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Neira JL, Palomino-Schätzlein M. Folding of the nascent polypeptide chain of a histidine phosphocarrier protein in vitro. Arch Biochem Biophys 2023; 736:109538. [PMID: 36738980 DOI: 10.1016/j.abb.2023.109538] [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: 12/19/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The phosphotransferase system (PTS), a metabolic pathway formed by five proteins, modulates the use of sugars in bacteria. The second protein in the chain is the histidine phosphocarrier, HPr, with the binding site at His15. The HPr kinase/phosphorylase (HPrK/P), involved in the bacterial use of carbon sources, phosphorylates HPr at Ser46, and it binds at its binding site. The regulator of sigma D protein (Rsd) also binds to HPr at His15. We have designed fragments of HPr, growing from its N-terminus and containing the His15. In this work, we obtained three fragments, HPr38, HPr58 and HPr70, comprising the first thirty-eight, fifty-eight and seventy residues of HPr, respectively. All fragments were mainly disordered, with evidence of a weak native-like, helical population around the binding site, as shown by fluorescence, far-ultraviolet circular dichroism, size exclusion chromatography and nuclear magnetic resonance. Although HPr38, HPr58 and HPr70 were disordered, they could bind to: (i) the N-terminal domain of first protein of the PTS, EIN; (ii) Rsd; and, (iii) HPrK/P, as shown by fluorescence and biolayer interferometry (BLI). The association constants for each protein to any of the fragments were in the low micromolar range, within the same range than those measured in the binding of HPr to each protein. Then, although acquisition of stable, native-like secondary and tertiary structures occurred at the last residues of the polypeptide, the ability to bind protein partners happened much earlier in the growing chain. Binding was related to the presence of the native-like structure around His15.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018, Zaragoza, Spain.
| | - Martina Palomino-Schätzlein
- ProtoQSAR SL, CEEI-Valencia, Parque Tecnológico de Valencia, Av. Benjamin Franklin 12 (Dep. 8), 46980, Paterna, Valencia, Spain
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2
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Salillas S, Galano-Frutos JJ, Mahía A, Maity R, Conde-Giménez M, Anoz-Carbonell E, Berlamont H, Velazquez-Campoy A, Touati E, Mamat U, Schaible UE, Gálvez JA, Díaz-de-Villegas MD, Haesebrouck F, Aínsa JA, Sancho J. Selective Targeting of Human and Animal Pathogens of the Helicobacter Genus by Flavodoxin Inhibitors: Efficacy, Synergy, Resistance and Mechanistic Studies. Int J Mol Sci 2021; 22:ijms221810137. [PMID: 34576300 PMCID: PMC8467567 DOI: 10.3390/ijms221810137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial resistant (AMR) bacteria constitute a global health concern. Helicobacter pylori is a Gram-negative bacterium that infects about half of the human population and is a major cause of peptic ulcer disease and gastric cancer. Increasing resistance to triple and quadruple H. pylori eradication therapies poses great challenges and urges the development of novel, ideally narrow spectrum, antimicrobials targeting H. pylori. Here, we describe the antimicrobial spectrum of a family of nitrobenzoxadiazol-based antimicrobials initially discovered as inhibitors of flavodoxin: an essential H. pylori protein. Two groups of inhibitors are described. One group is formed by narrow-spectrum compounds, highly specific for H. pylori, but ineffective against enterohepatic Helicobacter species and other Gram-negative or Gram-positive bacteria. The second group includes extended-spectrum antimicrobials additionally targeting Gram-positive bacteria, the Gram-negative Campylobacter jejuni, and most Helicobacter species, but not affecting other Gram-negative pathogens. To identify the binding site of the inhibitors in the flavodoxin structure, several H. pylori-flavodoxin variants have been engineered and tested using isothermal titration calorimetry. An initial study of the inhibitors capacity to generate resistances and of their synergism with antimicrobials commonly used in H. pylori eradication therapies is described. The narrow-spectrum inhibitors, which are expected to affect the microbiota less dramatically than current antimicrobial drugs, offer an opportunity to develop new and specific H. pylori eradication combinations to deal with AMR in H. pylori. On the other hand, the extended-spectrum inhibitors constitute a new family of promising antimicrobials, with a potential use against AMR Gram-positive bacterial pathogens.
