes, tris malonyl-C60 fullerene (C3) and polyhydroxylated-C60 fullerene (C60-OHn), were compared using direct optical stopped-flow kinetic measurements, together with three native superoxide dismutases (SODs), CuZnSOD, MnSOD, and FeSOD, at both pH 12.7 and 8.5. Computer modeling including both SOD catalytic steps and superoxide self-dismutation enabled the best choice of catalyst concentration with minimal contribution to the observed kinetic change from the substrate self-dismutation. Biexponential fitting to the kinetic data ranks the rate constant (M-1 s-1) in the order of PEG-HCCs > CuZnSOD ≈ MnSOD ≈ PEG-aGQDs ≈ PEG-bGQDs > FeSOD ≫ C3 > C60-OHn at pH 12.7 and MnSOD > CuZnSOD ≈ PEG-HCCs > FeSOD > PEG-aGQDs ≈ PEG-bGQDs ≫ C3 ≈ C60-OHn at pH 8.5. Nonlinear regression of the kinetic model above yielded the same ranking as the biexponential fit, but provided better mechanistic insight. The data obtained by freeze-quench EPR direct assay at pH 12.7 also yield the same ranking as stopped-flow data. This is a necessary assessment of a panel of proclaimed carbon nano SOD mimetics using the same two direct methods, revealing a dramatic, 3-4 orders of magnitude difference in SOD activity between PEG-HCCs/PEG-GQDs from soluble fullerenes.
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Affiliation(s)
- Gang Wu
- Division of Hematology, Department of Internal Medicine, University of Texas-McGovern Medical School, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Vladimir Berka
- Division of Hematology, Department of Internal Medicine, University of Texas-McGovern Medical School, 6431 Fannin Street, Houston, Texas 77030, United States
| | - Paul J. Derry
- Center for Translational Research in Inflammatory Diseases, Michel E. DeBakey VA Medical Center, 2002 Holcombe Boulevard, Houston, Texas 77030, United States
- Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, United States
| | - Kimberly Mendoza
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Eugenia Kakadiaris
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Trenton Roy
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Thomas A. Kent
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Institute of Biosciences and Technology, Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, Texas 77030, United States
- Stanley H. Appel Department of Neurology, Houston Methodist Hospital and Research Institute, 6560 Fannin Street, Houston, Texas 77030, United States
| | - James M. Tour
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Smalley-Curl Institute, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- The NanoCarbon Center, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department of Materials Science and NanoEngineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ah-Lim Tsai
- Division of Hematology, Department of Internal Medicine, University of Texas-McGovern Medical School, 6431 Fannin Street, Houston, Texas 77030, United States
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20
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Yang X, Bennett B, Holz RC. Insights into the catalytic mechanism of a bacterial hydrolytic dehalogenase that degrades the fungicide chlorothalonil. J Biol Chem 2019; 294:13411-13420. [PMID: 31331935 DOI: 10.1074/jbc.ra119.009094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Indexed: 11/06/2022] Open
Abstract
Chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile; TPN) is one of the most commonly used fungicides in the United States. Given TPN's widespread use, general toxicity, and potential carcinogenicity, its biodegradation has garnered significant attention. Here, we developed a direct spectrophotometric assay for the Zn(II)-dependent, chlorothalonil-hydrolyzing dehalogenase from Pseudomonas sp. CTN-3 (Chd), enabling determination of its metal-binding properties; pH dependence of the kinetic parameters k cat, Km , and k cat/Km ; and solvent isotope effects. We found that a single Zn(II) ion binds a Chd monomer with a Kd of 0.17 μm, consistent with inductively coupled plasma MS data for the as-isolated Chd dimer. We observed that Chd was maximally active toward chlorothalonil in the pH range 7.0-9.0, and fits of these data yielded a pK ES1 of 5.4 ± 0.2, a pK ES2 of 9.9 ± 0.1 (k'cat = 24 ± 2 s-1), a pK E1 of 5.4 ± 0.3, and a pK E2 of 9.5 ± 0.1 (k'cat/k' m = 220 ± 10 s-1 mm-1). Proton inventory studies indicated that one proton is transferred in the rate-limiting step of the reaction at pD 7.0. Fits of UV-visible stopped-flow data suggested a three-step model and provided apparent rate constants for intermediate formation (i.e. a k'2 of 35.2 ± 0.1 s-1) and product release (i.e. a k'3 of 1.1 ± 0.2 s-1), indicating that product release is the slow step in catalysis. On the basis of these results, along with those previously reported, we propose a mechanism for Chd catalysis.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881; Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401.
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21
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Visconti L, Malagrinò F, Gianni S, Toto A. Structural characterization of an on-pathway intermediate and transition state in the folding of the N-terminal SH2 domain from SHP2. FEBS J 2019; 286:4769-4777. [PMID: 31287606 DOI: 10.1111/febs.14990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/29/2019] [Accepted: 07/06/2019] [Indexed: 12/23/2022]
Abstract
Src Homology 2 (SH2) domains are a class of protein domains that present a conserved three-dimensional structure and possess a crucial role in mediating protein-protein interactions. Despite their importance and abundance in the proteome, knowledge about the folding properties of SH2 domain is limited. Here we present an extensive mutational analysis (Φ value analysis) of the folding pathway of the N-SH2 domain of the Src homology region 2 domain-containing phosphatase-2 (SHP2) protein, a 104 residues domain that presents the classical SH2 domain fold (two α-helices flanking a central β-sheet composed of 3-5 antiparallel β-strands), with a fundamental role in mediating the interaction of SHP2 with its substrates and triggering key metabolic pathways in the cell. By analysing folding kinetic data we demonstrated that the folding pathway of N-SH2 presents an obligatory on-pathway intermediate that accumulates during the folding reaction. The production of 24 conservative site-directed variants allowed us to perform a Φ value analysis, by which we could fully characterize the intermediate and the transition state native-like interactions, providing a detailed quantitative analysis of the folding pathway of N-SH2. Results highlight the presence of a hydrophobic nucleus that stabilizes the intermediate, leading to a higher degree of native-like interactions in the transition state. Data are discussed and compared with previous works on SH2 domains.
