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Vinzón SE, Lopez MV, Cafferata EGA, Soto AS, Berguer PM, Vazquez L, Nusblat L, Pontoriero AV, Belotti EM, Salvetti NR, Viale DL, Vilardo AE, Avaro MM, Benedetti E, Russo ML, Dattero ME, Carobene M, Sánchez-Lamas M, Afonso J, Heitrich M, Cristófalo AE, Otero LH, Baumeister EG, Ortega HH, Edelstein A, Podhajcer OL. Cross-protection and cross-neutralization capacity of ancestral and VOC-matched SARS-CoV-2 adenoviral vector-based vaccines. NPJ Vaccines 2023; 8:149. [PMID: 37794010 PMCID: PMC10550992 DOI: 10.1038/s41541-023-00737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
COVID-19 vaccines were originally designed based on the ancestral Spike protein, but immune escape of emergent Variants of Concern (VOC) jeopardized their efficacy, warranting variant-proof vaccines. Here, we used preclinical rodent models to establish the cross-protective and cross-neutralizing capacity of adenoviral-vectored vaccines expressing VOC-matched Spike. CoroVaxG.3-D.FR, matched to Delta Plus Spike, displayed the highest levels of nAb to the matched VOC and mismatched variants. Cross-protection against viral infection in aged K18-hACE2 mice showed dramatic differences among the different vaccines. While Delta-targeted vaccines fully protected mice from a challenge with Gamma, a Gamma-based vaccine offered only partial protection to Delta challenge. Administration of CorovaxG.3-D.FR in a prime/boost regimen showed that a booster was able to increase the neutralizing capacity of the sera against all variants and fully protect aged K18-hACE2 mice against Omicron BA.1, as a BA.1-targeted vaccine did. The neutralizing capacity of the sera diminished in all cases against Omicron BA.2 and BA.5. Altogether, the data demonstrate that a booster with a vaccine based on an antigenically distant variant, such as Delta or BA.1, has the potential to protect from a wider range of SARS-CoV-2 lineages, although careful surveillance of breakthrough infections will help to evaluate combination vaccines targeting antigenically divergent variants yet to emerge.
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Affiliation(s)
- Sabrina E Vinzón
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - María V Lopez
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Eduardo G A Cafferata
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariadna S Soto
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Paula M Berguer
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Luciana Vazquez
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Leonora Nusblat
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Andrea V Pontoriero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Eduardo M Belotti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Natalia R Salvetti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Diego L Viale
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariel E Vilardo
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Martin M Avaro
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Estefanía Benedetti
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mara L Russo
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - María E Dattero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mauricio Carobene
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Buenos Aires, Argentina
| | | | - Jimena Afonso
- Area de Bioterio, Fundación Instituto Leloir; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Mauro Heitrich
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Alejandro E Cristófalo
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
| | - Lisandro H Otero
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Instituto de Biotecnología Ambiental y Salud, CONICET, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Elsa G Baumeister
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Hugo H Ortega
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Alexis Edelstein
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina.
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2
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Laura Darriba M, Castro CP, Coria LM, Bruno L, Laura Cerutti M, Otero LH, Chemes LB, Rasia RM, Klinke S, Cassataro J, Pasquevich KA. A disordered region retains the full protease inhibitor activity and the capacity to induce CD8+ T cells in vivo of the oral vaccine adjuvant U-Omp19. Comput Struct Biotechnol J 2022; 20:5098-5114. [PMID: 36187929 PMCID: PMC9486555 DOI: 10.1016/j.csbj.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- M. Laura Darriba
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Celeste Pueblas Castro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lorena M. Coria
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Laura Bruno
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - M. Laura Cerutti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Juliana Cassataro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Karina A. Pasquevich
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
- Corresponding author.
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3
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Otero LH, Foscaldi S, Antelo GT, Rosano GL, Sirigu S, Klinke S, Defelipe LA, Sánchez-Lamas M, Battocchio G, Conforte V, Vojnov AA, Chavas LMG, Goldbaum FA, Mroginski MA, Rinaldi J, Bonomi HR. Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level. Sci Adv 2021; 7:eabh1097. [PMID: 34818032 PMCID: PMC8612531 DOI: 10.1126/sciadv.abh1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.
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Affiliation(s)
- Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Sabrina Foscaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giuliano T. Antelo
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Germán L. Rosano
- Unidad de Espectrometría de Masa, Instituto de Biología Molecular y Celular de Rosario, UEM-IBR, CONICET, Bv. 27 de Febrero (S2000EZP), Rosario, Argentina
| | - Serena Sirigu
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Lucas A. Defelipe
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85 (22607), Hamburg, Germany
| | - Maximiliano Sánchez-Lamas
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giovanni Battocchio
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Valeria Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Adrián A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Leonard M. G. Chavas
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Maria-Andrea Mroginski
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
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4
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Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG. Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. J Biol Chem 2021; 297:101175. [PMID: 34499924 PMCID: PMC8421091 DOI: 10.1016/j.jbc.2021.101175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 01/22/2023] Open
Abstract
The spike protein is the main protein component of the SARS-CoV-2 virion surface. The spike receptor-binding motif mediates recognition of the human angiotensin-converting enzyme 2 receptor, a critical step in infection, and is the preferential target for spike-neutralizing antibodies. Posttranslational modifications of the spike receptor-binding motif have been shown to modulate viral infectivity and host immune response, but these modifications are still being explored. Here we studied asparagine deamidation of the spike protein, a spontaneous event that leads to the appearance of aspartic and isoaspartic residues, which affect both the protein backbone and its charge. We used computational prediction and biochemical experiments to identify five deamidation hotspots in the SARS-CoV-2 spike protein. Asparagine residues 481 and 501 in the receptor-binding motif deamidate with a half-life of 16.5 and 123 days at 37 °C, respectively. Deamidation is significantly slowed at 4 °C, indicating a strong dependence of spike protein molecular aging on environmental conditions. Deamidation of the spike receptor-binding motif decreases the equilibrium constant for binding to the human angiotensin-converting enzyme 2 receptor more than 3.5-fold, yet its high conservation pattern suggests some positive effect on viral fitness. We propose a model for deamidation of the full SARS-CoV-2 virion illustrating how deamidation of the spike receptor-binding motif could lead to the accumulation on the virion surface of a nonnegligible chemically diverse spike population in a timescale of days. Our findings provide a potential mechanism for molecular aging of the spike protein with significant consequences for understanding virus infectivity and vaccine development.
