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Galano-Frutos JJ, Maity R, Iguarbe V, Aínsa JA, Velázquez-Campoy A, Schaible UE, Mamat U, Sancho J. L-Thyroxine and L-thyroxine-based antimicrobials against Streptococcus pneumoniae and other Gram-positive bacteria. Heliyon 2024; 10:e27982. [PMID: 38689973 PMCID: PMC11059415 DOI: 10.1016/j.heliyon.2024.e27982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Objectives The rise of antibiotic-resistant Streptococcus pneumoniae (Sp) poses a significant global health threat, urging the quest for novel antimicrobial solutions. We have discovered that the human hormone l-thyroxine has antibacterial properties. In order to explore its drugability we perform here the characterization of a series of l-thyroxine analogues and describe the structural determinants influencing their antibacterial efficacy. Method We performed a high-throughput screening of a library of compounds approved for use in humans, complemented with ITC assays on purified Sp-flavodoxin, to pinpoint molecules binding to this protein. Antimicrobial in vitro susceptibility assays of the hit compound (l-thyroxine) as well as of 13 l-thyroxine analogues were done against a panel of Gram-positive and Gram-negative bacteria. Toxicity of compounds on HepG2 cells was also assessed. A combined structure-activity and computational docking analysis was carried out to uncover functional groups crucial for the antimicrobial potency of these compounds. Results Human l-thyroxine binds to Sp-flavodoxin, forming a 1:1 complex of low micromolar Kd. While l-thyroxine specifically inhibited Sp growth, some derivatives displayed activity against other Gram-positive bacteria like Staphylococcus aureus and Enterococcus faecalis, while remaining inactive against Gram-negative pathogens. Neither l-thyroxine nor some selected derivatives exhibited toxicity to HepG2 cells. Conclusions l-thyroxine derivatives targeting bacterial flavodoxins represent a new and promising class of antimicrobials.
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Affiliation(s)
- Juan José Galano-Frutos
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR, Largo Francesco Vito 1, 00168, Rome, Italy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - Ritwik Maity
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - Verónica Iguarbe
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
| | - José Antonio Aínsa
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Facultad de Medicina, University of Zaragoza, Zaragoza 50009, Spain
- CIBER de Enfermedades Respiratorias–CIBERES, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ulrich E. Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, & Leibniz Research Alliance INFECTIONS, Borstel, Germany
- Biochemical Microbiology & Immunochemistry, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel Germany
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, & Leibniz Research Alliance INFECTIONS, Borstel, Germany
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, University of Zaragoza, Zaragoza 50009, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
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Liu S, Chen Y, Du T, Zhao W, Liu X, Zhang H, Yuan Q, Gao L, Dong Y, Gao X, Gong Y, Cao P. A dimer-monomer transition captured by the crystal structures of cyanobacterial apo flavodoxin. Biochem Biophys Res Commun 2023; 639:134-141. [PMID: 36493556 DOI: 10.1016/j.bbrc.2022.11.089] [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: 11/18/2022] [Accepted: 11/27/2022] [Indexed: 11/30/2022]
Abstract
In cyanobacteria and algae (but not plants), flavodoxin (Fld) replaces ferredoxin (Fd) under stress conditions to transfer electrons from photosystem I (PSI) to ferredoxin-NADP+ reductase (FNR) during photosynthesis. Fld constitutes a small electron carrier noncovalently bound to flavin mononucleotide (FMN), and also an ideal model for revealing the protein/flavin-binding mechanism because of its relative simplicity compared to other flavoproteins. Here, we report two crystal structures of apo-Fld from Synechococcus sp. PCC 7942, one dimeric structure of 2.09 Å and one monomeric structure of 1.84 Å resolution. Analytical ultracentrifugation showed that in solution, apo-Fld exists both as monomers and dimers. Our dimer structure contains two ligand-binding pockets separated by a distance of 45 Å, much longer than the previous structures of FMN-bound dimers. These results suggested a potential dimer-monomer transition mechanism of cyanobacterial apo-Fld. We further propose that the dimer represents the "standby" state to stabilize itself, while the monomer constitutes the "ready" state to bind FMN. Furthermore, we generated a new docking model of cyanobacterial Fld-FNR complex based on the recently reported cryo-EM structures, and mapped the special interactions between Fld and FNR in detail.