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Affiliation(s)
- Lorenzo Visconti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Francesca Malagrinò
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Italy
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22
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Sebastián M, Velázquez-Campoy A, Medina M. The RFK catalytic cycle of the pathogen Streptococcus pneumoniae shows species-specific features in prokaryotic FMN synthesis. J Enzyme Inhib Med Chem 2018; 33:842-849. [PMID: 29693467 PMCID: PMC6010069 DOI: 10.1080/14756366.2018.1461857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023] Open
Abstract
Emergence of multidrug-resistant bacteria forces us to explore new therapeutic strategies, and proteins involved in key metabolic pathways are promising anti-bacterial targets. Bifunctional flavin-adenine dinucleotide (FAD) synthetases (FADS) are prokaryotic enzymes that synthesise the flavin mononucleotide (FMN) and FAD cofactors. The FADS from the human pathogen Streptococcus pneumoniae (SpnFADS)-causative agent of pneumonia in humans - shows relevant catalytic dissimilarities compared to other FADSs. Here, by integrating thermodynamic and kinetic data, we present a global description of the riboflavin kinase activity of SpnFADS, as well as of the inhibition mechanisms regulating this activity. Our data shed light on biophysical determinants that modulate species-specific conformational changes leading to catalytically competent conformations, as well as binding rates and affinities of substrates versus products. This knowledge paves the way for the development of tools - that taking advantage of the regulatory dissimilarities during FMN biosynthesis in different species - might be used in the discovery of specific anti-pneumococcal drugs.
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Affiliation(s)
- María Sebastián
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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23
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Araújo P, Basílio N, Fernandes A, Mateus N, de Freitas V, Pina F, Oliveira J. Impact of Lignosulfonates on the Thermodynamic and Kinetic Parameters of Malvidin-3- O-glucoside in Aqueous Solutions. J Agric Food Chem 2018; 66:6382-6387. [PMID: 29870233 DOI: 10.1021/acs.jafc.8b02273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The interaction of malvidin-3- O-glucoside (1) and a lignosulfonate was studied by UV-visible spectroscopy, and the results obtained showed the formation of a complex between the negatively charged lignosulfonate and the flavylium cation form (AH+) of this anthocyanin at pH 1. The thermodynamic and kinetic parameters of 1 in the presence of a lignosulfonate were determined by UV-visible spectroscopy and stopped-flow techniques. The main differences were observed in the flavylium cation (AH+)/quinoidal base (A) equilibrium, the AH+ form being more stabilized than A (p Ka1 = 4.4 ± 0.1) compared with 1 in the absence of the lignosulfonate (p Ka1 = 3.9 ± 0.1). Furthermore, comparing the hydration ( kh = 0.028 s-1) and dehydration ( k-h = 40 M-1 s-1) processes of 1 in the presence of the lignosulfonate with the processes of 1 ( kh = 0.12 s-1 and k-h = 35 M-1 s-1) show that the hydration process is slower while the dehydration process is practically unaffected in the presence of the lignosulfonate.
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Affiliation(s)
- Paula Araújo
- ICETA/REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, 687 , 4169-007 Porto , Portugal
| | - Nuno Basílio
- REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Monte de Caparica , Portugal
| | - Ana Fernandes
- ICETA/REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, 687 , 4169-007 Porto , Portugal
| | - Nuno Mateus
- ICETA/REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, 687 , 4169-007 Porto , Portugal
| | - Victor de Freitas
- ICETA/REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, 687 , 4169-007 Porto , Portugal
| | - Fernando Pina
- REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química, Faculdade de Ciências e Tecnologia , Universidade NOVA de Lisboa , 2829-516 Monte de Caparica , Portugal
| | - Joana Oliveira
- ICETA/REQUIMTE - Laboratório Associado para a Química Verde, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, 687 , 4169-007 Porto , Portugal
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24
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Bortolini C, Klausen LH, Hoffmann SV, Jones NC, Saadeh D, Wang Z, Knowles TPJ, Dong M. Rapid Growth of Acetylated Aβ(16-20) into Macroscopic Crystals. ACS Nano 2018; 12:5408-5416. [PMID: 29771495 DOI: 10.1021/acsnano.8b00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aberrant assembly of the amyloid-β (Aβ) is responsible for the development of Alzheimer's disease, but can also be exploited to obtain highly functional biomaterials. The short Aβ fragment, KLVFF (Aβ16-20), is crucial for Aβ assembly and considered to be an Aβ aggregation inhibitor. Here, we show that acetylation of KLVFF turns it into an extremely fast self-assembling molecule, reaching macroscopic ( i.e., mm) size in seconds. We show that KLVFF is metastable and that the self-assembly can be directed toward a crystalline or fibrillar phase simply through chemical modification, via acetylation or amidation of the peptide. Amidated KLVFF can form amyloid fibrils; we observed folding events of such fibrils occurring in as little as 60 ms. The ability of single KLVFF molecules to rapidly assemble as highly ordered macroscopic structures makes it a promising candidate for applications as a rapid-forming templating material.
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Affiliation(s)
- Christian Bortolini
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Lasse Hyldgaard Klausen
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | | | - Nykola C Jones
- ISA, Department of Physics and Astronomy , Aarhus University , Aarhus 8000 , Denmark
| | - Daniela Saadeh
- Centre for Astronomy & Particle Theory , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Zegao Wang
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center , Aarhus University , Aarhus 8000 , Denmark
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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25
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Smirnova I, Kasho V, Jiang X, Chen HM, Withers SG, Kaback HR. Oversized galactosides as a probe for conformational dynamics in LacY. Proc Natl Acad Sci U S A 2018; 115:4146-51. [PMID: 29602806 DOI: 10.1073/pnas.1800706115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding kinetics of α-galactopyranoside homologs with fluorescent aglycones of different sizes and shapes were determined with the lactose permease (LacY) of Escherichia coli by FRET from Trp151 in the binding site of LacY to the fluorophores. Fast binding was observed with LacY stabilized in an outward-open conformation (kon = 4-20 μM-1·s-1), indicating unobstructed access to the binding site even for ligands that are much larger than lactose. Dissociation rate constants (koff) increase with the size of the aglycone so that Kd values also increase but remain in the micromolar range for each homolog. Phe27 (helix I) forms an apparent constriction in the pathway for sugar by protruding into the periplasmic cavity. However, replacement of Phe27 with a bulkier Trp does not create an obstacle in the pathway even for large ligands, since binding kinetics remain unchanged. High accessibility of the binding site is also observed in a LacY/nanobody complex with partially blocked periplasmic opening. Remarkably, E. coli expressing WT LacY catalyzes transport of α- or β-galactopyranosides with oversized aglycones such as bodipy or Aldol518, which may require an extra space within the occluded intermediate. The results confirm that LacY specificity is strictly directed toward the galactopyranoside ring and also clearly indicate that the opening on the periplasmic side is sufficiently wide to accommodate the large galactoside derivatives tested here. We conclude that the actual pathway for the substrate entering from the periplasmic side is wider than the pore diameter calculated in the periplasmic-open X-ray structures.