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Affiliation(s)
- Sandra Salillas
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Juan José Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Alejandro Mahía
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Ritwik Maity
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - María Conde-Giménez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
| | - Helena Berlamont
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (H.B.); (F.H.)
| | - Adrian Velazquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- ARAID Foundation, Government of Aragon, 50018 Zaragoza, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, CNRS UMR2001, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris, France;
| | - Uwe Mamat
- Cellular Microbiology, Program Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany; (U.M.); (U.E.S.)
| | - Ulrich E. Schaible
- Cellular Microbiology, Program Area Infections, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany; (U.M.); (U.E.S.)
| | - José A. Gálvez
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC—Departamento de Química Orgánica, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; (J.A.G.); (M.D.D.-d.-V.)
| | - María D. Díaz-de-Villegas
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC—Departamento de Química Orgánica, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; (J.A.G.); (M.D.D.-d.-V.)
| | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B9820 Merelbeke, Belgium; (H.B.); (F.H.)
| | - José A. Aínsa
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Departamento de Microbiología, Pediatría, Radiología y Salud Pública, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias—CIBERES, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; (S.S.); (J.J.G.-F.); (A.M.); (R.M.); (M.C.-G.); (E.A.-C.); (A.V.-C.); (J.A.A.)
- Departamento de Bioquímica y Biología Molecular y Celular, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence:
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Neira JL, Palomino-Schätzlein M, Hurtado-Gómez E, Ortore MG, Falcó A. An N-terminal half fragment of the histidine phosphocarrier protein, HPr, is disordered but binds to HPr partners and shows antibacterial properties. Biochim Biophys Acta Gen Subj 2021; 1865:130015. [PMID: 34537288 DOI: 10.1016/j.bbagen.2021.130015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/26/2021] [Accepted: 09/15/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The phosphotransferase system (PTS) modulates the preferential use of sugars in bacteria. It is formed by a protein cascade in which the first two proteins are general (namely enzyme I, EI, and the histidine phosphocarrier protein, HPr) and the others are sugar-specific permeases; the active site of HPr is His15. The HPr kinase/phosphorylase (HPrK/P), involved in the use of carbon sources in Gram-positive, phopshorylates HPr at a serine. The regulator of sigma D protein (Rsd) also binds to HPr. We are designing specific fragments of HPr, which can be used to interfere with those protein-protein interactions (PPIs), where the intact HPr intervenes. METHODS We obtained a fragment (HPr48) comprising the first forty-eight residues of HPr. HPr48 was disordered as shown by fluorescence, far-ultraviolet (UV) circular dichroism (CD), small angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR). RESULTS Secondary structure propensities, from the assigned backbone nuclei, further support the unfolded nature of the fragment. However, HPr48 was capable of binding to: (i) the N-terminal region of EI, EIN; (ii) the intact Rsd; and, (iii) HPrK/P, as shown by fluorescence, far-UV CD, NMR and biolayer interferometry (BLI). The association constants for each protein, as measured by fluorescence and BLI, were in the order of the low micromolar range, similar to those measured between the intact HPr and each of the other macromolecules. CONCLUSIONS Although HPr48 is forty-eight-residue long, it assisted antibiotics to exert antimicrobial activity. GENERAL SIGNIFICANCE HPr48 could be used as a lead compound in the development of new antibiotics, or, alternatively, to improve the efficiency of existing ones.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche (Alicante), Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | | | | | - María G Ortore
- Dipartimento DiSVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Alberto Falcó
- IDIBE, Universidad Miguel Hernández, 03202, Elche (Alicante), Spain.
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4
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Ortega-Alarcon D, Claveria-Gimeno R, Vega S, Jorge-Torres OC, Esteller M, Abian O, Velazquez-Campoy A. Influence of the disordered domain structure of MeCP2 on its structural stability and dsDNA interaction. Int J Biol Macromol 2021; 175:58-66. [PMID: 33548325 DOI: 10.1016/j.ijbiomac.2021.01.206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/17/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a transcriptional regulator and a chromatin-associated structural protein. MeCP2 deregulation results in two neurodevelopmental disorders: MeCP2 dysfunction is associated with Rett syndrome, while excess of activity is associated with MeCP2 duplication syndrome. MeCP2 is an intrinsically disordered protein (IDP) constituted by six structural domains with variable, small percentage of well-defined secondary structure. Two domains, methyl-CpG binding domain (MBD) and transcription repressor domain (TRD), are the elements responsible for dsDNA binding ability and recruitment of the gene transcription/silencing machinery, respectively. Previously we studied the influence of the completely disordered, MBD-flanking domains (N-terminal domain, NTD, and intervening domain, ID) on the structural and functional features of the MBD (Claveria-Gimeno, R. et al. Sci Rep. 2017, 7, 41,635). Here we report the biophysical study of the influence of the remaining domains (transcriptional repressor domain, TRD, and C-terminal domains, CTDα and CTDβ) on the structural stability of MBD and the dsDNA binding capabilities of MBD and ID. The influence of distant disordered domains on MBD properties makes it necessary to consider the NTD-MBD-ID variant as the minimal protein construct for studying dsDNA/chromatin binding properties, while the full-length protein should be considered for transcriptional regulation studies.
