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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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2
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Keitelman IA, Shiromizu CM, Zgajnar NR, Danielián S, Jancic CC, Martí MA, Fuentes F, Yancoski J, Vera Aguilar D, Rosso DA, Goris V, Buda G, Katsicas MM, Galigniana MD, Galletti JG, Sabbione F, Trevani AS. The interplay between serine proteases and caspase-1 regulates the autophagy-mediated secretion of Interleukin-1 beta in human neutrophils. Front Immunol 2022; 13:832306. [PMID: 36091026 PMCID: PMC9458071 DOI: 10.3389/fimmu.2022.832306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/09/2021] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Neutrophils play major roles against bacteria and fungi infections not only due to their microbicide properties but also because they release mediators like Interleukin-1 beta (IL-1β) that contribute to orchestrate the inflammatory response. This cytokine is a leaderless protein synthesized in the cytoplasm as a precursor (pro-IL-1β) that is proteolytically processed to its active isoform and released from human neutrophils by secretory autophagy. In most myeloid cells, pro-IL-1β is processed by caspase-1 upon inflammasome activation. Here we employed neutrophils from both healthy donors and patients with a gain-of-function (GOF) NLRP3-mutation to dissect IL-1β processing in these cells. We found that although caspase-1 is required for IL-1β secretion, it undergoes rapid inactivation, and instead, neutrophil serine proteases play a key role in pro-IL-1β processing. Our findings bring to light distinctive features of the regulation of caspase-1 activity in human neutrophils and reveal new molecular mechanisms that control human neutrophil IL-1β secretion.
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Affiliation(s)
- Irene A. Keitelman
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Carolina M. Shiromizu
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Nadia R. Zgajnar
- Laboratorio de receptores nucleares, Instituto de Biología y Medicina Experimental (IBYME)-CONICET, Buenos Aires, Argentina
| | - Silvia Danielián
- Laboratorio de Biología Molecular Inmunología, Hospital de Pediatría “Juan P. Garrahan”, Buenos Aires, Argentina
| | - Carolina C. Jancic
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) – CONICET, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Federico Fuentes
- Laboratorio de Microscopía, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Judith Yancoski
- Laboratorio de Biología Molecular Inmunología, Hospital de Pediatría “Juan P. Garrahan”, Buenos Aires, Argentina
| | - Douglas Vera Aguilar
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - David A. Rosso
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Verónica Goris
- Unidad de Genómica. Laboratorio de Biología Molecular de Inmunología, Hospital de Pediatría “Juan P. Garrahan”, Buenos Aires, Argentina
| | - Guadalupe Buda
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) – CONICET, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - María Martha Katsicas
- Servicio de Inmunología y Reumatología, Hospital de Pediatría “Juan P. Garrahan”, Buenos Aires, Argentina
| | - Mario D. Galigniana
- Laboratorio de receptores nucleares, Instituto de Biología y Medicina Experimental (IBYME)-CONICET, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Jeremías G. Galletti
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Florencia Sabbione
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
| | - Analia S. Trevani
- Laboratorio de Inmunidad Innata, Instituto de Medicina Experimental (IMEX) - CONICET, Academia Nacional de Medicina, Buenos Aires, Argentina
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Analia S. Trevani, ;
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Martin A, Fernandez MC, Cattaneo ER, Schuster CD, Venara M, Clément F, Berenstein A, Lombardi MG, Bergadá I, Gutierrez M, Martí MA, Gonzalez-Baro MR, Pennisi PA. Type 1 Insulin-Like Growth Factor Receptor Nuclear Localization in High-Grade Glioma Cells Enhances Motility, Metabolism, and In Vivo Tumorigenesis. Front Endocrinol (Lausanne) 2022; 13:849279. [PMID: 35574033 PMCID: PMC9094447 DOI: 10.3389/fendo.2022.849279] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Gliomas are the most frequent solid tumors in children. Among these, high-grade gliomas are less common in children than in adults, though they are similar in their aggressive clinical behavior. In adults, glioblastoma is the most lethal tumor of the central nervous system. Insulin-like growth factor 1 receptor (IGF1R) plays an important role in cancer biology, and its nuclear localization has been described as an adverse prognostic factor in different tumors. Previously, we have demonstrated that, in pediatric gliomas, IGF1R nuclear localization is significantly associated with high-grade tumors, worst clinical outcome, and increased risk of death. Herein we explore the role of IGF1R intracellular localization by comparing two glioblastoma cell lines that differ only in their IGF1R capacity to translocate to the nucleus. In vitro, IGF1R nuclear localization enhances glioblastoma cell motility and metabolism without affecting their proliferation. In vivo, IGF1R has the capacity to translocate to the nucleus and allows not only a higher proliferation rate and the earlier development of tumors but also renders the cells sensitive to OSI906 therapy. With this work, we provide evidence supporting the implications of the presence of IGF1R in the nucleus of glioma cells and a potential therapeutic opportunity for patients harboring gliomas with IGF1R nuclear localization.