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26
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Hathazi D, Scurtu F, Bischin C, Mot A, Attia AAA, Kongsted J, Silaghi-Dumitrescu R. The Reaction of Oxy Hemoglobin with Nitrite: Mechanism, Antioxidant-Modulated Effect, and Implications for Blood Substitute Evaluation. Molecules 2018; 23:molecules23020350. [PMID: 29414908 PMCID: PMC6017026 DOI: 10.3390/molecules23020350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/27/2022] Open
Abstract
The autocatalytic reaction between nitrite and the oxy form of globins involves free radicals. For myoglobin (Mb), an initial binding of nitrite to the iron-coordinated oxygen molecule was proposed; the resulting ferrous-peroxynitrate species was not detected, but its decay product, the high-valent ferryl form, was demonstrated in stopped-flow experiments. Reported here are the stopped flow spectra recorded upon mixing oxy Hb (native, as well as chemically-derivatized in the form of several candidates of blood substitutes) with a supraphysiological concentration of nitrite. The data may be fitted to a simple kinetic model involving a transient met-aqua form, in contrast to the ferryl detected in the case of Mb in a similar reaction sequence. These data are in line with a previous observation of a transient accumulation of ferryl Hb under auto-catalytic conditions at much lower concentrations of nitrite (Grubina, R. et al. J. Biol. Chem. 2007, 282, 12916). The simple model for fitting the stopped-flow data leaves a small part of the absorbance changes unaccounted for, unless a fourth species is invoked displaying features similar to the oxy and tentatively assigned as ferrous-peroxynitrate. Density functional theory (DFT) calculations support this latter assignment. The reaction allows for differentiating between the reactivities of various chemically modified hemoglobins, including candidates for blood substitutes. Polymerization of hemoglobin slows the nitrite-induced oxidation, in sharp contrast to oxidative-stress type reactions which are generally accelerated, not inhibited. Sheep hemoglobin is found to be distinctly more resistant to reaction with nitrite compared to bovine Hb, at large nitrite concentrations (stopped-flow experiments directly observing the oxy + nitrite reaction) as well as under auto-catalytic conditions. Copolymerization of Hb with bovine serum albumin (BSA) using glutaraldehyde leads to a distinct increase of the lag time compared to native Hb as well as to any other form of derivatization examined in the present study. The Hb-BSA copolymer also displays a slower initial reaction with nitrite under stopped-flow conditions, compared to native Hb.
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Affiliation(s)
- Denisa Hathazi
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
| | - Florina Scurtu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
| | - Cristina Bischin
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
| | - Augustin Mot
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
| | - Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania.
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Abstract
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The
mechanism of Aβ aggregation in the absence of metal ions
is well established, yet the role that Zn2+ and Cu2+, the two most studied metal ions, released during neurotransmission,
paly in promoting Aβ aggregation in the vicinity of neuronal
synapses remains elusive. Here we report the kinetics of Zn2+ binding to Aβ and Zn2+/Cu2+ binding
to Aβ-Cu to form ternary complexes under near physiological
conditions (nM Aβ, μM metal ions). We find that these
reactions are several orders of magnitude slower than Cu2+ binding to Aβ. Coupled reaction-diffusion simulations of the
interactions of synaptically released metal ions with Aβ show
that up to a third of Aβ is Cu2+-bound under repetitive
metal ion release, while any other Aβ-metal complexes (including
Aβ-Zn) are insignificant. We therefore conclude that Zn2+ is unlikely to play an important role in the very early
stages (i.e., dimer formation) of Aβ aggregation, contrary to
a widely held view in the subject. We propose that targeting the specific
interactions between Cu2+ and Aβ may be a viable
option in drug development efforts for early stages of AD.
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Affiliation(s)
- Thomas Branch
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mauricio Barahona
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Charlotte A. Dodson
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Liming Ying
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
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28
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You J, Li H, Lu XM, Li W, Wang PY, Dou SX, Xi XG. Effects of monovalent cations on folding kinetics of G-quadruplexes. Biosci Rep 2017; 37:BSR20170771. [PMID: 28588052 DOI: 10.1042/BSR20170771] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes are special structures existing at the ends of human telomeres,
the folding kinetics of which are essential for their functions, such as in the
maintenance of genome stability and the protection of chromosome ends. In the
present study, we investigated the folding kinetics of G-quadruplex in different
monovalent cation environments and determined the detailed kinetic parameters
for Na+- and K+-induced G-quadruplex folding, and for its
structural transition from the basket-type Na+ form to the
hybrid-type K+ form. More interestingly, although Li+ was
often used in previous studies of G-quadruplex folding as a control ion supposed
to have no effect, we have found that Li+ can actually influence the
folding kinetics of both Na+- and K+-induced
G-quadruplexes significantly and in different ways, by changing the folding
fraction of Na+-induced G-quadruplexes and greatly increasing the
folding rates of K+-induced G-quadruplexes. The present study may
shed new light on the roles of monovalent cations in G-quadruplex folding and
should be useful for further studies of the underlying folding mechanism.
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29
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Shrestha R, Chen X, Ramyar KX, Hayati Z, Carlson EA, Bossmann SH, Song L, Geisbrecht BV, Li P. Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata. ACS Catal 2016; 6:8036-8047. [PMID: 29308294 DOI: 10.1021/acscatal.6b01952] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases, in which a catalytic distal aspartate is involved in H2O2 activation to catalyze oxidations in acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds (J. Biol. Chem.2015, 290, 23447). Based on the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II-like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the crosslinking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal possibly due to its extremely small solvent accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.
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Affiliation(s)
| | | | | | - Zahra Hayati
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | | | | | - Likai Song
- National
High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
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Ghodsi F, Habibi-Khorassani SM, Shahraki M. Kinetic Spectrophotometric Method for the 1,4-Diionic Organophosphorus Formation in the Presence of Meldrum's Acid: Stopped-Flow Approach. Molecules 2016; 21:E1514. [PMID: 27845723 DOI: 10.3390/molecules21111514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 11/17/2022] Open
Abstract
The kinetics of the reaction between triphenylphosphine (TPP) and dimethyl acetylenedicarboxylate (DMAD) in the presence of Meldrum’s acid (MA) for the generation of the 1,4-diionic organophosphorus compound has been investigated using the stopped-flow and UV-VIS spectrophotometry techniques. The first step of the reaction between TPP and DMAD for the generation of (I1) in ethanol was followed by the stopped-flow apparatus. This step was recognized as a fast step. The reaction between the intermediate (I1) and MA showed first-order kinetics, and it was followed by the UV-VIS spectrophotometry technique. The activation parameters for the slow step of the proposed mechanism were determined using two linearized forms of the Eyring equation. From the temperature, concentration and solvent studies, the activation energy (Ea = 20.16 kJ·mol−1) and the related activation parameters (ΔG‡ = 71.17 ± 0.015 kJ·mol−1, ΔS‡ = −185.49 ± 0.026 J·mol−1 and ΔH‡ =17.72 ± 0.007 kJ·mol−1) were calculated. The experimental data indicated that the reaction was zero-order in MA and second-order overall. The proposed mechanism was confirmed with the observed kinetic data obtained from the UV-VIS and stopped-flow techniques.