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Affiliation(s)
- David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Rafael Claveria-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Olga C Jorge-Torres
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907, l'Hospitalet de Llobregat, Barcelona, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza 50018, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Fundación ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain.
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5
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Neira JL, Rizzuti B, Jiménez-Alesanco A, Abián O, Velázquez-Campoy A, Iovanna JL. The Paralogue of the Intrinsically Disordered Nuclear Protein 1 Has a Nuclear Localization Sequence that Binds to Human Importin α3. Int J Mol Sci 2020; 21:ijms21197428. [PMID: 33050086 PMCID: PMC7583046 DOI: 10.3390/ijms21197428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 02/07/2023] Open
Abstract
Numerous carrier proteins intervene in protein transport from the cytoplasm to the nucleus in eukaryotic cells. One of those is importin α, with several human isoforms; among them, importin α3 (Impα3) features a particularly high flexibility. The protein NUPR1L is an intrinsically disordered protein (IDP), evolved as a paralogue of nuclear protein 1 (NUPR1), which is involved in chromatin remodeling and DNA repair. It is predicted that NUPR1L has a nuclear localization sequence (NLS) from residues Arg51 to Gln74, in order to allow for nuclear translocation. We studied in this work the ability of intact NUPR1L to bind Impα3 and its depleted species, ∆Impα3, without the importin binding domain (IBB), using fluorescence, isothermal titration calorimetry (ITC), circular dichroism (CD), nuclear magnetic resonance (NMR), and molecular docking techniques. Furthermore, the binding of the peptide matching the isolated NLS region of NUPR1L (NLS-NUPR1L) was also studied using the same methods. Our results show that NUPR1L was bound to Imp α3 with a low micromolar affinity (~5 μM). Furthermore, a similar affinity value was observed for the binding of NLS-NUPR1L. These findings indicate that the NLS region, which was unfolded in isolation in solution, was essentially responsible for the binding of NUPR1L to both importin species. This result was also confirmed by our in silico modeling. The binding reaction of NLS-NUPR1L to ∆Impα3 showed a larger affinity (i.e., lower dissociation constant) compared with that of Impα3, confirming that the IBB could act as an auto-inhibition region of Impα3. Taken together, our findings pinpoint the theoretical predictions of the NLS region in NUPR1L and, more importantly, suggest that this IDP relies on an importin for its nuclear translocation.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, Arcavacata di Rende, 87036 Cosenza, Italy;
| | - Ana Jiménez-Alesanco
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; (A.J.-A.); (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Gobierno de Aragon, 50009 Zaragoza, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
- Correspondence: (J.L.N.); (J.L.I.); Tel.: +34-966-65-8475 (J.L.N.); +33(0)491-82-8803 (J.L.I.)
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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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7
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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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8
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Kinetic and thermodynamic effects of phosphorylation on p53 binding to MDM2. Sci Rep 2019; 9:693. [PMID: 30679555 PMCID: PMC6345774 DOI: 10.1038/s41598-018-36589-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/15/2018] [Indexed: 02/03/2023] Open
Abstract
p53 is frequently mutated in human cancers. Its levels are tightly regulated by the E3 ubiquitin ligase MDM2. The complex between MDM2 and p53 is largely formed by the interaction between the N-terminal domain of MDM2 and the N-terminal transactivation (TA) domain of p53 (residues 15–29). We investigated the kinetic and thermodynamic basis of the MDM2/p53 interaction by using wild-type and mutant variants of the TA domain. We focus on the effects of phosphorylation at positions Thr18 and Ser20 including their substitution with phosphomimetics. Conformational propensities of the isolated peptides were investigated using in silico methods and experimentally by circular dichroism and 1H-NMR in aqueous solution. Both experimental and computational analyses indicate that the p53 peptides are mainly disordered in aqueous solution, with evidence of nascent helix around the Ser20-Leu25 region. Both phosphorylation and the phosphomimetics at Thr18 result in a decrease in the binding affinity by ten- to twenty-fold when compared to the wild-type. Phosphorylation and phosphomimetics at Ser20 result in a smaller decrease in the affinity. Mutation of Lys24 and Leu25 also disrupts the interaction. Our results may be useful for further development of peptide-based drugs targeting the MDM2/p53 interaction.