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Affiliation(s)
- Shuwen Liu
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Yuanyuan Chen
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Tianming Du
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Wencong Zhao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Xuejing Liu
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Heng Zhang
- Center for Multidisciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Qing Yuan
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Liang Gao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Yuhui Dong
- Center for Multidisciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China
| | - Xueyun Gao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China.
| | - Yong Gong
- Center for Multidisciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing, 100049, China.
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing, 100124, China.
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Khowdiary MM, Taha NA, Saleh NM, Elhenawy AA. Synthesis of Novel Nano-Sulfonamide Metal-Based Corrosion Inhibitor Surfactants. MATERIALS 2022; 15:ma15031146. [PMID: 35161090 PMCID: PMC8838271 DOI: 10.3390/ma15031146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/13/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023]
Abstract
The synthesis of novel corrosion inhibitors and biocide metal complex nanoparticle surfactants was achieved through the reaction of sulfonamide with selenious acid to produce a quaternary ammonium salt. Platinum and cobalt surfactants were then formed by complexing the first products with platinum (II) or cobalt (II) ions. The surface properties of these surfactants were then investigated, and the free energy of form micelles (ΔGomic) and adsorption (ΔGoads) was determined. The obtained cationic compounds were evaluated as corrosion inhibitors for carbon steel dissolution in 1N HCl medium. The results of gravimetric and electrochemical measurements showed that the obtained inhibitors were excellent corrosion inhibitors. The anti-sulfate-reducing bacteria activity known to cause corrosion of oil pipes was obtained by the inhibition zone diameter method for the prepared compounds, which were measured against sulfate-reducing bacteria. FTIR spectra, elemental analysis, H1 NMR spectrum, and 13C labeling were performed to ensure the purity of the prepared compounds.
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Affiliation(s)
- Manal M. Khowdiary
- Chemistry Department, Faculty of Applied Science, Umm Al-Qura University Branch El Lieth, Makkah al-Mukarramah 24382, Saudi Arabia
- Applied Surfactant Laboratory, Egyptian Petroleum Research Institute, Cairo 11727, Egypt
- Correspondence: (M.M.K.); (N.A.T.); Tel.: +966-583-307-941 (M.M.K.); +20-100-528-9679 (N.A.T.)
| | - Nahla A. Taha
- Modeling and Simulation Research Department, Advanced Technology and New Materials Research Institute, City of Scientific Research and Technological Applications (SRTA-CITY), New Borg El-Arab City 21934, Egypt
- Correspondence: (M.M.K.); (N.A.T.); Tel.: +966-583-307-941 (M.M.K.); +20-100-528-9679 (N.A.T.)
| | - Nashwa M. Saleh
- Egypt Department of Chemistry, Faculty of Science, Al-Azhar University (Girls Branch), Youssef Abbas Str., Cairo 11651, Egypt;
| | - Ahmed A. Elhenawy
- Department of Chemistry, Faculty of Science and Arts in Al-Mukhwah, Al-Baha University, Al Bahah 65511, Saudi Arabia;
- Chemistry Department, Al-Azhar University, Cairo 11651, Egypt
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Favero LM, Chideroli RT, Ferrari NA, Azevedo VADC, Tiwari S, Lopera-Barrero NM, Pereira UDP. In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae. Front Genet 2020; 11:1024. [PMID: 33005185 PMCID: PMC7484375 DOI: 10.3389/fgene.2020.01024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022] Open
Abstract
Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.
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Affiliation(s)
- Leonardo Mantovani Favero
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Roberta Torres Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Natália Amoroso Ferrari
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
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5
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Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. Int J Mol Sci 2020; 21:ijms21051881. [PMID: 32164177 PMCID: PMC7084853 DOI: 10.3390/ijms21051881] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Flavodoxins are small soluble electron transfer proteins widely present in bacteria and absent in vertebrates. Flavodoxins participate in different metabolic pathways and, in some bacteria, they have been shown to be essential proteins representing promising therapeutic targets to fight bacterial infections. Using purified flavodoxin and chemical libraries, leads can be identified that block flavodoxin function and act as bactericidal molecules, as it has been demonstrated for Helicobacter pylori (Hp), the most prevalent human gastric pathogen. Increasing antimicrobial resistance by this bacterium has led current therapies to lose effectiveness, so alternative treatments are urgently required. Here, we summarize, with a focus on flavodoxin, opportunities for pharmacological intervention offered by the potential protein targets described for this bacterium and provide information on other gastrointestinal pathogens and also on bacteria from the gut microbiota that contain flavodoxin. The process of discovery and development of novel antimicrobials specific for Hp flavodoxin that is being carried out in our group is explained, as it can be extrapolated to the discovery of inhibitors specific for other gastric pathogens. The high specificity for Hp of the antimicrobials developed may be of help to reduce damage to the gut microbiota and to slow down the development of resistant Hp mutants.