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Hu H, Luo C, Zheng YG. Transient Kinetics Define a Complete Kinetic Model for Protein Arginine Methyltransferase 1. J Biol Chem 2016; 291:26722-26738. [PMID: 27834681 DOI: 10.1074/jbc.m116.757625] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/10/2016] [Indexed: 12/31/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are the enzymes responsible for posttranslational methylation of protein arginine residues in eukaryotic cells, particularly within the histone tails. A detailed mechanistic model of PRMT-catalyzed methylation is currently lacking, but it is essential for understanding the functions of PRMTs in various cellular pathways and for efficient design of PRMT inhibitors as potential treatments for a range of human diseases. In this work, we used stopped-flow fluorescence in combination with global kinetic simulation to dissect the transient kinetics of PRMT1, the predominant type I arginine methyltransferase. Several important mechanistic insights were revealed. The cofactor and the peptide substrate bound to PRMT1 in a random manner and then followed a kinetically preferred pathway to generate the catalytic enzyme-cofactor-substrate ternary complex. Product release proceeded in an ordered fashion, with peptide dissociation followed by release of the byproduct S-adenosylhomocysteine. Importantly, the dissociation rate of the monomethylated intermediate from the ternary complex was much faster than the methyl transfer. Such a result provided direct evidence for distributive arginine dimethylation, which means the monomethylated substrate has to be released to solution and rebind with PRMT1 before it undergoes further methylation. In addition, cofactor binding involved a conformational transition, likely an open-to-closed conversion of the active site pocket. Further, the histone H4 peptide bound to the two active sites of the PRMT1 homodimer with differential affinities, suggesting a negative cooperativity mechanism of substrate binding. These findings provide a new mechanistic understanding of how PRMTs interact with their substrates and transfer methyl groups.
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Affiliation(s)
- Hao Hu
- From the Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia 30602 and
| | - Cheng Luo
- the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Y George Zheng
- From the Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia 30602 and
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Kuznetsov NA, Lebedeva NA, Kuznetsova AA, Rechkunova NI, Dyrkheeva NS, Kupryushkin MS, Stetsenko DA, Pyshnyi DV, Fedorova OS, Lavrik OI. Pre-steady state kinetics of DNA binding and abasic site hydrolysis by tyrosyl-DNA phosphodiesterase 1. J Biomol Struct Dyn 2016; 35:2314-2327. [PMID: 27687298 DOI: 10.1080/07391102.2016.1220331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) processes DNA 3'-end-blocking modifications, possesses DNA and RNA 3'-nucleosidase activity and is also able to hydrolyze an internal apurinic/apyrimidinic (AP) site and its synthetic analogs. The mechanism of Tdp1 interaction with DNA was analyzed using pre-steady state stopped-flow kinetics with tryptophan, 2-aminopurine and Förster resonance energy transfer fluorescence detection. Phosphorothioate or tetramethyl phosphoryl guanidine groups at the 3'-end of DNA have been used to prevent 3'-nucleosidase digestion by Tdp1. DNA binding and catalytic properties of Tdp1 and its mutants H493R (Tdp1 mutant SCAN1) and H263A have been compared. The data indicate that the initial step of Tdp1 interaction with DNA includes binding of Tdp1 to the DNA ends followed by the 3'-nucleosidase reaction. In the case of DNA containing AP site, three steps of fluorescence variation were detected that characterize (i) initial binding the enzyme to the termini of DNA, (ii) the conformational transitions of Tdp1 and (iii) search for and recognition of the AP-site in DNA, which leads to the formation of the catalytically active complex and to the AP-site cleavage reaction. Analysis of Tdp1 interaction with single- and double-stranded DNA substrates shows that the rates of the 3'-nucleosidase and AP-site cleavage reactions have similar values in the case of single-stranded DNA, whereas in double-stranded DNA, the cleavage of the AP-site proceeds two times faster than 3'-nucleosidase digestion. Therefore, the data show that the AP-site cleavage reaction is an essential function of Tdp1 which may comprise an independent of AP endonuclease 1 AP-site repair pathway.
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Affiliation(s)
- Nikita A Kuznetsov
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Natalia A Lebedeva
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Alexandra A Kuznetsova
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia
| | - Nadejda I Rechkunova
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Nadezhda S Dyrkheeva
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia
| | - Maxim S Kupryushkin
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia
| | - Dmitry A Stetsenko
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia
| | - Dmitrii V Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Olga S Fedorova
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
| | - Olga I Lavrik
- a Institute of Chemical Biology and Fundamental Medicine , Siberian Branch of the Russian Academy of Sciences , Novosibirsk 630090 , Russia.,b Department of Natural Sciences , Novosibirsk State University , Novosibirsk 630090 , Russia
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Singh SP, Koc KN, Stodola JL, Galletto R. A Monomer of Pif1 Unwinds Double-Stranded DNA and It Is Regulated by the Nature of the Non-Translocating Strand at the 3'-End. J Mol Biol 2016; 428:1053-1067. [PMID: 26908222 DOI: 10.1016/j.jmb.2016.02.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 11/17/2022]
Abstract
Using a DNA polymerase coupled assay and FRET (Förster resonance energy transfer)-based helicase assays, in this work, we show that a monomer of Saccharomyces cerevisiae Pif1 can unwind dsDNA (double-stranded DNA). The helicase activity of a Pif1 monomer is modulated by the nature of the 3'-ssDNA (single-stranded DNA) tail of the substrate and its effect on a Pif1-dependent re-winding activity that is coupled to the opening of dsDNA. We propose that, in addition to the ssDNA site on the protein that interacts with the translocating strand, Pif1 has a second site that binds the 3'-ssDNA of the substrate. Interaction of DNA with this site modulates the degree to which re-winding counteracts unwinding. Depending on the nature of the 3'-tail and the length of the duplex DNA to be unwound, this activity is sufficiently strong to mask the helicase activity of a monomer. In excess Pif1 over the DNA, the Pif1-dependent re-winding of the opened DNA strongly limits unwinding, independent of the 3'-tail. We propose that, in this case, binding of DNA to the second site is precluded and modulation of the Pif1-dependent re-winding activity is largely lost.