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9
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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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10
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Neira JL, Hornos F, Cozza C, Cámara-Artigas A, Abián O, Velázquez-Campoy A. The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments. Arch Biochem Biophys 2017; 639:26-37. [PMID: 29288053 DOI: 10.1016/j.abb.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
Abstract
The phosphotransferase system (PTS) controls the preferential use of sugars in bacteria and it is also involved in other processes, such as chemotaxis. It is formed by a protein cascade in which the first two proteins are general (namely, EI and HPr) and the others are sugar-specific permeases. The Rsd protein binds specifically to the RNA polymerase (RNAP) σ70 factor. We first characterized the conformational stability of Escherichia coli Rsd. And second, we delineated the binding regions of Streptomyces coelicolor, HPrsc, and E. coli Rsd, by using fragments derived from each protein. To that end, we used several biophysical probes, namely, fluorescence, CD, NMR, ITC and BLI. Rsd had a free energy of unfolding of 15 kcal mol-1 at 25 °C, and a thermal denaturation midpoint of 103 °C at pH 6.5. The affinity between Rsd and HPrsc was 2 μM. Interestingly enough, the isolated helical-peptides, comprising the third (RsdH3) and fourth (RsdH4) Rsd helices, also interacted with HPrsc in a specific manner, and with affinities similar to that of the whole Rsd. Moreover, the isolated peptide of HPrsc, HPr9-30, comprising the active site, His15, also was bound to intact Rsd with similar affinity. Therefore, binding between Rsd and HPrsc was modulated by the two helices H3 and H4 of Rsd, and the regions around the active site of HPrsc. This implies that specific fragments of Rsd and HPrsc can be used to interfere with other protein-protein interactions (PPIs) of each other protein.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain.
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain
| | - Concetta Cozza
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, Almería, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.
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11
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Houwman JA, van Mierlo CPM. Folding of proteins with a flavodoxin-like architecture. FEBS J 2017; 284:3145-3167. [PMID: 28380286 DOI: 10.1111/febs.14077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022]
Abstract
The flavodoxin-like fold is a protein architecture that can be traced back to the universal ancestor of the three kingdoms of life. Many proteins share this α-β parallel topology and hence it is highly relevant to illuminate how they fold. Here, we review experiments and simulations concerning the folding of flavodoxins and CheY-like proteins, which share the flavodoxin-like fold. These polypeptides tend to temporarily misfold during unassisted folding to their functionally active forms. This susceptibility to frustration is caused by the more rapid formation of an α-helix compared to a β-sheet, particularly when a parallel β-sheet is involved. As a result, flavodoxin-like proteins form intermediates that are off-pathway to native protein and several of these species are molten globules (MGs). Experiments suggest that the off-pathway species are of helical nature and that flavodoxin-like proteins have a nonconserved transition state that determines the rate of productive folding. Folding of flavodoxin from Azotobacter vinelandii has been investigated extensively, enabling a schematic construction of its folding energy landscape. It is the only flavodoxin-like protein of which cotranslational folding has been probed. New insights that emphasize differences between in vivo and in vitro folding energy landscapes are emerging: the ribosome modulates MG formation in nascent apoflavodoxin and forces this polypeptide toward the native state.