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Salillas S, Alías M, Michel V, Mahía A, Lucía A, Rodrigues L, Bueno J, Galano-Frutos JJ, De Reuse H, Velázquez-Campoy A, Carrodeguas JA, Sostres C, Castillo J, Aínsa JA, Díaz-de-Villegas MD, Lanas Á, Touati E, Sancho J. Design, Synthesis, and Efficacy Testing of Nitroethylene- and 7-Nitrobenzoxadiazol-Based Flavodoxin Inhibitors against Helicobacter pylori Drug-Resistant Clinical Strains and in Helicobacter pylori-Infected Mice. J Med Chem 2019; 62:6102-6115. [DOI: 10.1021/acs.jmedchem.9b00355] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sandra Salillas
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Miriam Alías
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
| | - Valérie Michel
- Helicobacter Pathogenesis Unit, Department of Microbiology, CNRS ERL6002, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris 75724, France
| | - Alejandro Mahía
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Ainhoa Lucía
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Liliana Rodrigues
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | | | - Juan José Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Hilde De Reuse
- Helicobacter Pathogenesis Unit, Department of Microbiology, CNRS ERL6002, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris 75724, France
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
- Fundación ARAID, Gobierno de Aragón, Zaragoza 50009, Spain
| | - José Alberto Carrodeguas
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Carlos Sostres
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | | | - José Antonio Aínsa
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | | | - Ángel Lanas
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
| | - Eliette Touati
- Helicobacter Pathogenesis Unit, Department of Microbiology, CNRS ERL6002, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris 75724, France
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, Zaragoza 50018, Spain
- Aragon Health Research Institute (IIS Aragón), Zaragoza 50009, Spain
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7
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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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8
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Arai S, Shibazaki C, Adachi M, Maeda Y, Tahara T, Kato T, Miyazaki H, Kuroki R. The non-glycosylated N-terminal domain of human thrombopoietin is a molten globule under native conditions. FEBS J 2019; 286:1717-1733. [PMID: 30675759 DOI: 10.1111/febs.14765] [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: 10/02/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
Abstract
Human thrombopoietin (hTPO) is a primary hematopoietic growth factor that regulates megakaryocytopoiesis and platelet production. The non-glycosylated form of 1-163 residues of hTPO (hTPO163 ) including the N-terminal active site domain (1-153 residues) is a candidate for treating thrombocytopenia. However, the autoantigenicity level of hTPO163 is higher than that of the full-length glycosylated hTPO (ghTPO332 ). In order to clarify the structural and physicochemical properties of hTPO163 , circular dichroism (CD) and differential scanning calorimetry (DSC) analyses were performed. CD analysis indicated that hTPO163 undergoes an induced-fit conformational change (+19.0% for helix and -16.7% for β-strand) upon binding to the neutralizing antibody TN1 in a manner similar to the coupled folding and binding mechanism. Moreover, DSC analysis showed that the thermal transition process of hTPO163 is a multistate transition; hTPO163 is thermally stabilized upon receptor (c-Mpl) binding, as indicated with raising the midpoint (Tm ) temperature of the transition by at least +9.5 K. The conformational variability and stability of hTPO163 indicate that hTPO163 exists as a molten globule under native conditions, which may enable the induced-fit conformational change according to the type of ligands (antibodies and receptor). Additionally, CD and computational analyses indicated that the C-terminal domain (154-332 residues) and glycosylation assists the folding of the N-terminal domain. These observations suggest that the antibody affinity and autoantigenicity of hTPO163 might be reduced, if the conformational variability of hTPO163 is restricted by mutation and/or by the addition of C-terminal domain with glycosylation to keep its conformation suitable for the c-Mpl recognition.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), Tokai, Japan
| | - Chie Shibazaki
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), Tokai, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), Tokai, Japan
| | | | | | - Takashi Kato
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | | | - Ryota Kuroki
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Japan
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Kapoor I, Nair SK. Structure-Guided Analyses of a Key Enzyme Involved in the Biosynthesis of an Antivitamin. Biochemistry 2018; 57:5282-5288. [PMID: 30125480 DOI: 10.1021/acs.biochem.8b00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RosB catalyzes the formation of 8-aminoriboflavin 5'-phosphate (AFP), the key intermediate in roseoflavin biosynthesis, from the metabolic precursors riboflavin 5'-phosphate (RP, also known as FMN) and glutamate. The conversion of the aromatic methyl group at position 8 in RP into the aromatic amine in AFP occurs via two intermediates, namely, the aldehyde 8-formyl-RP and the acid 8-carboxy-RP. To gain insights into the mechanism for this chemically challenging transformation, we utilized a structure-based approach to identify active site variants of RosB that stall the reaction at various points along the reaction coordinate. Crystal structures of individual variants in complex with different reaction intermediates, identified via mass spectroscopic analysis, illuminate conformational changes that occur at the active site during multistep conversion. These studies provide a plausible route for the progression of the reaction and a molecular rationale for the mechanism of this unusual biocatalyst.
