1
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Mothersole RG, Macdonald M, Kolesnikov M, Murphy MEP, Wolthers KR. Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin. Protein Sci 2019; 28:1460-1472. [PMID: 31116469 DOI: 10.1002/pro.3661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 11/08/2022]
Abstract
Flavodoxins are small flavin mononucleotide (FMN)-containing proteins that mediate a variety of electron transfer processes. The primary sequence of flavodoxin from Fusobacterium nucleatum, a pathogenic oral bacterium, is marked with a number of distinct features including a glycine to lysine (K13) substitution in the highly conserved phosphate-binding loop (T/S-X-T-G-X-T), variation in the aromatic residues that sandwich the FMN cofactor, and a more even distribution of acidic and basic residues. The Eox/sq (oxidized/semiquinone; -43 mV) and Esq/hq (semiquinone/hydroquinone; -256 mV) are the highest recorded reduction potentials of known long-chain flavodoxins. These more electropositive values are a consequence of the apoprotein binding to the FMN hydroquinone anion with ~70-fold greater affinity compared to the oxidized form of the cofactor. Inspection of the FnFld crystal structure revealed the absence of a hydrogen bond between the protein and the oxidized FMN N5 atom, which likely accounts for the more electropositive Eox/sq . The more electropositive Esq/hq is likely attributed to only one negatively charged group positioned within 12 Å of the FMN N1. We show that natural substitutions of highly conserved residues partially account for these more electropositive reduction potentials.
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Affiliation(s)
- Robert G Mothersole
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Marta Macdonald
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
| | - Maxim Kolesnikov
- Department of Microbiology and Immunology, University at the British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University at the British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University at the British Columbia, Kelowna, British Columbia, V1V 1V7, Canada
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2
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Gudim I, Lofstad M, van Beek W, Hersleth HP. High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus. Protein Sci 2019; 27:1439-1449. [PMID: 29722453 PMCID: PMC6153408 DOI: 10.1002/pro.3436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 02/03/2023]
Abstract
Flavodoxins (Flds) are small proteins that shuttle electrons in a range of reactions in microorganisms. Flds contain a redox‐active cofactor, a flavin mononucleotide (FMN), and it is well established that when Flds are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilizing the one‐electron reduced state. Here, we present high‐resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidized (ox) and one‐electron reduced (semiquinone, sq) state. We observe a mixture of conformers in the oxidized state; a 50:50 distribution between the established oxidized conformation where the peptide bond is pointing away from the flavin, and a conformation where the peptide bond is pointing toward the flavin, approximating the conformation in the semiquinone state. We use single‐crystal spectroscopy to demonstrate that the mixture of conformers is not caused by radiation damage to the crystal. This is the first time that such a mixture of conformers is reported in a wild‐type Fld. We therefore carried out a survey of published Fld structures, which show that several proteins have a pronounced conformational flexibility of this peptide bond. The degree of flexibility seems to be modulated by the presence, or absence, of stabilizing interactions between the peptide bond carbonyl and its surrounding amino acids. We hypothesize that the degree of conformational flexibility will affect the Fld ox/sq redox potential.
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Affiliation(s)
- Ingvild Gudim
- Department of Biosciences, Section for Biochemistry and Molecular Biology, Department of Biosciences should be before Section for Biochemistry and Molecular Biology, University of Oslo, Oslo, Norway
| | - Marie Lofstad
- Department of Biosciences, Section for Biochemistry and Molecular Biology, Department of Biosciences should be before Section for Biochemistry and Molecular Biology, University of Oslo, Oslo, Norway
| | - Wouter van Beek
- Swiss-Norwegian Beam Lines, European Synchrotron Radiation Facility, Grenoble, France
| | - Hans-Petter Hersleth
- Department of Biosciences, Section for Biochemistry and Molecular Biology, Department of Biosciences should be before Section for Biochemistry and Molecular Biology, University of Oslo, Oslo, Norway.,Department of Chemistry, Section for Chemical Life Sciences, University of Oslo, Oslo, Norway
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3
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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4
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Lamazares E, Vega S, Ferreira P, Medina M, Galano-Frutos JJ, Martínez-Júlvez M, Velázquez-Campoy A, Sancho J. Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate. Phys Chem Chem Phys 2018; 19:19021-19031. [PMID: 28702545 DOI: 10.1039/c7cp02606d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions. Wild type apoflavodoxin populates under native conditions a partly unfolded conformation (10% of molecules) whose unstructured region includes the binding sites for the FMN cofactor and for redox partner proteins. We recently engineered a thermostable variant where the intermediate is no longer detectable. Using the wild type and variant, we assess the relevance of the intermediate comparing folding kinetics, cofactor binding kinetics, cofactor affinity, X-ray structure, intrinsic dynamics, redox potential of the apoflavodoxin-cofactor complex (Fld), its affinity for partner protein FNR, and electron transfer rate within the Fld/FNR physiological complex. Our data strongly suggest the intermediate state, conserved in long-chain apoflavodoxins, is not required for the correct assembly of flavodoxin nor does it contribute to shape its electron transfer properties. This analysis can be applied to evaluate other native basin intermediates.