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Affiliation(s)
- Joseline A Houwman
- Laboratory of Biochemistry, Wageningen University and Research, The Netherlands
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12
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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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13
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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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14
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On the link between conformational changes, ligand binding and heat capacity. Biochim Biophys Acta Gen Subj 2016; 1860:868-878. [DOI: 10.1016/j.bbagen.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
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15
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Hernández O, Araque P, Tamayo D, Restrepo A, Herrera S, Mcewen JG, Pelaez C, Almeida AJ. Alternative oxidase plays an important role in Paracoccidioides brasiliensis cellular homeostasis and morphological transition. Med Mycol 2015; 53:205-14. [DOI: 10.1093/mmy/myu091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Flavodoxin cofactor binding induces structural changes that are required for protein-protein interactions with NADP(+) oxidoreductase and pyruvate formate-lyase activating enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2512-9. [PMID: 24016774 DOI: 10.1016/j.bbapap.2013.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/27/2013] [Accepted: 08/30/2013] [Indexed: 11/23/2022]
Abstract
Flavodoxin (Fld) conformational changes, thermal stability, and cofactor binding were studied using circular dichroism (CD), isothermal titration calorimetry (ITC), and limited proteolysis. Thermodynamics of apo and holo-Fld folding were examined to discern the features of this important electron transfer protein and to provide data on apo-Fld. With the exception of fluorescence and UV-vis binding experiments with its cofactor flavin mononucleotide (FMN), apo-Fld is almost completely uncharacterized in Escherichia coli. Fld is more structured when the FMN cofactor is bound; the association is tight and driven by enthalpy of binding. Surface plasmon resonance binding experiments were carried out under anaerobic conditions for both apo- and holo-Fld and demonstrate the importance of structure and conformation for the interaction with binding partners. Holo-Fld is capable of associating with NADP(+)-dependent flavodoxin oxidoreductase (FNR) and pyruvate formate-lyase activating enzyme (PFL-AE) whereas there is no detectable interaction between apo-Fld and either protein. Limited proteolysis experiments were analyzed by LC-MS to identify the regions in Fld that are involved in conformation changes upon cofactor binding. Docking software was used to model the Fld/PFL-AE complex to understand the interactions between these two proteins and gain insight into electron transfer reactions from Fld to PFL-AE.
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17
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Galano JJ, Alías M, Pérez R, Velázquez-Campoy A, Hoffman PS, Sancho J. Improved Flavodoxin Inhibitors with Potential Therapeutic Effects against Helicobacter pylori Infection. J Med Chem 2013; 56:6248-58. [DOI: 10.1021/jm400786q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Juan J. Galano
- Departamento
de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
| | - Miriam Alías
- Departamento
de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
| | - Reyes Pérez
- Departamento
de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
| | - Adrian Velázquez-Campoy
- Departamento
de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
- Fundación ARAID, Gobierno de Aragon, Aragon, Spain
| | - Paul S. Hoffman
- Department of Medicine, Division
of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, Virginia
22908, United States
| | - Javier Sancho
- Departamento
de Bioquímica
y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
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18
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Aprile FA, Dhulesia A, Stengel F, Roodveldt C, Benesch JLP, Tortora P, Robinson CV, Salvatella X, Dobson CM, Cremades N. Hsp70 oligomerization is mediated by an interaction between the interdomain linker and the substrate-binding domain. PLoS One 2013; 8:e67961. [PMID: 23840795 PMCID: PMC3696110 DOI: 10.1371/journal.pone.0067961] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/24/2013] [Indexed: 12/21/2022] Open
Abstract
Oligomerization in the heat shock protein (Hsp) 70 family has been extensively documented both in vitro and in vivo, although the mechanism, the identity of the specific protein regions involved and the physiological relevance of this process are still unclear. We have studied the oligomeric properties of a series of human Hsp70 variants by means of nanoelectrospray ionization mass spectrometry, optical spectroscopy and quantitative size exclusion chromatography. Our results show that Hsp70 oligomerization takes place through a specific interaction between the interdomain linker of one molecule and the substrate-binding domain of a different molecule, generating dimers and higher-order oligomers. We have found that substrate binding shifts the oligomerization equilibrium towards the accumulation of functional monomeric protein, probably by sequestering the helical lid sub-domain needed to stabilize the chaperone: substrate complex. Taken together, these findings suggest a possible role of chaperone oligomerization as a mechanism for regulating the availability of the active monomeric form of the chaperone and for the control of substrate binding and release.