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Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis. PLoS One 2017; 12:e0189319. [PMID: 29216329 PMCID: PMC5720691 DOI: 10.1371/journal.pone.0189319] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
Fusobacterium spp. present in the oral and gut flora is carcinogenic and is associated with the risk of pancreatic and colorectal cancers. Fusobacterium spp. is also implicated in a broad spectrum of human pathologies, including Crohn’s disease and ulcerative colitis (UC). Here we report the complete genome sequence of Fusobacterium varium Fv113-g1 (genome size, 3.96 Mb) isolated from a patient with UC. Comparative genome analyses totally suggested that Fv113-g1 is basically assigned as F. varium, in particular, it could be reclassified as notable F. varium subsp. similar to F. ulcerans because of partial shared orthologs. Compared with the genome sequences of F. varium ATCC 27725 (genome size, 3.30 Mb) and other strains of Fusobacterium spp., Fv113-g1 possesses many accessary pan-genome sequences with noteworthy multiple virulence factors, including 44 autotransporters (type V secretion system, T5SS) and 13 Fusobacterium adhesion (FadA) paralogs involved in potential mucosal inflammation. Indeed, transcriptome analysis demonstrated that Fv113-g1-specific accessary genes, such as multiple T5SS and fadA paralogs, showed notably increased expression with D-MEM cultivation than with brain heart infusion broth. This implied that growth condition may enhance the expression of such potential virulence factors, leading to remarkable survival against other gut microorganisms and to the pathogenicity to human intestinal epithelium.
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Plegaria JS, Sutter M, Ferlez B, Aussignargues C, Niklas J, Poluektov OG, Fromwiller C, TerAvest M, Utschig LM, Tiede DM, Kerfeld CA. Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment. Biochemistry 2017; 56:5679-5690. [PMID: 28956602 DOI: 10.1021/acs.biochem.7b00682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles that encapsulate enzymes involved in CO2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Metabolosomes share a common core of enzymes and a distinct signature enzyme for substrate degradation that defines the function of the BMC (e.g., propanediol or ethanolamine utilization BMCs, or glycyl-radical enzyme microcompartments). Loci encoding metabolosomes also typically contain genes for proteins that support organelle function, such as regulation, transport of substrate, and cofactor (e.g., vitamin B12) synthesis and recycling. Flavoproteins are frequently among these ancillary gene products, suggesting that these redox active proteins play an undetermined function in many metabolosomes. Here, we report the first characterization of a BMC-associated flavodoxin (Fld1C), a small flavoprotein, derived from the noncanonical 1,2-propanediol utilization BMC locus (PDU1C) of Lactobacillus reuteri. The 2.0 Å X-ray structure of Fld1C displays the α/β flavodoxin fold, which noncovalently binds a single flavin mononucleotide molecule. Fld1C is a short-chain flavodoxin with redox potentials of -240 ± 3 mV oxidized/semiquinone and -344 ± 1 mV semiquinone/hydroquinone versus the standard hydrogen electrode at pH 7.5. It can participate in an electron transfer reaction with a photoreductant to form a stable semiquinone species. Collectively, our structural and functional results suggest that PDU1C BMCs encapsulate Fld1C to store and transfer electrons for the reactivation and/or recycling of the B12 cofactor utilized by the signature enzyme.
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Affiliation(s)
- Jefferson S Plegaria
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Clément Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Jens Niklas
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Oleg G Poluektov
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Ciara Fromwiller
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michaela TerAvest
- Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
| | - Lisa M Utschig
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - David M Tiede
- Solar Energy Conversion Group, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University , East Lansing, Michigan 48824, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.,Department of Biochemistry & Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States.,Berkeley Synthetic Biology Institute , Berkeley, California 94720, United States
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