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Arratia LM, Bermudes-Contreras JD, Juarez-Monroy JA, Romero-Macías EA, Luna-Rojas JC, López-Hidalgo M, Vega AV, Zamorano-Carrillo A. Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of Na V1.2 and Na V1.6. Sci Rep 2024; 14:6761. [PMID: 38514708 PMCID: PMC10957924 DOI: 10.1038/s41598-024-57117-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Voltage-gated sodium channels (NaV) are pivotal proteins responsible for initiating and transmitting action potentials. Emerging evidence suggests that proteolytic cleavage of sodium channels by calpains is pivotal in diverse physiological scenarios, including ischemia, brain injury, and neuropathic pain associated with diabetes. Despite this significance, the precise mechanism by which calpains recognize sodium channels, especially given the multiple calpain isoforms expressed in neurons, remains elusive. In this work, we show the interaction of Calpain-10 with NaV's C-terminus through a yeast 2-hybrid assay screening of a mouse brain cDNA library and in vitro by GST-pulldown. Later, we also obtained a structural and dynamic hypothesis of this interaction by modeling, docking, and molecular dynamics simulation. These results indicate that Calpain-10 interacts differentially with the C-terminus of NaV1.2 and NaV1.6. Calpain-10 interacts with NaV1.2 through domains III and T in a stable manner. In contrast, its interaction with NaV1.6 involves domains II and III, which could promote proteolysis through the Cys-catalytic site and C2 motifs.
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Affiliation(s)
- Luis Manuel Arratia
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Juan David Bermudes-Contreras
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Jorge Armando Juarez-Monroy
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Erik Alan Romero-Macías
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Doctorado en Ciencias Biomédicas, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Julio Cesar Luna-Rojas
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Maestría en Neurobiología, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Ana Victoria Vega
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico.
| | - Absalom Zamorano-Carrillo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico.
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Ramírez-Salinas GL, García-Machorro J, Rojas-Hernández S, Campos-Rodríguez R, de Oca ACM, Gomez MM, Luciano R, Zimic M, Correa-Basurto J. Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies. Arch Virol 2020; 165:891-911. [PMID: 32060794 PMCID: PMC7222995 DOI: 10.1007/s00705-020-04537-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/11/2019] [Indexed: 02/01/2023]
Abstract
Pandemics caused by influenza A virus (IAV) are responsible for the deaths of millions of humans around the world. One of these pandemics occurred in Mexico in 2009. Despite the impact of IAV on human health, there is no effective vaccine. Gene mutations and translocation of genome segments of different IAV subtypes infecting a single host cell make the development of a universal vaccine difficult. The design of immunogenic peptides using bioinformatics tools could be an interesting strategy to increase the success of vaccines. In this work, we used the predicted amino acid sequences of the neuraminidase (NA) and hemagglutinin (HA) proteins of different IAV subtypes to perform multiple alignments, epitope predictions, molecular dynamics simulations, and experimental validation. Peptide selection was based on the following criteria: promiscuity, protein surface exposure, and the degree of conservation among different medically relevant IAV strains. These peptides were tested using immunological assays to test their ability to induce production of antibodies against IAV. We immunized rabbits and mice and measured the levels of IgG and IgA antibodies in serum samples and nasal washes. Rabbit antibodies against the peptides P11 and P14 (both of which are hybrids of NA and HA) recognized HA from both group 1 (H1, H2, and H5) and group 2 (H3 and H7) IAV and also recognized the purified NA protein from the viral stock (influenza A Puerto Rico/916/34). IgG antibodies from rabbits immunized with P11 and P14 were capable of recognizing viral particles and inhibited virus hemagglutination. Additionally, intranasal immunization of mice with P11 and P14 induced specific IgG and IgA antibodies in serum and nasal mucosa, respectively. Interestingly, the IgG antibodies were found to have neutralizing capability. In conclusion, the peptides designed through in silico studies were validated in experimental assays.
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Affiliation(s)
- G Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Jazmín García-Machorro
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rafael Campos-Rodríguez
- Laboratorio de Bioquímica. Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Arturo Contis-Montes de Oca
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Miguel Medina Gomez
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rocío Luciano
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
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Demolombe V, de Brevern AG, Molina F, Lavigne G, Granier C, Moreau V. Benchmarking the PEPOP methods for mimicking discontinuous epitopes. BMC Bioinformatics 2019; 20:738. [PMID: 31888437 PMCID: PMC6937815 DOI: 10.1186/s12859-019-3189-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 11/04/2019] [Indexed: 11/18/2022] Open
Abstract
Background Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances. Results Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method. Conclusion The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.
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Affiliation(s)
- Vincent Demolombe
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Alexandre G de Brevern
- INSERM UMR-S 1134, DSIMB, F-75739, Paris, France.,Univ Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR 1134, F-75739, Paris, France.,INTS, F-75739, Paris, France.,Laboratoire d'Excellence GR-Ex, F75737, Paris, France
| | - Franck Molina
- Sys2Diag UMR 9005 CNRS/ALCEDIAGComplex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184, Montpellier Cedex 4, France
| | | | - Claude Granier
- Sys2Diag UMR 9005 CNRS/ALCEDIAGComplex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184, Montpellier Cedex 4, France
| | - Violaine Moreau
- CNRS, UMR5048, INSERM, U1054, Université Montpellier, Centre de Biochimie Structurale, 29, route de Navacelles, 34090, Montpellier, France.
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Rojas-Osornio SA, Cruz-Hernández TR, Drago-Serrano ME, Campos-Rodríguez R. Immunity to influenza: Impact of obesity. Obes Res Clin Pract 2019; 13:419-429. [PMID: 31542241 DOI: 10.1016/j.orcp.2019.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/14/2019] [Accepted: 05/19/2019] [Indexed: 12/27/2022]
Abstract
Obesity is a health concern that is recognized as a critical factor for vulnerability to influenza A/pdmH1N1 virus infection, with epidemiological and clinical impacts. In humans, obesity induces disturbances in inflammatory and immune responses to the influenza virus and in some cases, this leads to severe complications, with fatal outcomes. Obesity impairs immunity by altering the response of cytokines, resulting in a decrease in the cytotoxic cell response of immunocompetent cells which have a key anti-viral role. Additionally, obesity seems to disturb the balance of endocrine hormones, such as leptin, that affect the interplay between metabolic and immune systems. This contribution focuses on reviewing the current epidemiologic data for the immune response to immunity in obese humans and animal models. In doing so, we aim to provide potential mechanisms to enhance immunity to influenza A/pdmH1N1 virus infection and protective factors in obese people.
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Affiliation(s)
- Sandra Angélica Rojas-Osornio
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico
| | - Teresita Rocío Cruz-Hernández
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico
| | - Maria Elisa Drago-Serrano
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Unidad Xochimilco. Calzada del Hueso No. 1100, CP 04960, CDMX, Mexico
| | - Rafael Campos-Rodríguez
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, CP 11340, CDMX, Mexico.
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Farrokhi M, Dabirzadeh M, Fadaee E, Beni AA, Saadatpour Z, Rezaei A, Heidari Z. Polymorphism in Leptin and Leptin Receptor Genes May Modify Leptin Levels and Represent Risk Factors for Multiple Sclerosis. Immunol Invest 2016; 45:328-35. [DOI: 10.3109/08820139.2016.1157811] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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