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Affiliation(s)
- Francesco A. Aprile
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Anne Dhulesia
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Stengel
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Cintia Roodveldt
- CABIMER-Andalusian Center for Molecular Biology and Regenerative Medicine (Consejo Superior de Investigaciones Científicas-University of Seville-UPO-Junta de Andalucia), Seville, Spain
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Paolo Tortora
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Xavier Salvatella
- Joint BSC-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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19
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The stability of 2-state, 3-state and more-state proteins from simple spectroscopic techniques... plus the structure of the equilibrium intermediates at the same time. Arch Biochem Biophys 2013; 531:4-13. [DOI: 10.1016/j.abb.2012.10.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/22/2012] [Accepted: 10/28/2012] [Indexed: 11/20/2022]
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20
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Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case. PLoS Comput Biol 2012; 8:e1002647. [PMID: 22927805 PMCID: PMC3426563 DOI: 10.1371/journal.pcbi.1002647] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/18/2012] [Indexed: 11/29/2022] Open
Abstract
The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an “activated” form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered protein. Our results allow us to speculate that proteins with a well packed core connected by long loops might behave as partially disordered proteins under native conditions, or alternatively behave as three state folders. Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins. A simplistic view of protein structure tends to emphasize the opposition between the native state and the denatured ensemble of unfolded conformations. In addition to these extreme conformations, proteins subjected to a variety of perturbations often populate alternative partly unfolded conformations, some of which are close in energy to the native state and, accordingly, can be populated under native or quasi-native conditions. There is increasing evidence that these “perturbed” conformations participate in protein function or, in some cases, are related to the outcome of folding diseases. We have used the “state of the art” molecular dynamics combined with a variety of experimental techniques to characterize for the first time, to our knowledge, the thermal intermediate of a three-state folding protein (apoflavodoxin). Based on our results we have been able to suggest a general mechanism of thermal unfolding in complex proteins and to determine interesting links between thermal intermediates and partially unfolded proteins.
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21
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Hernandez O, Garcia AM, Almeida AJ, Tamayo D, Gonzalez A, Restrepo A, McEwen JG. Gene expression during activation of Paracoccidioides brasiliensis conidia. Yeast 2011; 28:771-81. [PMID: 21960298 DOI: 10.1002/yea.1902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/13/2011] [Accepted: 08/05/2011] [Indexed: 11/12/2022] Open
Abstract
This study focuses on gene expression during crucial biological phenomena of the dimorphic fungal human pathogen Paracoccidioides brasiliensis, the conidia-to-yeast (C-Y) transition and the conidia-to-mycelia (C-M) germination. We studied 10 genes involved in different cellular functions: oxidative stress response (alternative oxidase (AOX), superoxide dismutase (SOD), flavodoxin, conserved hypothetical protein (Y20)); cell metabolism (glyceraldehyde-3-phosphate dehydrogenase (GADPH), cholestenol Delta-isomerase (ChDI), glycine dehydrogenase (GDh)) and heat shock response (Heat shock protein 90 (HSP90)), and cell synthesis and wall structure (glucan synthase-1 (GS-1), α-1,3-glucan synthase (αGS), and mannosyltransferase (MT)). Gene expression was measured during the first 72 h and 96 h of C-Y and C-M, respectively, previously shown to be a fundamental time frame for the consolidation of these cellular processes. The gene expression of AOX, GAPDH, HSP90, MT, αGS, and GDh was significantly increased during the C-Y transition, while SOD, ChDI, GAPDH, MT, GDh, and GS-1 were increased during C-M germination. Additionally, some were highly expressed in each process: AOX, HSP90, and αGS during C-Y; SOD, ChDI, and GS-1 during C-M. Altogether, these data add new information regarding gene expression during the C-Y and C-M processes. Future research will be targeted to further characterize the true relevance of the studied genes during the morphological transition, either during adaptation to the environment or to the infected host.
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Affiliation(s)
- O Hernandez
- Biology Institute, University of Antioquia, Medellín, Colombia.
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Ayuso-Tejedor S, Abián O, Velázquez-Campoy A, Sancho J. Mechanism of FMN Binding to the Apoflavodoxin from Helicobacter pylori. Biochemistry 2011; 50:8703-11. [PMID: 21910456 DOI: 10.1021/bi201025y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Flavodoxins are bacterial electron transport proteins whose redox competence is due to the presence of a tightly but noncovalently bound FMN molecule. While the thermodynamics of the complex are understood, the mechanism of association between the apoflavodoxin and the redox cofactor is not so clear. We investigate here the mechanism of FMN binding to the apoflavodoxin from Helicobacter pylori, an essential protein that is being used as a target to develop antimicrobials. This flavodoxin is structurally peculiar as it lacks the typical bulky residue interacting with the FMN re face but bears instead a small alanine. FMN binding is biphasic, regardless of the presence of phosphate molecules in solution, while riboflavin binding takes place in a single step, the rate constant of which coincides with the fast phase of FMN binding. A mutational study at the isoalloxazine and phosphate subsites for FMN binding clearly indicates that FMN association is always limited by interaction with the isoalloxazine subsite because mutating residues that interact with the phosphate moiety of FMN in the native complex hardly changes the observed rate constants and amplitudes. In contrast, replacing tyr92, which interacts with the isoalloxazine, greatly lowers the rate constants. Our analysis indicates that the two FMN binding phases observed are related neither with alternative or sequential interaction with the two binding subsites nor with the presence of bound phosphate. It is possible that they reflect the intrinsic conformational heterogeneity of the apoflavodoxin ensemble.