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Affiliation(s)
- Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Lucas A Defelipe
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lucio Aliperti
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Stephan Niebling
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Tânia F Custódio
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Christian Löw
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - María García-Alai
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany; Centre for Structural Systems Biology, Hamburg, Germany
| | - Ignacio E Sánchez
- Laboratorio de Fisiología de Proteínas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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5
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Rivelli Antonelli JF, Santander VS, Nigra AD, Monesterolo NE, Previtali G, Primo E, Otero LH, Casale CH. Prevention of tubulin/aldose reductase association delays the development of pathological complications in diabetic rats. J Physiol Biochem 2021; 77:565-576. [PMID: 34097242 DOI: 10.1007/s13105-021-00820-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
In recent studies, we found that compounds derived from phenolic acids (CAFs) prevent the formation of the tubulin/aldose reductase complex and, consequently, may decrease the occurrence or delay the development of secondary pathologies associated with aldose reductase activation in diabetes mellitus. To verify this hypothesis, we determined the effect of CAFs on Na+,K+-ATPase tubulin-dependent activity in COS cells, ex vivo cataract formation in rat lenses and finally, to evaluate the antidiabetic effect of CAFs, diabetes mellitus was induced in Wistar rats, they were treated with different CAFs and four parameters were determinates: cataract formation, erythrocyte deformability, nephropathy and blood pressure. After confirming that CAFs are able to prevent the association between aldose reductase and tubulin, we found that treatment of diabetic rats with these compounds decreased membrane-associated acetylated tubulin, increased NKA activity, and thus reversed the development of four AR-activated complications of diabetes mellitus determined in this work. Based on these results, the existence of a new physiological mechanism is proposed, in which tubulin is a key regulator of aldose reductase activity. This mechanism can explain the incorrect functioning of aldose reductase and Na+,K+-ATPase, two key enzymes in the pathogenesis of diabetes mellitus. Moreover, we found that such alterations can be prevented by CAFs, which are able to dissociate tubulin/aldose reductase complex.
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Affiliation(s)
- Juan F Rivelli Antonelli
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Verónica S Santander
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Ayelen D Nigra
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Noelia E Monesterolo
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Gabriela Previtali
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Emilianao Primo
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina
| | - Lisandro H Otero
- Instituto de Investigaciones Bioquímicas de Buenos Aires, IIBBA, CONICET - Fundación Instituto Leloir, Av Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - César H Casale
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, 5800, Córdoba, CP, Argentina.
- INBIAS CONICET-UNRC, Instituto de Biotecnología Ambiental y Salud, Campus UNRC, Río Cuarto, 5800, Córdoba, CP, Argentina.
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6
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Cagnoni AJ, Primo ED, Klinke S, Cano ME, Giordano W, Mariño KV, Kovensky J, Goldbaum FA, Uhrig ML, Otero LH. Crystal structures of peanut lectin in the presence of synthetic β-N- and β-S-galactosides disclose evidence for the recognition of different glycomimetic ligands. Acta Crystallogr D Struct Biol 2020; 76:1080-1091. [PMID: 33135679 DOI: 10.1107/s2059798320012371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/08/2020] [Indexed: 11/11/2022]
Abstract
Carbohydrate-lectin interactions are involved in important cellular recognition processes, including viral and bacterial infections, inflammation and tumor metastasis. Hence, structural studies of lectin-synthetic glycan complexes are essential for understanding lectin-recognition processes and for the further design of promising chemotherapeutics that interfere with sugar-lectin interactions. Plant lectins are excellent models for the study of the molecular-recognition process. Among them, peanut lectin (PNA) is highly relevant in the field of glycobiology because of its specificity for β-galactosides, showing high affinity towards the Thomsen-Friedenreich antigen, a well known tumor-associated carbohydrate antigen. Given this specificity, PNA is one of the most frequently used molecular probes for the recognition of tumor cell-surface O-glycans. Thus, it has been extensively used in glycobiology for inhibition studies with a variety of β-galactoside and β-lactoside ligands. Here, crystal structures of PNA are reported in complex with six novel synthetic hydrolytically stable β-N- and β-S-galactosides. These complexes disclosed key molecular-binding interactions of the different sugars with PNA at the atomic level, revealing the roles of specific water molecules in protein-ligand recognition. Furthermore, binding-affinity studies by isothermal titration calorimetry showed dissociation-constant values in the micromolar range, as well as a positive multivalency effect in terms of affinity in the case of the divalent compounds. Taken together, this work provides a qualitative structural rationale for the upcoming synthesis of optimized glycoclusters designed for the study of lectin-mediated biological processes. The understanding of the recognition of β-N- and β-S-galactosides by PNA represents a benchmark in protein-carbohydrate interactions since they are novel synthetic ligands that do not belong to the family of O-linked glycosides.