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Affiliation(s)
- Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katrina N Koc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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Gray RD, Trent JO, Chaires JB. Folding and unfolding pathways of the human telomeric G-quadruplex. J Mol Biol 2014; 426:1629-50. [PMID: 24487181 DOI: 10.1016/j.jmb.2014.01.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 11/30/2022]
Abstract
Sequence analogs of human telomeric DNA such as d[AGGG(TTAGGG)3] (Tel22) fold into monomeric quadruplex structures in the presence of a suitable cation. To investigate the pathway for unimolecular quadruplex formation, we monitored the kinetics of K(+)-induced folding of Tel22 by circular dichroism (CD), intrinsic 2-aminopurine fluorescence, and fluorescence resonance energy transfer (FRET). The results are consistent with a four-step pathway U ↔ I1 ↔ I2 ↔ I3 ↔ F where U and F represent unfolded and folded conformational ensembles and I1, I2, and I3 are intermediates. Previous kinetic studies have shown that I1 is formed in a rapid pre-equilibrium and may consist of an ensemble of "prefolded" hairpin structures brought about by cation-induced electrostatic collapse of the DNA. The current study shows that I1 converts to I2 with a relaxation time τ1=0.1s at 25 °C in 25 mM KCl. The CD spectrum of I2 is characteristic of an antiparallel quadruplex that could form as a result of intramolecular fold-over of the I1 hairpins. I3 is relatively slowly formed (τ2≈3700s) and has CD and FRET properties consistent with those expected of a triplex structure as previously observed in equilibrium melting studies. I3 converts to F with τ3≈750s. Identical pathways with different kinetic constants involving a rapidly formed antiparallel intermediate were observed with oligonucleotides forming mixed parallel/antiparallel hybrid-1 and hybrid-2 topologies {e.g. d[TTGGG(TTAGGG)3A] and d[TAGGG(TTAGGG)3TT]}. Aspects of the kinetics of unfolding were also monitored by the spectroscopic methods listed above and by time-resolved fluorescence lifetime measurements using a complementary strand trap assay. These experiments reveal a slow, rate-limiting step along the unfolding pathway.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
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Qin ZJ, Shimizu A, Li J, Ikeguchi M, Shinjo M, Kihara H. α-helix formation rate of oligopeptides at subzero temperatures. Biophysics (Nagoya-shi) 2014; 10:9-13. [PMID: 27493493 PMCID: PMC4629656 DOI: 10.2142/biophysics.10.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/24/2014] [Indexed: 12/01/2022] Open
Abstract
In 1999, Clarke et al. ((1999) Proc. Natl. Acad. Sci. USA 96, 7232–7237) reported that the nucleation rate of α-helix of oligopeptide AK16 is as slow as 60 ms. In the present study, we measured the nucleation rate of oligopeptide, C17 (DLTDDIMCVKKILDKVG, corresponding to α-helical region of 84th to 100th amino acids of bovine α-lactalbumin) using the same method as Clarke et al. We found only initial bursts of the increase of α-helices at temperatures higher than −50°C in the presence of 70% methanol. The result with AK16 was the same as Clarke et al. reported. We also found that the folding rate of polyglutamic acid is too fast to be detected by the stopped-flow apparatus at 4°C. These results demonstrate that the α-helix formation rates in C17, AK16 and polyglutamic acid are shorter than the dead time of the stopped-flow apparatus (6 ms).
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Affiliation(s)
- Zhi-Jie Qin
- Department of Physics, Kansai Medical University, 2-5-1, Shin-Machi, Hirakata, Osaka 573-1010, Japan
| | - Akio Shimizu
- Department of Environmental Engineering for Symbiosis, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Jinsong Li
- Department of Physics, Kansai Medical University, 2-5-1, Shin-Machi, Hirakata, Osaka 573-1010, Japan
| | - Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan
| | - Masaji Shinjo
- Department of Physics, Kansai Medical University, 2-5-1, Shin-Machi, Hirakata, Osaka 573-1010, Japan
| | - Hiroshi Kihara
- Department of Physics, Kansai Medical University, 2-5-1, Shin-Machi, Hirakata, Osaka 573-1010, Japan
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Esadze A, Iwahara J. Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process. J Mol Biol 2013; 426:230-44. [PMID: 24076422 DOI: 10.1016/j.jmb.2013.09.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/25/2023]
Abstract
Kinetic characterizations of protein translocation on DNA are nontrivial because the simultaneous presence of multiple different mechanisms makes it difficult to extract the information specific to a particular translocation mechanism. In this study, we have developed new approaches for the kinetic investigations of proteins' sliding and intersegment transfer (also known as "direct transfer") in the target DNA search process. Based on the analytical expression of the mean search time for the discrete-state stochastic model, we derived analytical forms of the apparent rate constant kapp for protein-target association in systems involving competitor DNA and the intersegment transfer mechanism. Our analytical forms of kapp facilitate the experimental determination of the kinetic rate constants for intersegment transfer and sliding in the target association process. Using stopped-flow fluorescence data for the target association kinetics along with the analytical forms of kapp, we have studied the translocation of the Egr-1 zinc-finger protein in the target DNA association process. Sliding was analyzed using the DNA-length-dependent kapp data. Using the dependence of kapp on the concentration of competitor DNA, we determined the second-order rate constant for intersegment transfer. Our results indicate that a major pathway in the target association process for the Egr-1 zinc-finger protein is the one involving intersegment transfer to a nonspecific site and the subsequent sliding to the target.
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Affiliation(s)
- Alexandre Esadze
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA.
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Mizukami T, Xu M, Cheng H, Roder H, Maki K. Nonuniform chain collapse during early stages of staphylococcal nuclease folding detected by fluorescence resonance energy transfer and ultrarapid mixing methods. Protein Sci 2013; 22:1336-48. [PMID: 23904284 DOI: 10.1002/pro.2320] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 11/07/2022]
Abstract
The development of tertiary structure during folding of staphylococcal nuclease (SNase) was studied by time-resolved fluorescence resonance energy transfer measured using continuous- and stopped-flow techniques. Variants of this two-domain protein containing intradomain and interdomain fluorescence donor/acceptor pairs (Trp and Cys-linked fluorophore or quencher) were prepared to probe the intradomain and interdomain structural evolution accompanying SNase folding. The intra-domain donor/acceptor pairs are within the β-barrel domain (Trp27/Cys64 and Trp27/Cys97) and the interdomain pair is between the α-helical domain and the β-barrel domain (Trp140/Cys64). Time-resolved energy transfer efficiency accompanying folding and unfolding at different urea concentrations was measured over a time range from 30 μs to ≈ 10 s. Information on average donor/acceptor distances at different stages of the folding process was obtained by using a quantitative kinetic modeling approach. The average distance for the donor/acceptor pairs in the β-barrel domain decreases to nearly native values whereas that of the interdomain donor/acceptor pairs remains unchanged in the earliest intermediate (<500 μs of refolding). This indicates a rapid nonuniform collapse resulting in an ensemble of heterogeneous conformations in which the central region of the β-barrel domain is well developed while the C-terminal α-helical domain remains disordered. The distance between Trp140 and Cys64 decreases to native values on the 100-ms time scale, indicating that the α-helical domain docks onto the preformed β-barrel at a late stage of the folding. In addition, the unfolded state is found to be more compact under native conditions, suggesting that changes in solvent conditions may induce a nonspecific hydrophobic collapse.