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Affiliation(s)
- Ayelen Martin
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - María Celia Fernandez
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Elizabeth R. Cattaneo
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Claudio D. Schuster
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - Marcela Venara
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Florencia Clément
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Ariel Berenstein
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, CONICET, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | | | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Mariana Gutierrez
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, Argentina
| | - María R. Gonzalez-Baro
- Instituto de Investigaciones Bioquímicas de La Plata, CONICET, Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Patricia A. Pennisi
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” CONICET—FEI—División de Endocrinología, Hospital de Niños R. Gutierrez, Buenos Aires, Argentina
- *Correspondence: Patricia A. Pennisi,
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Castro S, Brunello FG, Sansó G, Scaglia P, Esnaola Azcoiti M, Izquierdo A, Villegas F, Bergadá I, Ropelato MG, Martí MA, Rey RA, Grinspon RP. Delayed Puberty Due to a WDR11 Truncation at Its N-Terminal Domain Leading to a Mild Form of Ciliopathy Presenting With Dissociated Central Hypogonadism: Case Report. Front Pediatr 2022; 10:887658. [PMID: 35722485 PMCID: PMC9204026 DOI: 10.3389/fped.2022.887658] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/21/2022] [Indexed: 11/25/2022] Open
Abstract
Pubertal delay in males is frequently due to constitutional delay of growth and puberty, but pathologic hypogonadism should be considered. After general illnesses and primary testicular failure are ruled out, the main differential diagnosis is central (or hypogonadotropic) hypogonadism, resulting from a defective function of the gonadotropin-releasing hormone (GnRH)/gonadotropin axis. Ciliopathies arising from defects in non-motile cilia are responsible for developmental disorders affecting the sense organs and the reproductive system. WDR11-mediated signaling in non-motile cilia is critical for fetal development of GnRH neurons. Only missense variants of WDR11 have been reported to date in patients with central hypogonadism, suggesting that nonsense variants could lead to more complex phenotypes. We report the case of a male patient presenting with delayed puberty due to Kallmann syndrome (central hypogonadism associated with hyposmia) in whom the next-generation sequencing analysis identified a novel heterozygous base duplication, leading to a frameshift and a stop codon in the N-terminal region of WDR11. The variant was predicted to undergo nonsense-mediated decay and classified as probably pathogenic following the American College of Medical Genetics and Genomics (ACMG) criteria. This is the first report of a variant in the WDR11 N-terminal region predicted to lead to complete expression loss that, contrary to expectations, led to a mild form of ciliopathy resulting in isolated Kallmann syndrome.
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Affiliation(s)
- Sebastián Castro
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Franco G Brunello
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Gabriela Sansó
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Paula Scaglia
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Esnaola Azcoiti
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Agustín Izquierdo
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Florencia Villegas
- Servicio de Genética, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Gabriela Ropelato
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Rodolfo A Rey
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Unidad de Medicina Traslacional, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.,Departamento de Biología Celular, Histología, Facultad de Medicina, Universidad de Buenos Aires, Embriología y Genética, Buenos Aires, Argentina
| | - Romina P Grinspon
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
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5
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Gergics P, Smith C, Bando H, Jorge AAL, Rockstroh-Lippold D, Vishnopolska SA, Castinetti F, Maksutova M, Carvalho LRS, Hoppmann J, Martínez Mayer J, Albarel F, Braslavsky D, Keselman A, Bergadá I, Martí MA, Saveanu A, Barlier A, Abou Jamra R, Guo MH, Dauber A, Nakaguma M, Mendonca BB, Jayakody SN, Ozel AB, Fang Q, Ma Q, Li JZ, Brue T, Pérez Millán MI, Arnhold IJP, Pfaeffle R, Kitzman JO, Camper SA. High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency. Am J Hum Genet 2021; 108:1526-1539. [PMID: 34270938 DOI: 10.1016/j.ajhg.2021.06.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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] [Received: 01/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary hormone deficiency occurs in ∼1:4,000 live births. Approximately 3% of the cases are due to mutations in the alpha isoform of POU1F1, a pituitary-specific transcriptional activator. We found four separate heterozygous missense variants in unrelated individuals with hypopituitarism that were predicted to affect a minor isoform, POU1F1 beta, which can act as a transcriptional repressor. These variants retain repressor activity, but they shift splicing to favor the expression of the beta isoform, resulting in dominant-negative loss of function. Using a high-throughput splicing reporter assay, we tested 1,070 single-nucleotide variants in POU1F1. We identified 96 splice-disruptive variants, including 14 synonymous variants. In separate cohorts, we found two additional synonymous variants nominated by this screen that co-segregate with hypopituitarism. This study underlines the importance of evaluating the impact of variants on splicing and provides a catalog for interpretation of variants of unknown significance in POU1F1.