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Affiliation(s)
- Alejandro J Cagnoni
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental, IBYME-CONICET, Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Emiliano D Primo
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, INBIAS-CONICET, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - María E Cano
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
| | - Walter Giordano
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, INBIAS-CONICET, Ruta Nacional 36 Km 601, 5800 Río Cuarto, Córdoba, Argentina
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental, IBYME-CONICET, Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - José Kovensky
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources (LG2A)-CNRS UMR 7378, Université de Picardie Jules Verne, 33 Rue Saint Leu, 80039 Amiens CEDEX, France
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - María Laura Uhrig
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
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Giglio ML, Ituarte S, Milesi V, Dreon MS, Brola TR, Caramelo J, Ip JCH, Maté S, Qiu JW, Otero LH, Heras H. Exaptation of two ancient immune proteins into a new dimeric pore-forming toxin in snails. J Struct Biol 2020; 211:107531. [PMID: 32446810 DOI: 10.1016/j.jsb.2020.107531] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022]
Abstract
The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles, however MACPFs with pore-forming toxic function in venoms and poisons are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that can affect the digestive and nervous systems of potential predators. We report the three-dimensional structure of PmPV2, at 17.2 Å resolution determined by negative-stain electron microscopy and its solution structure by small angle X-ray scattering (SAXS). We found that PV2s differ from nearly all MACPFs in two respects: it is a dimer in solution and protomers combine two immune proteins into an AB toxin. The MACPF chain is linked by a single disulfide bond to a tachylectin chain, and two heterodimers are arranged head-to-tail by non-covalent forces in the native protein. MACPF domain is fused with a putative new Ct-accessory domain exclusive to invertebrates. The tachylectin is a six-bladed β-propeller, similar to animal tectonins. We experimentally validated the predicted functions of both subunits and demonstrated for the first time that PV2s are true pore-forming toxins. The tachylectin "B" delivery subunit would bind to target membranes, and then the MACPF "A" toxic subunit would disrupt lipid bilayers forming large pores altering the plasma membrane conductance. These results indicate that PV2s toxicity evolved by linking two immune proteins where their combined preexisting functions gave rise to a new toxic entity with a novel role in defense against predation. This structure is an unparalleled example of protein exaptation.
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Affiliation(s)
- M L Giglio
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina
| | - S Ituarte
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina
| | - V Milesi
- Instituto de Estudios Inmunológicos y Fisiopatológicos, IIFP CONICET CCT La Plata - UNLP, Facultad de Ciencias Exactas, 1900 La Plata, Argentina
| | - M S Dreon
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina
| | - T R Brola
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina
| | - J Caramelo
- Instituto de Investigaciones Bioquímicas de Buenos Aires, IIBBA, CONICET - Fundación Instituto Leloir, Av Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - J C H Ip
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China
| | - S Maté
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina
| | - J W Qiu
- Department of Biology, Hong Kong Baptist University, 224 Waterloo Road, Hong Kong, China
| | - L H Otero
- Instituto de Investigaciones Bioquímicas de Buenos Aires, IIBBA, CONICET - Fundación Instituto Leloir, Av Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina; Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina.
| | - H Heras
- Instituto de Investigaciones Bioquímicas de La Plata "Prof. Dr. Rodolfo R. Brenner", INIBIOLP, CONICET CCT La Plata - Universidad Nacional de La Plata (UNLP), Facultad de Ciencias Médicas,1900 La Plata, Argentina; Cátedra de Química Biologica, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata (UNLP), 1900 La Plata, Argentina.
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Zylberman V, Sanguineti S, Pontoriero AV, Higa SV, Cerutti ML, Morrone Seijo SM, Pardo R, Muñoz L, Acuña Intrieri ME, Alzogaray VA, Avaro MM, Benedetti E, Berguer PM, Bocanera L, Bukata L, Bustelo MS, Campos AM, Colonna M, Correa E, Cragnaz L, Dattero ME, Dellafiore M, Foscaldi S, González JV, Guerra LL, Klinke S, Labanda MS, Lauché C, López JC, Martínez AM, Otero LH, Peyric EH, Ponziani PF, Ramondino R, Rinaldi J, Rodríguez S, Russo JE, Russo ML, Saavedra SL, Seigelchifer M, Sosa S, Vilariño C, López Biscayart P, Corley E, Spatz L, Baumeister EG, Goldbaum FA. Development of a hyperimmune equine serum therapy for COVID-19 in Argentina. Medicina (B Aires) 2020; 80 Suppl 3:1-6. [PMID: 32658841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Abstract
The disease named COVID-19, caused by the SARS-CoV-2 coronavirus, is currently generating a global pandemic. Vaccine development is no doubt the best long-term immunological approach, but in the current epidemiologic and health emergency there is a need for rapid and effective solutions. Convalescent plasma is the only antibody-based therapy available for COVID-19 patients to date. Equine polyclonal antibodies (EpAbs) put forward a sound alternative. The new generation of processed and purified EpAbs containing highly purified F(ab')2 fragments demonstrated to be safe and well tolerated. EpAbs are easy to manufacture allowing a fast development and scaling up for a treatment. Based on these ideas, we present a new therapeutic product obtained after immunization of horses with the receptor-binding domain of the viral Spike glycoprotein. Our product shows around 50 times more potency in in vitro seroneutralization assays than the average of convalescent plasma. This result may allow us to test the safety and efficacy of this product in a phase 2/3 clinical trial to be conducted in July 2020 in the metropolitan area of Buenos Aires, Argentina.