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Affiliation(s)
- Emilio Lamazares
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Patricia Ferreira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan J Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Fundación ARAID, Gobierno de Aragón, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
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5
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Kurzbach D, Flamm AG, Sára T. Network representation of protein interactions-Experimental results. Protein Sci 2016; 25:1628-36. [PMID: 27272395 PMCID: PMC5338234 DOI: 10.1002/pro.2964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 01/23/2023]
Abstract
A graph theoretical analysis of nuclear magnetic resonance (NMR) data of six different protein interactions has been presented. The representation of the protein interaction data as a graph or network reveals that all of the studied interactions are based on a common functional concept. They all involve a single densely packed hub of functionally correlated residues that mediate the ligand binding events. This is found independent of the kind of protein (folded or unfolded) or ligand (protein, polymer or small molecule). Furthermore, the power of the graph analysis is demonstrated at the examples of the Calmodulin (CaM)/Calcium and the Cold Shock Protein A (CspA)/RNA interaction. The presented approach enables the precise determination of multiple binding sites for the respective ligand molecules.
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Affiliation(s)
- Dennis Kurzbach
- Departement de Chimie, Ecole Normale SuperieurePSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolecules (LBM)24 rue Lhomond75005ParisFrance
| | - Andrea G. Flamm
- Department for Structural and Computational BiologyUniversity of ViennaCampus Vienna BioCenter 5Vienna1030Austria
| | - Tomáš Sára
- Department for Structural and Computational BiologyUniversity of ViennaCampus Vienna BioCenter 5Vienna1030Austria
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6
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Kurzbach D. Network representation of protein interactions: Theory of graph description and analysis. Protein Sci 2016; 25:1617-27. [PMID: 27272236 DOI: 10.1002/pro.2963] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022]
Abstract
A methodological framework is presented for the graph theoretical interpretation of NMR data of protein interactions. The proposed analysis generalizes the idea of network representations of protein structures by expanding it to protein interactions. This approach is based on regularization of residue-resolved NMR relaxation times and chemical shift data and subsequent construction of an adjacency matrix that represents the underlying protein interaction as a graph or network. The network nodes represent protein residues. Two nodes are connected if two residues are functionally correlated during the protein interaction event. The analysis of the resulting network enables the quantification of the importance of each amino acid of a protein for its interactions. Furthermore, the determination of the pattern of correlations between residues yields insights into the functional architecture of an interaction. This is of special interest for intrinsically disordered proteins, since the structural (three-dimensional) architecture of these proteins and their complexes is difficult to determine. The power of the proposed methodology is demonstrated at the example of the interaction between the intrinsically disordered protein osteopontin and its natural ligand heparin.
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Affiliation(s)
- Dennis Kurzbach
- Departement de Chimie, Ecole Normale Superieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolecules (LBM), 24 rue Lhomond, 75005 Paris, France
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7
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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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8
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Ye Q, Fu W, Hu Y, Jin C. Long-chain flavodoxin FldB from Escherichia coli. JOURNAL OF BIOMOLECULAR NMR 2014; 60:283-288. [PMID: 25380767 DOI: 10.1007/s10858-014-9874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Qian Ye
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
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