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Affiliation(s)
- Takuya Mizukami
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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Haque MM, Tejero J, Bayachou M, Wang ZQ, Fadlalla M, Stuehr DJ. Thermodynamic characterization of five key kinetic parameters that define neuronal nitric oxide synthase catalysis. FEBS J 2013; 280:4439-53. [PMID: 23789902 DOI: 10.1111/febs.12404] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/30/2022]
Abstract
NO synthase (NOS) enzymes convert L-arginine to NO in two sequential reactions whose rates (k(cat1) and k(cat2)) are both limited by the rate of ferric heme reduction (k(r)). An enzyme ferric heme-NO complex forms as an immediate product complex and then undergoes either dissociation (at a rate that we denote as k(d)) to release NO in a productive manner, or reduction (k(r)) to form a ferrous heme-NO complex that must react with O2 (at a rate that we denote as k(ox)) in a NO dioxygenase reaction that regenerates the ferric enzyme. The interplay of these five kinetic parameters (k(cat1), k(cat2), k(r), k(d) and k(ox)) determines NOS specific activity, O2 concentration response, and pulsatile versus steady-state NO generation. In the present study, we utilized stopped-flow spectroscopy and single catalytic turnover methods to characterize the individual temperature dependencies of the five kinetic parameters of rat neuronal NOS. We then incorporated the measured kinetic values into computer simulations of the neuronal NOS reaction using a global kinetic model to comprehensively model its temperature-dependent catalytic behaviours. The results obtained provide new mechanistic insights and also reveal that the different temperature dependencies of the five kinetic parameters significantly alter neuronal NOS catalytic behaviours and NO release efficiency as a function of temperature.
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Romero E, Robinson R, Sobrado P. Monitoring the reductive and oxidative half-reactions of a flavin-dependent monooxygenase using stopped-flow spectrophotometry. J Vis Exp 2012:3803. [PMID: 22453826 PMCID: PMC3415168 DOI: 10.3791/3803] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus siderophore A (SidA) is an FAD-containing monooxygenase that catalyzes the hydroxylation of ornithine in the biosynthesis of hydroxamate siderophores that are essential for virulence (e.g. ferricrocin or N',N",N'''-triacetylfusarinine C). The reaction catalyzed by SidA can be divided into reductive and oxidative half-reactions. In the reductive half-reaction, the oxidized FAD bound to Af SidA, is reduced by NADPH. In the oxidative half-reaction, the reduced cofactor reacts with molecular oxygen to form a C4a-hydroperoxyflavin intermediate, which transfers an oxygen atom to ornithine. Here, we describe a procedure to measure the rates and detect the different spectral forms of SidA using a stopped-flow instrument installed in an anaerobic glove box. In the stopped-flow instrument, small volumes of reactants are rapidly mixed, and after the flow is stopped by the stop syringe, the spectral changes of the solution placed in the observation cell are recorded over time. In the first part of the experiment, we show how we can use the stopped-flow instrument in single mode, where the anaerobic reduction of the flavin in Af SidA by NADPH is directly measured. We then use double mixing settings where Af SidA is first anaerobically reduced by NADPH for a designated period of time in an aging loop, and then reacted with molecular oxygen in the observation cell. In order to perform this experiment, anaerobic buffers are necessary because when only the reductive half-reaction is monitored, any oxygen in the solutions will react with the reduced flavin cofactor and form a C4a-hydroperoxyflavin intermediate that will ultimately decay back into the oxidized flavin. This would not allow the user to accurately measure rates of reduction since there would be complete turnover of the enzyme. When the oxidative half-reaction is being studied the enzyme must be reduced in the absence of oxygen so that just the steps between reduction and oxidation are observed. One of the buffers used in this experiment is oxygen saturated so that we can study the oxidative half-reaction at higher concentrations of oxygen. These are often the procedures carried out when studying either the reductive or oxidative half-reactions with flavin-containing monooxygenases. The time scale of the pre-steady-state experiments performed with the stopped-flow is milliseconds to seconds, which allow the determination of intrinsic rate constants and the detection and identification of intermediates in the reaction. The procedures described here can be applied to other flavin-dependent monooxygenases.
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Affiliation(s)
- Elvira Romero
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Virginia, USA
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Abu-Soud HM, Maitra D, Byun J, Souza CEA, Banerjee J, Saed GM, Diamond MP, Andreana PR, Pennathur S. The reaction of HOCl and cyanocobalamin: corrin destruction and the liberation of cyanogen chloride. Free Radic Biol Med 2012; 52:616-625. [PMID: 22138102 PMCID: PMC3786219 DOI: 10.1016/j.freeradbiomed.2011.10.496] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 12/17/2022]
Abstract
Overproduction of hypochlorous acid (HOCl) has been associated with the development of a variety of disorders such as inflammation, heart disease, pulmonary fibrosis, and cancer through its ability to modify various biomolecules. HOCl is a potent oxidant generated by the myeloperoxidase-hydrogen peroxide-chloride system. Recently, we have provided evidence to support the important link between higher levels of HOCl and heme destruction and free iron release from hemoglobin and RBCs. Our current findings extend this work and show the ability of HOCl to mediate the destruction of metal-ion derivatives of tetrapyrrole macrocyclic rings, such as cyanocobalamin (Cobl), a common pharmacological form of vitamin B12. Cyanocobalamin is a water-soluble vitamin that plays an essential role as an enzyme cofactor and antioxidant, modulating nucleic acid metabolism and gene regulation. It is widely used as a therapeutic agent and supplement, because of its efficacy and stability. In this report, we demonstrate that although Cobl can be an excellent antioxidant, exposure to high levels of HOCl can overcome the beneficial effects of Cobl and generate proinflammatory reaction products. Our rapid kinetic, HPLC, and mass spectrometric analyses showed that HOCl can mediate corrin ring destruction and liberate cyanogen chloride (CNCl) through a mechanism that initially involves α-axial ligand replacement in Cobl to form a chlorinated derivative, hydrolysis, and cleavage of the phosphonucleotide moiety. Additionally, it can liberate free Co, which can perpetuate metal-ion-induced oxidant stress. Taken together, these results are the first report of the generation of toxic molecular products through the interaction of Cobl with HOCl.