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Affiliation(s)
- Vanesa Zylberman
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | | | - Andrea V Pontoriero
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | - Sandra V Higa
- Instituto Biológico Argentino S.A.I.C., Buenos Aires, Argentina
| | - María L Cerutti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- CRIP -Centro de Rediseño e Ingeniería de Proteínas UNSAM, Campus Miguelete, San Martín, Provincia de Buenos Aires, Argentina
| | | | - Romina Pardo
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
| | - Luciana Muñoz
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
| | - María E Acuña Intrieri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
- CRIP -Centro de Rediseño e Ingeniería de Proteínas UNSAM, Campus Miguelete, San Martín, Provincia de Buenos Aires, Argentina
| | - Vanina A Alzogaray
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Martín M Avaro
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | - Estefanía Benedetti
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | - Paula M Berguer
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Lucas Bukata
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
| | | | - Ana M Campos
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | - Mariana Colonna
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
| | - Elisa Correa
- mAbxience, Munro, Provincia de Buenos Aires, Argentina
| | - Lucía Cragnaz
- mAbxience, Munro, Provincia de Buenos Aires, Argentina
| | - María E Dattero
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | | | - Sabrina Foscaldi
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | | | - Sebastián Klinke
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - María S Labanda
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Juan C López
- Instituto Biológico Argentino S.A.I.C., Buenos Aires, Argentina
| | | | - Lisandro H Otero
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Elías H Peyric
- Instituto Biológico Argentino S.A.I.C., Buenos Aires, Argentina
| | | | | | - Jimena Rinaldi
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | | | - Javier E Russo
- Instituto Biológico Argentino S.A.I.C., Buenos Aires, Argentina
| | - Mara L Russo
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | | | | | - Santiago Sosa
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Claudio Vilariño
- >CRIP -Centro de Rediseño e Ingeniería de Proteínas UNSAM, Campus Miguelete, San Martín, Provincia de Buenos Aires, Argentina
| | | | | | - Linus Spatz
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
| | - Elsa G Baumeister
- Servicio Virosis Respiratorias INEI-ANLIS Malbrán, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Centro Nacional de Influenza de OMS, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Inmunova S.A., San Martín, Provincia de Buenos Aires, Argentina
- CRIP -Centro de Rediseño e Ingeniería de Proteínas UNSAM, Campus Miguelete, San Martín, Provincia de Buenos Aires, Argentina
- Laboratorio de Inmunología y Microbiología Molecular, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
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Klinke S, Rinaldi J, Goldbaum FA, Suarez S, Otero LH. An All-Inclusive and Straightway Laboratory Activity to Solve the Three-Dimensional Crystal Structure of a Protein. Biochem Mol Biol Educ 2019; 47:700-707. [PMID: 31444958 DOI: 10.1002/bmb.21296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/26/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
X-ray crystallography provides structural information of molecules at the atomic level, being a central technique at the forefront of science and technology. However, crystallography teaching is not usually implemented in biochemistry lab classes due to its complex execution by nonexpert users. Here, we report the basic step-by-step workflow performed by crystallographers in order to solve the three-dimensional structure of a protein. All these activities were executed in a course for Latin-American graduate students with no previous knowledge on X-ray crystallography entitled "Crystallography in Structural Biology: why do we need a protein crystal, and how do we get it?." We would like to share our experience with the educational research community, with the main purpose being to enrich teaching in biochemistry and structural molecular biology by performing a series of interesting laboratory and computer experiments. © 2019 International Union of Biochemistry and Molecular Biology, 47(6):700-707, 2019.
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Affiliation(s)
- Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - Sebastián Suarez
- Departamento de Química Inorgánica, Analítica y Química, Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA, Buenos Aires, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
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Espinoza-Cara A, Zitare U, Alvarez-Paggi D, Klinke S, Otero LH, Murgida DH, Vila AJ. Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis. Chem Sci 2018; 9:6692-6702. [PMID: 30310603 PMCID: PMC6115626 DOI: 10.1039/c8sc01444b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/27/2018] [Indexed: 12/30/2022] Open
Abstract
Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.
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Affiliation(s)
- Andrés Espinoza-Cara
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
| | - Ulises Zitare
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Damián Alvarez-Paggi
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir , IIBBA-CONICET , Buenos Aires , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica , Analítica y Química Física-INQUIMAE , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires-CONICET , Buenos Aires , Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) , Rosario , Argentina .
- Área Biofísica , Departamento de Química Biológica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Rosario , Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM. , Buenos Aires , Argentina
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Primo ED, Otero LH, Ruiz F, Klinke S, Giordano W. The disruptive effect of lysozyme on the bacterial cell wall explored by an in-silico structural outlook. Biochem Mol Biol Educ 2018; 46:83-90. [PMID: 29131507 DOI: 10.1002/bmb.21092] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/22/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine. Such exercises typically do not include structural data. We describe here a sequence of computer tasks designed to illustrate and reinforce both physiological and structural concepts involved in lysozyme effects on the bacterial cell-wall structure. This lab class usually lasts 3.5 hours. First, the instructor presents introductory concepts of the bacterial cell wall and the effect of lysozyme on its structure. Then, students are taught to use computer modeling to visualize the three-dimensional structure of a lysozyme in complex with bacterial cell-wall fragments. Finally, the lysozyme inhibitory effect on a bacterial culture is optionally proposed as a simple microbiological assay. The computer lab exercises described here give students a realistic understanding of the disruptive effect of lysozymes on the bacterial cell wall, a crucial component in bacterial survival. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):83-90, 2018.
