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Anion-specific interaction with human NQO1 inhibits flavin binding. Int J Biol Macromol 2019; 126:1223-1233. [PMID: 30615965 DOI: 10.1016/j.ijbiomac.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
Abstract
Ion binding to biomacromolecules can modulate their activity and stability in vivo. It is of particular interest to understand the structural and energetic basis of anion binding to functional sites of biomacromolecules. In this work, binding of anions to the FAD binding pocket of human NAD(P)H:quinone oxidoreductase 1 (NQO1), a flavoprotein associated with cancer due to a common polymorphism causing a P187S amino acid substitution, was investigated. It is known that NQO1 stability in vivo is strongly modulated by binding of its flavin cofactor. Herein, binding and protein stability analyses were carried out to show that anion binding to the apo-state of NQO1 P187S inhibits FAD binding with increasing strength following the chaotropic behavior of anions. These inhibitory effects were significant for some anions even at low millimolar concentrations. Additional pH dependent analyses suggested that protonation of histidine residues in the FAD binding pocket was not critical for anion or flavin binding. Overall, this detailed biophysical analysis helps to understanding how anions modulate NQO1 functionality in vitro, thus allowing hypothesize that NQO1 stability in vivo could be modulated by differential anion binding and subsequent inhibition of FAD binding.
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2
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Thermodynamics of cooperative binding of FAD to human NQO1: Implications to understanding cofactor-dependent function and stability of the flavoproteome. Arch Biochem Biophys 2017; 636:17-27. [PMID: 29100982 DOI: 10.1016/j.abb.2017.10.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/23/2023]
Abstract
The stability of human flavoproteins strongly depends on flavin levels, although the structural and energetic basis of this relationship is poorly understood. Here, we report an in-depth analysis on the thermodynamics of FAD binding to one of the most representative examples of such relationship, NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a dimeric enzyme that tightly binds FAD, which triggers large structural changes upon binding. A common cancer-associated polymorphism (P187S) severely compromises FAD binding. We show that FAD binding is described well by a thermodynamic model explicitly incorporating binding cooperativity when applied to different sets of calorimetric analyses and NQO1 variants, thus providing insight on the effects in vitro and in cells of cancer-associated P187S, its suppressor mutation H80R and the role of NQO1 C-terminal domain to modulate binding cooperativity and energetics. Furthermore, we show that FAD binding to NQO1 is very sensitive to physiologically relevant environmental conditions, such as the presence of phosphate buffer and salts. Overall, our results contribute to understanding at the molecular level the link between NQO1 stability and fluctuations of FAD levels intracellularly, and supports the notion that FAD binding energetics and cooperativity are fundamentally linked with the dynamic nature of apo-NQO1 conformational ensemble.
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3
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Rodríguez-Cárdenas Á, Rojas AL, Conde-Giménez M, Velázquez-Campoy A, Hurtado-Guerrero R, Sancho J. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target. PLoS One 2016; 11:e0161020. [PMID: 27649488 PMCID: PMC5029806 DOI: 10.1371/journal.pone.0161020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022] Open
Abstract
Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91-100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld.
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Affiliation(s)
- Ángela Rodríguez-Cárdenas
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adriana L. Rojas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - María Conde-Giménez
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
- * E-mail: (RHG); (JS)
| | - Javier Sancho
- Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain
- * E-mail: (RHG); (JS)
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4
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Galano-Frutos JJ, Morón MC, Sancho J. The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin. Phys Chem Chem Phys 2016; 17:28635-46. [PMID: 26443502 DOI: 10.1039/c5cp04504e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.
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Affiliation(s)
- Juan J Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC). Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
| | - M Carmen Morón
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas-Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain and Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC). Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
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5
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Dutta SK, Serrano P, Geralt M, Axelrod HL, Xu Q, Lesley SA, Godzik A, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K. Cofactor-induced reversible folding of Flavodoxin-4 from Lactobacillus acidophilus. Protein Sci 2015; 24:1600-8. [PMID: 26177955 DOI: 10.1002/pro.2743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/06/2022]
Abstract
Flavodoxins in combination with the flavin mononucleotide (FMN) cofactor play important roles for electron transport in prokaryotes. Here, novel insights into the FMN-binding mechanism to flavodoxins-4 were obtained from the NMR structures of the apo-protein from Lactobacillus acidophilus (YP_193882.1) and comparison of its complex with FMN. Extensive reversible conformational changes were observed upon FMN binding and release. The NMR structure of the FMN complex is in agreement with the crystal structure (PDB ID: 3EDO) and exhibits the characteristic flavodoxin fold, with a central five-stranded parallel β-sheet and five α-helices forming an α/β-sandwich architecture. The structure differs from other flavoproteins in that helix α2 is oriented perpendicular to the β-sheet and covers the FMN-binding site. This helix reversibly unfolds upon removal of the FMN ligand, which represents a unique structural rearrangement among flavodoxins.
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Affiliation(s)
- Samit Kumar Dutta
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Pedro Serrano
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Michael Geralt
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Herbert L Axelrod
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Qingping Xu
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Scott A Lesley
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121
| | - Adam Godzik
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, 92037.,Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, 92093
| | - Ashley M Deacon
- Joint Center for Structural Genomics, La Jolla, California, 92037.,SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, California, 94025
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Ian A Wilson
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
| | - Kurt Wüthrich
- Joint Center for Structural Genomics, La Jolla, California, 92037.,Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California, 92037.,Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California, 92037
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6
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Hamdane D, Bou-Nader C, Cornu D, Hui-Bon-Hoa G, Fontecave M. Flavin-Protein Complexes: Aromatic Stacking Assisted by a Hydrogen Bond. Biochemistry 2015; 54:4354-64. [PMID: 26120776 DOI: 10.1021/acs.biochem.5b00501] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-catalyzed reactions often rely on a noncovalently bound cofactor whose reactivity is tuned by its immediate environment. Flavin cofactors, the most versatile catalyst encountered in biology, are often maintained within the protein throughout numbers of complex ionic and aromatic interactions. Here, we have investigated the role of π-π stacking and hydrogen bond interactions between a tyrosine and the isoalloxazine moiety of the flavin adenine dinucleotide (FAD) in an FAD-dependent RNA methyltransferase. Combining several static and time-resolved spectroscopies as well as biochemical approaches, we showed that aromatic stacking is assisted by a hydrogen bond between the phenol group and the amide of an adjacent active site loop. A mechanism of recognition and binding of the redox cofactor is proposed.
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Affiliation(s)
- Djemel Hamdane
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Charles Bou-Nader
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - David Cornu
- ‡INSERM U779, 78 Rue du Général Leclerc, 94275 Le Kremlin-Bicêtre, France
| | - Gaston Hui-Bon-Hoa
- §Plateforme IMAGIF, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 1 avenue de le terrasse, 91191 Gif Sur Yvette, France
| | - Marc Fontecave
- †Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, France 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France
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