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Affiliation(s)
- Husam M Abu-Soud
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA; Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Dhiman Maitra
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jaeman Byun
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Carlos Eduardo A Souza
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jashoman Banerjee
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Ghassan M Saed
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael P Diamond
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Peter R Andreana
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Maitra D, Byun J, Andreana PR, Abdulhamid I, Saed GM, Diamond MP, Pennathur S, Abu-Soud HM. Mechanism of hypochlorous acid-mediated heme destruction and free iron release. Free Radic Biol Med 2011; 51:364-73. [PMID: 21466849 PMCID: PMC3378337 DOI: 10.1016/j.freeradbiomed.2011.03.040] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 03/25/2011] [Accepted: 03/29/2011] [Indexed: 11/23/2022]
Abstract
Here, we show that hypochlorous acid (HOCl), a potent neutrophil-generated oxidant, can mediate destruction of free heme (Ht) and the heme precursor, protoporphyrin IX (PPIX). Ht displays a broad Soret absorbance peak centered at 365 and 394 nm, indicative of the presence of monomer and μ-oxo-dimer. Oxidation of Ht by HOCl was accompanied by a marked decrease in the Soret absorption peak and release of free iron. Kinetic measurements showed that the Ht-HOCl reaction was triphasic. The first two phases were HOCl concentration dependent and attributable to HOCl binding to the monomeric and dimeric forms. The third phase was HOCl concentration independent and attributed to Ht destruction with the release of free iron. HPLC and LC-ESI-MS analyses of the Ht-HOCl reaction revealed the formation of a number of degradation products, resulting from the cleavage or modification of one or more carbon-methene bridges of the porphyrin ring. Similar studies with PPIX showed that HOCl also mediated tetrapyrrole ring destruction. Collectively, this work demonstrates the ability of HOCl to modulate destruction of heme, through a process that occurs independent of the iron molecule that resides in the porphyrin center. This phenomenon may play a role in HOCl-mediated oxidative injury in pathological conditions.
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Affiliation(s)
- Dhiman Maitra
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jaeman Byun
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter R. Andreana
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Ibrahim Abdulhamid
- Department of Pediatrics, Children's Hospital of Michigan, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Ghassan M. Saed
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael P. Diamond
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Husam M. Abu-Soud
- Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Corresponding Author: Husam M. Abu-Soud, Ph.D., Wayne State University School of Medicine, Department of Obstetrics and Gynecology, The C.S. Mott Center for Human Growth and Development, 275 E. Hancock, Detroit, MI 48201, Tel: 313 577-6178; Fax: 313 577-8554;
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Abstract
The on and off rates corresponding to the binding of two test anions (acetate, AcO(-), and dihydrogen phosphate, H(2)PO(4)(-), studied as their tetrabutylammonium salts) to diprotonated cyclo[8]pyrrole have been determined in CH(3)CN using stopped-flow analyses carried out at various temperatures. For dihydrogen phosphate, this afforded the activation enthalpies and entropies associated with both off and on processes. The different dynamic behavior seen for these test anions underscores the utility of kinetic analyses as a possible new tool for the advanced characterization of anion receptors.
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Affiliation(s)
- Elizabeth Karnas
- Department of Chemistry & Biochemistry, University Station-A5300, The University of Texas, Austin, Texas 78712-0165, USA
| | - Sung Kuk Kim
- Department of Chemistry & Biochemistry, University Station-A5300, The University of Texas, Austin, Texas 78712-0165, USA
| | - Kenneth A. Johnson
- Department of Chemistry & Biochemistry, University Station-A5300, The University of Texas, Austin, Texas 78712-0165, USA
| | - Jonathan L. Sessler
- Department of Chemistry & Biochemistry, University Station-A5300, The University of Texas, Austin, Texas 78712-0165, USA
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
| | - Kei Ohkubo
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shunichi Fukuzumi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Bioinspired Science, Ewha Womans University, Seoul, 120-750, Korea
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Mijailovich SM, Li X, del Alamo JC, Griffiths RH, Kecman V, Geeves MA. Resolution and uniqueness of estimated parameters of a model of thin filament regulation in solution. Comput Biol Chem 2010; 34:19-33. [PMID: 20060364 PMCID: PMC6089521 DOI: 10.1016/j.compbiolchem.2009.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Revised: 11/24/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022]
Abstract
The estimation of chemical kinetic rate constants for any non-trivial model is complex due to the nonlinear effects of second order chemical reactions. We developed an algorithm to accomplish this goal based on the Damped Least Squares (DLS) inversion method and then tested the effectiveness of this method on the McKillop-Geeves (MG) model of thin filament regulation. The kinetics of MG model is defined by a set of nonlinear ordinary differential equations (ODEs) that predict the evolution of troponin-tropomyosin-actin and actin-myosin states. The values of the rate constants are estimated by integrating these ODEs numerically and fitting them to a series of stopped-flow pyrene fluorescence transients of myosin-S1 fragment binding to regulated actin in solution. The accuracy and robustness of the estimated rate constants are evaluated for DLS and two other methods, namely quasi-Newton (QN) and simulated annealing (SA). The comparison of these methods revealed that SA provides the best estimates of the model parameters because of its global optimization scheme. However it converges slowly and does quantify the uniqueness of the estimated parameters. On the other hand the QN method converges rapidly but only if the initial guess of the parameters is close to the optimum values, otherwise it diverges. Overall, the DLS method proves to be the most convenient method. It converges fast and was able to provide excellent estimates of kinetic parameters. Furthermore, DLS provides the model resolution matrix, which quantifies the interdependence of model parameters thereby evaluating the uniqueness of their estimated values. This property is essential for estimating of the dependence of the model parameters on experimental conditions (e.g. Ca(2+) concentration) when it is assessed from noisy experimental data such as pyrene fluorescence from stopped-flow transients. The advantages of the DLS method observed in this study should be further examined in other physicochemical systems to firmly establish the observed effectiveness of DSL vs. the other parameter estimation methods.
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Affiliation(s)
- Srboljub M Mijailovich
- Molecular and Integrative Physiological Sciences, Dept. of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA.