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Affiliation(s)
- Emiliano D Primo
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, RN36 601, Argentina
| | - Lisandro H Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires, Argentina
| | - Francisco Ruiz
- Departamento de Microbiología e Inmunología, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, RN36 601, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires, Argentina
| | - Walter Giordano
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, RN36 601, Argentina
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12
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Soldano A, Klinke S, Otero LH, Rivera M, Catalano-Dupuy DL, Ceccarelli EA. Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism. PLoS One 2017; 12:e0182535. [PMID: 28771589 PMCID: PMC5542595 DOI: 10.1371/journal.pone.0182535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/19/2017] [Indexed: 11/25/2022] Open
Abstract
Heme oxygenase from Leptospira interrogans is an important virulence factor. During catalysis, redox equivalents are provided to this enzyme by the plastidic-type ferredoxin-NADP+ reductase also found in L. interrogans. This process may have evolved to aid this bacterial pathogen to obtain heme-iron from their host and enable successful colonization. Herein we report the crystal structure of the heme oxygenase-heme complex at 1.73 Å resolution. The structure reveals several distinctive features related to its function. A hydrogen bonded network of structural water molecules that extends from the catalytic site to the protein surface was cleared observed. A depression on the surface appears to be the H+ network entrance from the aqueous environment to the catalytic site for O2 activation, a key step in the heme oxygenase reaction. We have performed a mutational analysis of the F157, located at the above-mentioned depression. The mutant enzymes were unable to carry out the complete degradation of heme to biliverdin since the reaction was arrested at the verdoheme stage. We also observed that the stability of the oxyferrous complex, the efficiency of heme hydroxylation and the subsequent conversion to verdoheme was adversely affected. These findings underscore a long-range communication between the outer fringes of the hydrogen-bonded network of structural waters and the heme active site during catalysis. Finally, by analyzing the crystal structures of ferredoxin-NADP+ reductase and heme oxygenase, we propose a model for the productive association of these proteins.
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Affiliation(s)
- Anabel Soldano
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Mario Rivera
- Department of Chemistry and Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas, United States of America
| | - Daniela L. Catalano-Dupuy
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail:
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13
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Fernández I, Otero LH, Klinke S, Carrica MDC, Goldbaum FA. Snapshots of Conformational Changes Shed Light into the NtrX Receiver Domain Signal Transduction Mechanism. J Mol Biol 2015; 427:3258-3272. [DOI: 10.1016/j.jmb.2015.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/11/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
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14
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Bouley R, Kumarasiri M, Peng Z, Otero LH, Song W, Suckow MA, Schroeder VA, Wolter WR, Lastochkin E, Antunes NT, Pi H, Vakulenko S, Hermoso JA, Chang M, Mobashery S. Discovery of antibiotic (E)-3-(3-carboxyphenyl)-2-(4-cyanostyryl)quinazolin-4(3H)-one. J Am Chem Soc 2015; 137:1738-41. [PMID: 25629446 DOI: 10.1021/jacs.5b00056] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the face of the clinical challenge posed by resistant bacteria, the present needs for novel classes of antibiotics are genuine. In silico docking and screening, followed by chemical synthesis of a library of quinazolinones, led to the discovery of (E)-3-(3-carboxyphenyl)-2-(4-cyanostyryl)quinazolin-4(3H)-one (compound 2) as an antibiotic effective in vivo against methicillin-resistant Staphylococcus aureus (MRSA). This antibiotic impairs cell-wall biosynthesis as documented by functional assays, showing binding of 2 to penicillin-binding protein (PBP) 2a. We document that the antibiotic also inhibits PBP1 of S. aureus, indicating a broad targeting of structurally similar PBPs by this antibiotic. This class of antibiotics holds promise in fighting MRSA infections.
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Affiliation(s)
- Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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15
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Klinke S, Otero LH, Rinaldi J, Sosa S, Guimarães BG, Shepard WE, Goldbaum FA, Bonomi HR. Crystallization and preliminary X-ray characterization of the full-length bacteriophytochrome from the plant pathogen Xanthomonas campestris pv. campestris. Acta Crystallogr F Struct Biol Commun 2014; 70:1636-9. [PMID: 25484215 PMCID: PMC4259229 DOI: 10.1107/s2053230x14023243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/21/2014] [Indexed: 11/11/2022] Open
Abstract
Phytochromes give rise to the largest photosensor family known to date. However, they are underrepresented in the Protein Data Bank. Plant, cyanobacterial, fungal and bacterial phytochromes share a canonical architecture consisting of an N-terminal photosensory module (PAS2-GAF-PHY domains) and a C-terminal variable output module. The bacterium Xanthomonas campestris pv. campestris, a worldwide agricultural pathogen, codes for a single bacteriophytochrome (XccBphP) that has this canonical architecture, bearing a C-terminal PAS9 domain as the output module. Full-length XccBphP was cloned, expressed and purified to homogeneity by nickel-NTA affinity and size-exclusion chromatography and was then crystallized at room temperature bound to its cofactor biliverdin. A complete native X-ray diffraction data set was collected to a maximum resolution of 3.25 Å. The crystals belonged to space group P43212, with unit-cell parameters a = b = 103.94, c = 344.57 Å and a dimer in the asymmetric unit. Refinement is underway after solving the structure by molecular replacement.