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Affiliation(s)
- S Ayuso-Tejedor
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza 50009, Spain
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23
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Abian O, Vega S, Neira JL, Velazquez-Campoy A. Conformational stability of hepatitis C virus NS3 protease. Biophys J 2011; 99:3811-20. [PMID: 21112306 DOI: 10.1016/j.bpj.2010.10.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 11/17/2022] Open
Abstract
The hepatitis C virus NS3 protease is responsible for the processing of the nonstructural region of viral precursor polyprotein in infected hepatic cells. NS3 has been considered a target for drug discovery for a long time. NS3 is a zinc-dependent serine protease. However, the zinc ion is not involved in the catalytic mechanism, because it is bound far away from the active site. Thus, zinc is essential for the structural integrity of the protein and it is considered to have a structural role. The first thermodynamic study on the conformational equilibrium and stability of NS3 and the effect of zinc on such equilibrium is presented here. In agreement with a previous calorimetric study on the binding of zinc to NS3, the global unfolding heat capacity is dominated by the zinc dissociation step, suggesting that the binding of zinc induces a significant structural rearrangement of the protein. In addition, contrary to other homologous zinc-dependent proteases, the zinc-free NS3 protease is not completely unstructured. It is apparent that the conformational landscape of hepatitis C virus NS3 protease is fairly complex due to its intrinsic plasticity, and to the interactions with its different effectors (zinc and the accessory viral protein NS4A) and their modulation of the population of the different conformational states.
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Affiliation(s)
- Olga Abian
- Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain.
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24
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Dhulesia A, Cremades N, Kumita JR, Hsu STD, Mossuto MF, Dumoulin M, Nietlispach D, Akke M, Salvatella X, Dobson CM. Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution. J Am Chem Soc 2010; 132:15580-8. [PMID: 20958028 PMCID: PMC2974344 DOI: 10.1021/ja103524m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Indexed: 12/22/2022]
Abstract
The partial unfolding of human lysozyme underlies its conversion from the soluble state into amyloid fibrils observed in a fatal hereditary form of systemic amyloidosis. To understand the molecular origins of the disease, it is critical to characterize the structural and physicochemical properties of the amyloidogenic states of the protein. Here we provide a high-resolution view of the unfolding process at low pH for three different lysozyme variants, the wild-type protein and the mutants I56T and I59T, which show variable stabilities and propensities to aggregate in vitro. Using a range of biophysical techniques that includes differential scanning calorimetry and nuclear magnetic resonance spectroscopy, we demonstrate that thermal unfolding under amyloidogenic solution conditions involves a cooperative loss of native tertiary structure, followed by progressive unfolding of a compact, molten globule-like denatured state ensemble as the temperature is increased. The width of the temperature window over which the denatured ensemble progressively unfolds correlates with the relative amyloidogenicity and stability of these variants, and the region of lysozyme that unfolds first maps to that which forms the core of the amyloid fibrils formed under similar conditions. Together, these results present a coherent picture at atomic resolution of the initial events underlying amyloid formation by a globular protein.
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25
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Ayuso-Tejedor S, Nishikori S, Okuno T, Ogura T, Sancho J. FtsH cleavage of non-native conformations of proteins. J Struct Biol 2010; 171:117-24. [DOI: 10.1016/j.jsb.2010.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 05/01/2010] [Accepted: 05/03/2010] [Indexed: 11/17/2022]
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26
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Ayuso-Tejedor S, Angarica VE, Bueno M, Campos LA, Abián O, Bernadó P, Sancho J, Jiménez MA. Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins. J Mol Biol 2010; 400:922-34. [PMID: 20553732 DOI: 10.1016/j.jmb.2010.05.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/13/2010] [Accepted: 05/21/2010] [Indexed: 11/27/2022]
Abstract
Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity.
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Affiliation(s)
- Sara Ayuso-Tejedor
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain
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27
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Duckworth MJ, Okoli AS, Mendz GL. Novel Helicobacter pylori therapeutic targets: the unusual suspects. Expert Rev Anti Infect Ther 2009; 7:835-67. [PMID: 19735225 DOI: 10.1586/eri.09.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the current status of the discovery and development of anti-Helicobacter therapies requires an overview of the searches for therapeutic targets performed to date. A summary is given of the very substantial body of work conducted in the quest to find Helicobacter pylori genes that could be suitable candidates for therapeutic intervention. The products of most of these genes perform metabolic functions, and others have roles in growth, cell motility and colonization. The genes identified as potential targets have been organized into three categories according to their degree of characterization. A short description and evaluation is provided of the main candidates in each category. Investigations of potential therapeutic targets have generated a wealth of information about the physiology and genetics of H. pylori, and its interactions with the host, but have yielded little by way of new therapies.