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Zuberek J, Kubacka D, Jablonowska A, Jemielity J, Stepinski J, Sonenberg N, Darzynkiewicz E. Weak binding affinity of human 4EHP for mRNA cap analogs. RNA 2007; 13:691-7. [PMID: 17369309 PMCID: PMC1852817 DOI: 10.1261/rna.453107] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ribosome recruitment to the majority of eukaryotic mRNAs is facilitated by the interaction of the cap binding protein, eIF4E, with the mRNA 5' cap structure. eIF4E stimulates translation through its interaction with a scaffolding protein, eIF4G, which helps to recruit the ribosome. Metazoans also contain a homolog of eIF4E, termed 4EHP, which binds the cap structure, but not eIF4G, and thus cannot stimulate translation, but it instead inhibits the translation of only one known, and possibly subset mRNAs. To understand why 4EHP does not inhibit general translation, we studied the binding affinity of 4EHP for cap analogs using two methods: fluorescence titration and stopped-flow measurements. We show that 4EHP binds cap analogs m(7)GpppG and m(7)GTP with 30 and 100 lower affinity than eIF4E. Thus, 4EHP cannot compete with eIF4E for binding to the cap structure of most mRNAs.
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Affiliation(s)
- Joanna Zuberek
- Department of Biophysics, Institute of Experimental Physics, Warsaw University, 02-089 Warsaw, Poland
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45
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Zhu J, Egawa T, Yeh SR, Yu L, Yu CA. Simultaneous reduction of iron-sulfur protein and cytochrome b(L) during ubiquinol oxidation in cytochrome bc(1) complex. Proc Natl Acad Sci U S A 2007; 104:4864-9. [PMID: 17360398 PMCID: PMC1829230 DOI: 10.1073/pnas.0607812104] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Indexed: 11/18/2022] Open
Abstract
The key step of the protonmotive Q-cycle mechanism of the cytochrome bc(1) complex is the bifurcated oxidation of ubiquinol at the Qp site. It was postulated that the iron-sulfur protein (ISP) accepts the first electron from ubiquinol to generate ubisemiquinone anion to reduce b(L). Because of the difficulty of following the reduction of ISP optically, direct evidence for the early involvement of ISP in ubiquinol oxidation is not available. Using the ultra-fast microfluidic mixer and the freeze-quenching device, coupled with EPR, we have been able to determine the presteady-state kinetics of ISP and cytochrome b(L) reduction by ubiquinol. The first-phase reduction of ISP starts as early as 100 micros with a t(1/2) of 250 micros. A similar reduction kinetic is also observed for cytochrome b(L), indicating a simultaneous reduction of both ISP and b(L). These results are consistent with the fact that no ubisemiquinone was detected at the Qp site during oxidation of ubiquinol. Under the same conditions, by using stopped flow, the reduction rates of cytochromes b(H) and c(1) were 403 s(-1) (t(1/2) 1.7 ms) and 164 s(-1) (t(1/2) 4.2 ms), respectively.
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Affiliation(s)
- Jian Zhu
- *Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078; and
| | - Tsuyoshi Egawa
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Linda Yu
- *Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078; and
| | - Chang-An Yu
- *Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078; and
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Baryshnikova EN, Melnik BS, Finkelstein AV, Semisotnov GV, Bychkova VE. Three-state protein folding: experimental determination of free-energy profile. Protein Sci 2005; 14:2658-67. [PMID: 16155199 PMCID: PMC2253297 DOI: 10.1110/ps.051402705] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Revised: 06/18/2005] [Accepted: 07/06/2005] [Indexed: 10/25/2022]
Abstract
When considering protein folding with a transient intermediate, a difficulty arises as to determination of the rates of separate transitions. Here we overcome this problem, using the kinetic studies of the unfolding/refolding reactions of the three-state protein apomyoglobin as a model. Amplitudes of the protein refolding kinetic burst phase corresponding to the transition from the unfolded (U) to intermediate (I) state, that occurs prior to the native state (N) formation, allow us to estimate relative populations of the rapidly converting states at various final urea concentrations. On the basis of these proportions, a complicated experimental chevron plot has been deconvolved into the urea-dependent rates of the I<-->N and U<-->N transitions to give the dependence of free energies of the main transition state and of all three (N, I, and U) stable states on urea concentration.
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Affiliation(s)
- Ekaterina N Baryshnikova
- Institute of Protein Research (Moscow office), Room 104, Vavilova Street 34, Moscow, GSP 1, 117334, Russia
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Apiyo D, Wittung-Stafshede P. Presence of the cofactor speeds up folding of Desulfovibrio desulfuricans flavodoxin. Protein Sci 2002; 11:1129-35. [PMID: 11967369 PMCID: PMC2373544 DOI: 10.1110/ps.3840102] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2001] [Revised: 01/07/2002] [Accepted: 02/06/2002] [Indexed: 10/14/2022]
Abstract
Flavodoxin is an alpha/beta protein with a noncovalently bound flavin-mononucleotide (FMN) cofactor. The apo-protein adopts a structure identical to that of the holo-form, although there is more dynamics in the FMN-binding loops. The equilibrium unfolding processes of Azotobacter vinelandii apo-flavodoxin, and Desulfovibrio desulfuricans ATCC strain 27774 apo- and holo-flavodoxins involve rather stable intermediates. In contrast, we here show that both holo- and apo-forms of flavodoxin from D. desulfuricans ATCC strain 29577 (75% sequence similarity with the strain 27774 protein) unfold in two-state equilibrium processes. Moreover, the FMN cofactor remains bound to the unfolded holo-protein. The folding and unfolding kinetics for holo-flavodoxin exhibit two-state behavior, albeit an additional slower phase is present at very low denaturant concentrations. The extrapolated folding time in water for holo-flavodoxin, approximately 280 microsec, is in excellent agreement with that predicted from the protein's native-state topology. Unlike the holo-protein behavior, the folding and unfolding reactions for apo-flavodoxin are best described by two kinetic phases, with rates differing approximately 15-fold, suggesting the presence of a kinetic intermediate. Both folding phases for apo-flavodoxin are orders of magnitude slower (40- and 530-fold, respectively) than that for the holo-protein. We conclude that polypeptide-cofactor interactions in the unfolded state of D. desulfuricans strain 29577 flavodoxin alter the kinetic-folding path towards two-state and speed up the folding reaction.
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Affiliation(s)
- David Apiyo
- Chemistry Department, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118, USA
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Abstract
A "temporal gradient apparatus" has been developed that allows the motility of bacteria to be studied after they have been subjected to a sudden change from one uniform concentration of attractant to another. A sudden decrease elicits the tumbling response observed with spatial gradients; it was found, however, that a sudden increase also elicits a response, namely supercoordinated swimming. This demonstrates that chemotaxis is achieved by modulation of the incidence of tumbling both above and below its steady-state value. The initial responses gradually revert to the steady-state motility pattern characteristic of a uniform distribution of attractant. The apparent detection of a spatial gradient by the bacteria therefore involves an actual detection of a temporal gradient experienced as a result of movement through space. Potential models for the chemotactic response based on some "memory" mechanism are discussed.
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