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Affiliation(s)
- Sebastián Klinke
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
| | - Santiago Sosa
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
| | - Beatriz G. Guimarães
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
| | - William E. Shepard
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
| | - Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA–CONICET, Avenida Patricias Argentinas 435, Buenos Aires, C1405BWE Buenos Aires, Argentina
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16
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Aran M, Smal C, Pellizza L, Gallo M, Otero LH, Klinke S, Goldbaum FA, Ithurralde ER, Bercovich A, Mac Cormack WP, Turjanski AG, Cicero DO. Solution and crystal structure of BA42, a protein from the Antarctic bacteriumBizionia argentinensiscomprised of a stand-alone TPM domain. Proteins 2014; 82:3062-78. [DOI: 10.1002/prot.24667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/01/2014] [Accepted: 08/06/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Aran
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Clara Smal
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Leonardo Pellizza
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Mariana Gallo
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Patricias Argentinas 435 (C1405BWE); Buenos Aires Argentina
| | - Esteban R. Ithurralde
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, e INQUIMAE-CONICET, Intendente Güiraldes 2160 (C1428EGA); Buenos Aires Argentina
| | - Andrés Bercovich
- Biosidus S.A., Constitución 4234 (C1254ABX); Buenos Aires Argentina
| | | | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, e INQUIMAE-CONICET, Intendente Güiraldes 2160 (C1428EGA); Buenos Aires Argentina
| | - Daniel O. Cicero
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma “Tor Vergata”, via della Ricerca Scientifica SNC (00133); Rome Italy
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17
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Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. Structural basis for the broad specificity of a new family of amino-acid racemases. ACTA ACUST UNITED AC 2013; 70:79-90. [PMID: 24419381 DOI: 10.1107/s1399004713024838] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/05/2013] [Indexed: 02/02/2023]
Abstract
Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.
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Affiliation(s)
- Akbar Espaillat
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Noelia Bernardo-García
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | | | - Lisandro H Otero
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Laura Álvarez
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Miguel A de Pedro
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | | | - Brigid M Davis
- Division of Infectious Diseases, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Felipe Cava
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
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18
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Otero LH, Rojas-Altuve A, Llarrull LI, Carrasco-López C, Kumarasiri M, Lastochkin E, Fishovitz J, Dawley M, Hesek D, Lee M, Johnson JW, Fisher JF, Chang M, Mobashery S, Hermoso JA. How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function. Proc Natl Acad Sci U S A 2013; 110:16808-13. [PMID: 24085846 PMCID: PMC3800995 DOI: 10.1073/pnas.1300118110] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expression of penicillin binding protein 2a (PBP2a) is the basis for the broad clinical resistance to the β-lactam antibiotics by methicillin-resistant Staphylococcus aureus (MRSA). The high-molecular mass penicillin binding proteins of bacteria catalyze in separate domains the transglycosylase and transpeptidase activities required for the biosynthesis of the peptidoglycan polymer that comprises the bacterial cell wall. In bacteria susceptible to β-lactam antibiotics, the transpeptidase activity of their penicillin binding proteins (PBPs) is lost as a result of irreversible acylation of an active site serine by the β-lactam antibiotics. In contrast, the PBP2a of MRSA is resistant to β-lactam acylation and successfully catalyzes the DD-transpeptidation reaction necessary to complete the cell wall. The inability to contain MRSA infection with β-lactam antibiotics is a continuing public health concern. We report herein the identification of an allosteric binding domain--a remarkable 60 Å distant from the DD-transpeptidase active site--discovered by crystallographic analysis of a soluble construct of PBP2a. When this allosteric site is occupied, a multiresidue conformational change culminates in the opening of the active site to permit substrate entry. This same crystallographic analysis also reveals the identity of three allosteric ligands: muramic acid (a saccharide component of the peptidoglycan), the cell wall peptidoglycan, and ceftaroline, a recently approved anti-MRSA β-lactam antibiotic. The ability of an anti-MRSA β-lactam antibiotic to stimulate allosteric opening of the active site, thus predisposing PBP2a to inactivation by a second β-lactam molecule, opens an unprecedented realm for β-lactam antibiotic structure-based design.