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Affiliation(s)
- Megan J Duckworth
- School of Medicine, Sydney, The University of Notre Dame Australia, 160 Oxford Street, Darlinghurst, NSW 2010, Australia.
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28
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Cremades N, Velázquez-Campoy A, Martínez-Júlvez M, Neira JL, Pérez-Dorado I, Hermoso J, Jiménez P, Lanas A, Hoffman PS, Sancho J. Discovery of specific flavodoxin inhibitors as potential therapeutic agents against Helicobacter pylori infection. ACS Chem Biol 2009; 4:928-38. [PMID: 19725577 DOI: 10.1021/cb900166q] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Helicobacter pylori establishes life-long infections in the gastric mucosa of over 1 billion people worldwide. In many cases, without specific antimicrobial intervention, H. pylori infected individuals will develop type B gastritis, chronic peptic ulcers and, more rarely, gastric neoplasias. Conventional antimicrobial therapy has been complicated by dramatic increases in resistance to macrolides, metronidazole and fluoroquinolones. Here, we report the development of novel therapeutics that specifically target the unique flavodoxin component of an essential metabolic pathway of H. pylori. With the use of high-throughput screening methodology, we have tested 10,000 chemicals and have identified 29 compounds that bind flavodoxin, four of which interrupted in vitro electron transfer to flavodoxin physiological partners. Three of these compounds are bactericidal and promisingly selective for H. pylori. The minimal inhibitory concentrations of two of them are 10 times lower than their minimal cytotoxic concentrations for HeLa cells. Importantly, neither of the four inhibitors is toxic for mice after administration of 1-10 mg kg(-1) doses twice a day for 5 days. Enzymatic, thermodynamic and structural characterization of the inhibitor-flavodoxin complexes suggests these compounds could act by modifying the redox potentials of flavodoxin. These newly discovered inhibitors represent promising selective leads against the different diseases associated to H. pylori infection.
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Affiliation(s)
- Nunilo Cremades
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
- Fundación Aragón I+D (ARAID-BIFI), Diputación General de Aragón, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
| | - José L. Neira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Inmaculada Pérez-Dorado
- Grupo de Crystalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Juan Hermoso
- Grupo de Crystalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | | | - Angel Lanas
- IACS, CIBERehd, University of Zaragoza, Spain
| | - Paul S. Hoffman
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia 22908
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain
- Biocomputation and Complex Systems Physics Institute (BIFI)-Unidad Asociada al IQFR-CSIC, 50009 Zaragoza, Spain
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29
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Molten globule and native state ensemble of Helicobacter pylori flavodoxin: can crowding, osmolytes or cofactors stabilize the native conformation relative to the molten globule? Biophys J 2008; 95:1913-27. [PMID: 18441031 DOI: 10.1529/biophysj.108.130153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Partly unfolded protein conformations close in energy to the native state may be involved in protein functioning and also be related to folding diseases, but yet their structure and energetics are poorly understood. One such conformation, the monomeric and well-behaved molten globule of Helicobacter pylori apoflavodoxin, is here investigated to provide, in a wide pH interval, a complete thermodynamic description of its unfolding equilibrium and the equilibrium linking molten globule and native state. All thermodynamic and molecular properties of the molten globule here analyzed are characteristic of a partly unfolded conformation, and their differences with those of the native state are typically quantitative rather than qualitative. The stability data depict a native state ensemble where the relative populations of the different intermediates are strongly modulated by pH. Whereas the molten globule is dominant at pH 2.0, at neutral pH it is just the least stable of three partly unfolded intermediates populated by this protein. It is of interest that the energy rank of these intermediates at pH 7.0 is consistent with their likelihood to overcome the native state and become the more stable conformation when the native state protein is subjected to heat or mutation stress. Given the small volume difference between molten globule and native state, neither crowding agents nor osmolytes can drive the molten globule back to the native state. This observation, which is in qualitative accord with predictions of simple excluded volume theory, indicates that molecular crowding in vivo is not an effective mechanism to minimize partial unfolding events leading to equilibrium intermediates.
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