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Affiliation(s)
- Lisandro H. Otero
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Alzoray Rojas-Altuve
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Leticia I. Llarrull
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Cesar Carrasco-López
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
| | - Malika Kumarasiri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jennifer Fishovitz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Matthew Dawley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jarrod W. Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano,” Consejo Superior de Investigaciones Cientificas, 28006 Madrid, Spain; and
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19
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Sánchez DG, Otero LH, Hernández CM, Serra AL, Encarnación S, Domenech CE, Lisa AT. A Pseudomonas aeruginosa PAO1 acetylcholinesterase is encoded by the PA4921 gene and belongs to the SGNH hydrolase family. Microbiol Res 2011; 167:317-25. [PMID: 22192836 DOI: 10.1016/j.micres.2011.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 11/19/2011] [Accepted: 11/21/2011] [Indexed: 11/17/2022]
Abstract
Through the use of molecular and biochemical experiments and bioinformatic tools, this work demonstrates that the PA4921 gene of the Pseudomonas aeruginosa PAO1 genome is a gene responsible for cholinesterase (ChoE) activity. Similar to the acetylcholinesterase (AchE) of Zea mays, this ChoE belongs to the SGNH hydrolase family. In mature ChoE, i.e., without a signal peptide, (18)Ser, (78)Gly, (127)N, and (268)H are conserved aminoacyl residues. Acetylthiocholine (ATC) and propionylthiocholine (PTC) are substrates of this enzyme, but butyrylcholine is an inhibitor. The enzyme also catalyzes the hydrolysis of the artificial esters p-nitrophenyl propionate (pNPP) and p-nitrophenyl butyrate (pNPB) but with lower catalytic efficiency with respect to ATC or PTC. The second difference is that pNPP and pNPB did not produce inhibition at high substrate concentrations, as occurred with ATC and PTC. These differences plus preliminary biochemical and kinetic studies with alkylammonium compounds led us to propose that this enzyme is an acetylcholinesterase (AchE) or propionylcholinesterase. Studies performed with the purified recombinant enzyme indicated that the substrate saturation curves and the catalytic mechanism are similar to those properties described for mammalian AchEs. Therefore, the results of this work suggest that the P. aeruginosa ChoE is an AchE that may also be found in Pseudomonas fluorescens.
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Affiliation(s)
- Diego G Sánchez
- Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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20
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Beassoni PR, Otero LH, Boetsch C, Domenech CE, González-Nilo FD, Lisa AT. Site-directed mutations and kinetic studies show key residues involved in alkylammonium interactions and reveal two sites for phosphorylcholine in Pseudomonas aeruginosa phosphorylcholine phosphatase. Biochim Biophys Acta 2011; 1814:858-63. [PMID: 21515416 DOI: 10.1016/j.bbapap.2011.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 03/17/2011] [Accepted: 04/01/2011] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa phosphorylcholine phosphatase (PchP) catalyzes the hydrolysis of phosphorylcholine (Pcho) to produce choline and inorganic phosphate. PchP belongs to the haloacid dehalogenase superfamily (HAD) and possesses the three characteristic motifs of this family: motif I ((31)D and (33)D), motif II ((166)S), and motif III ((242)K, (261)G, (262)D and (267)D), which fold to form the catalytic site that binds the metal ion and the phosphate moiety of Pcho. Based on comparisons to the PHOSPHO1 and PHOSPHO2 human enzymes and the choline-binding proteins of Gram-(+) bacteria, we selected residues (42)E and (43)E and the aromatic triplet (82)YYY(84) for site-directed mutagenesis to study the interactions with Pcho and p-nitrophenylphosphate as substrates of PchP. Because mutations in (42)E, (43)E and the three tyrosine residues affect both the substrate affinity and the inhibitory effect produced by high Pcho concentrations, we postulate that two sites, one catalytic and one inhibitory, are present in PchP and that they are adjacent and share residues.
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Affiliation(s)
- Paola R Beassoni
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, X5800BYA Río Cuarto, Córdoba, Argentina.
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Otero LH, Beassoni PR, Domenech CE, Lisa AT, Albert A. Crystallization and preliminary X-ray diffraction analysis of Pseudomonas aeruginosa phosphorylcholine phosphatase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:957-60. [PMID: 20693680 PMCID: PMC2917303 DOI: 10.1107/s1744309110024061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 06/21/2010] [Indexed: 11/10/2022]
Abstract
Pseudomonas aeruginosa phosphorylcholine phosphatase (PchP) catalyzes the hydrolysis of phosphorylcholine to produce choline and inorganic phosphate. Phosphorylcholine is released by the action of haemolytic phospholipase C (PlcH) on phosphatidylcholine or sphingomyelin. PchP belongs to the HAD superfamily and its activity is dependent on Mg2+, Zn2+ or Cu2+. The possible importance of PchP in the pathogenesis of P. aeruginosa, the lack of information about its structure and its low identity to other members of this family led us to attempt its crystallization in order to solve its three-dimensional structure. Crystals of the protein have been grown and diffraction data have been obtained to 2.7 A resolution. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a=137.16, b=159.15, c=73.31 A, beta=117.89 degrees. Statistical analysis of the unit-cell contents and the self-rotation function suggest a tetrameric state of the molecule with 222 point-group symmetry.
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Affiliation(s)
- Lisandro H. Otero
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, Río Cuarto 5800, Córdoba, Argentina
| | - Paola R. Beassoni
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, Río Cuarto 5800, Córdoba, Argentina
| | - Carlos E. Domenech
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, Río Cuarto 5800, Córdoba, Argentina
| | - Angela T. Lisa
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Ruta Nacional 36 Km 601, Río Cuarto 5800, Córdoba, Argentina
| | - Armando Albert
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química Física ‘Rocasolano’, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid E-28006, Spain
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22
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Otero LH, Beassoni PR, Lisa AT, Domenech CE. Transition from octahedral to tetrahedral geometry causes the activation or inhibition by Znf2+ of Pseudomonas aeruginosa phosphorylcholine phosphatase. Biometals 2010; 23:307-14. [PMID: 20135339 DOI: 10.1007/s10534-010-9289-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 01/10/2010] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa phosphorylcholine phosphatase (PchP) catalyzes the hydrolysis of phosphorylcholine, which is produced by the action of hemolytic phospholipase C on phosphatidylcholine or sphyngomielin, to generate choline and inorganic phosphate. Among divalent cations, its activity is dependent on Mg(2+) or Zn(2+). Mg(2+) produced identical activation at pH 5.0 and 7.4, but Zn(2+) was an activator at pH 5.0 and became an inhibitor at pH 7.4. At this higher pH, very low concentrations of Zn(2+) inhibited enzymatic activity even in the presence of saturating Mg(2+) concentrations. Considering experimental and theoretical physicochemical calculations performed by different authors, we conclude that at pH 5.0, Mg(2+) and Zn(2+) are hexacoordinated in an octahedral arrangement in the PchP active site. At pH 7.4, Mg(2+) conserves the octahedral coordination maintaining enzymatic activity. The inhibition produced by Zn(2+) at 7.4 is interpreted as a change from octahedral to tetrahedral coordination geometry which is produced by hydrolysis of the [Zn(2+)L(2)(-1)L(2)(0) (H(2)O)(2)] complex.
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Affiliation(s)
- Lisandro H Otero
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, 5800 Río Cuarto, Córdoba, Argentina
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23
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Beassoni PR, Berti FPD, Otero LH, Risso VA, Ferreyra RG, Lisa AT, Domenech CE, Ermácora MR. Preparation and biophysical characterization of recombinant Pseudomonas aeruginosa phosphorylcholine phosphatase. Protein Expr Purif 2010; 71:153-9. [PMID: 20064618 DOI: 10.1016/j.pep.2010.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 01/03/2010] [Accepted: 01/05/2010] [Indexed: 12/01/2022]
Abstract
Pseudomonas aeruginosa infections constitute a widespread health problem with high economical and social impact, and the phosphorylcholine phosphatase (PchP) of this bacterium is a potential target for antimicrobial treatment. However, drug design requires high-resolution structural information and detailed biophysical knowledge not available for PchP. An obstacle in the study of PchP is that current methods for its expression and purification are suboptimal and allowed only a preliminary kinetic characterization of the enzyme. Herein, we describe a new procedure for the efficient preparation of recombinant PchP overexpressed in Escherichia coli. The enzyme is purified from urea solubilized inclusion bodies and refolded by dialysis. The product of PchP refolding is a mixture of native PchP and a kinetically-trapped, alternatively-folded aggregate that is very slowly converted into the native state. The properly folded and fully active enzyme is isolated from the refolding mixture by size-exclusion chromatography. PchP prepared by the new procedure was subjected to chemical and biophysical characterization, and its basic optical, hydrodynamic, metal-binding, and catalytic properties are reported. The unfolding of the enzyme was also investigated, and its thermal stability was determined. The obtained information should help to compare PchP with other phosphatases and to obtain a better understanding of its catalytic mechanism. In addition, preliminary trials showed that PchP prepared by the new protocol is suitable for crystallization, opening the way for high-resolution studies of the enzyme structure.
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Affiliation(s)
- Paola R Beassoni
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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Beassoni PR, Otero LH, Lisa AT, Domenech CE. Using a molecular model and kinetic experiments in the presence of divalent cations to study the active site and catalysis of Pseudomonas aeruginosa phosphorylcholine phosphatase. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2008; 1784:2038-44. [DOI: 10.1016/j.bbapap.2008.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 07/26/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
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Beassoni PR, Otero LH, Massimelli MJ, Lisa AT, Domenech CE. Critical active-site residues identified by site-directed mutagenesis in Pseudomonas aeruginosa phosphorylcholine phosphatase, a new member of the haloacid dehalogenases hydrolase superfamily. Curr Microbiol 2006; 53:534-9. [PMID: 17106798 DOI: 10.1007/s00284-006-0365-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 08/17/2006] [Indexed: 11/27/2022]
Abstract
Pseudomonas aeruginosa phosphorylcholine phosphatase (PChP), the product of the PA5292 gene, is synthesized when the bacteria are grown with choline, betaine, dimethylglycine, or carnitine. In the presence of Mg(2+), PChP catalyzes the hydrolysis of both phosphorylcholine (PCh) and p-nitrophenylphosphate (p-NPP). PCh saturation curve analysis of the enzyme with or without the signal peptide indicated that the peptide was the fundamental factor responsible for decreasing the affinity of the second site of PChP for PCh, either at pH 5.0 or pH 7.4. PChP contained three conserved motifs characteristic of the haloacid dehalogenases superfamily. In the PChP without the signal peptide, motifs I, II, and III correspond to the residues (31)DMDNT(35), (166)SAA(168), and K(242)/(261)GDTPDSD(267), respectively. To determine the catalytic importance of the D31, D33, T35, S166, K242, D262, D265, and D267 on the enzyme activity, site-directed mutagenesis was performed. D31, D33, D262, and D267 were identified as the more important residues for catalysis. D265 and D267 may be involved in the stabilization of motif III, or might contribute to substrate specificity. The substitution of T35 by S35 resulted in an enzyme with a low PChP activity, but conserves the catalytic sites involved in the hydrolysis of PCh (K(m1) 0.03 mM: , K(m2) 0.5 mM: ) or p-NPP (K(m) 2.1 mM: ). Mutating either S166 or K242 revealed that these residues are also important to catalyze the hydrolysis of both substrates. The substitution of lysine by arginine or by glutamine revealed the importance of the positive charged group, either from the amino or guanidinium groups, because K242Q was inactive, whereas K242R was a functional enzyme.
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Affiliation(s)
- Paola R Beassoni
- Biologia Molecular, Universidad Nacional de Rio Cuarto, km 601, Ruta 36, Rio Cuarto, 5800, Argentina
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