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Affiliation(s)
- Peter Gergics
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Cathy Smith
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Hironori Bando
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Alexander A L Jorge
- Genetic Endocrinology Unit (LIM25), Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Denise Rockstroh-Lippold
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany
| | - Sebastian A Vishnopolska
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Frederic Castinetti
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - Mariam Maksutova
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Luciani Renata Silveira Carvalho
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Julia Hoppmann
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany
| | - Julián Martínez Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Frédérique Albarel
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - Debora Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ana Keselman
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá," FEI - CONICET - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires, CABA C1428EHA, Argentina
| | - Alexandru Saveanu
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Laboratory of Molecular Biology, Marseille 13385, France
| | - Anne Barlier
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Laboratory of Molecular Biology, Marseille 13385, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Michael H Guo
- Division of Endocrinology, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Dauber
- Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marilena Nakaguma
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Berenice B Mendonca
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Sajini N Jayakody
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - A Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Qing Fang
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Thierry Brue
- Aix Marseille University, AP-HM, INSERM, Marseille Medical Genetics, Marmara Institute, La Conception Hospital, Department of Endocrinology, Marseille 13005, France
| | - María Ines Pérez Millán
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, CABA CE1428EHA, Argentina
| | - Ivo J P Arnhold
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM/42, Division of Endocrinology, Hospital das Clinicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Roland Pfaeffle
- Department of Women's and Child Health, Division of Pediatric Endocrinology, University Hospital Leipzig, Leipzig 04103, Germany; Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA.
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6
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Serral F, Castello FA, Sosa EJ, Pardo AM, Palumbo MC, Modenutti C, Palomino MM, Lazarowski A, Auzmendi J, Ramos PIP, Nicolás MF, Turjanski AG, Martí MA, Fernández Do Porto D. From Genome to Drugs: New Approaches in Antimicrobial Discovery. Front Pharmacol 2021; 12:647060. [PMID: 34177572 PMCID: PMC8219968 DOI: 10.3389/fphar.2021.647060] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 01/31/2023] Open
Abstract
Decades of successful use of antibiotics is currently challenged by the emergence of increasingly resistant bacterial strains. Novel drugs are urgently required but, in a scenario where private investment in the development of new antimicrobials is declining, efforts to combat drug-resistant infections become a worldwide public health problem. Reasons behind unsuccessful new antimicrobial development projects range from inadequate selection of the molecular targets to a lack of innovation. In this context, increasingly available omics data for multiple pathogens has created new drug discovery and development opportunities to fight infectious diseases. Identification of an appropriate molecular target is currently accepted as a critical step of the drug discovery process. Here, we review how diverse layers of multi-omics data in conjunction with structural/functional analysis and systems biology can be used to prioritize the best candidate proteins. Once the target is selected, virtual screening can be used as a robust methodology to explore molecular scaffolds that could act as inhibitors, guiding the development of new drug lead compounds. This review focuses on how the advent of omics and the development and application of bioinformatics strategies conduct a "big-data era" that improves target selection and lead compound identification in a cost-effective and shortened timeline.
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Affiliation(s)
- Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Florencia A Castello
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- 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, Ciudad Universitaria, Buenos Aires, Argentina
| | - Agustín M Pardo
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Miranda Clara Palumbo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carlos Modenutti
- 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, Ciudad Universitaria, Buenos Aires, Argentina
| | - María Mercedes Palomino
- 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, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Lazarowski
- Departamento de Bioquímica Clínica, Instituto de Investigaciones en Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jerónimo Auzmendi
- Departamento de Bioquímica Clínica, Instituto de Investigaciones en Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Ivan P Ramos
- Centro de Integração de Dados e Conhecimentos para Saúde (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Adrián G Turjanski
- 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, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A Martí
- 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, Ciudad Universitaria, Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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7
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Modenutti CP, Blanco Capurro JI, Ibba R, Alonzi DS, Song MN, Vasiljević S, Kumar A, Chandran AV, Tax G, Marti L, Hill JC, Lia A, Hensen M, Waksman T, Rushton J, Rubichi S, Santino A, Martí MA, Zitzmann N, Roversi P. Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase. Structure 2021; 29:357-370.e9. [PMID: 33352114 PMCID: PMC8024514 DOI: 10.1016/j.str.2020.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/07/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022]
Abstract
UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2). CtUGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements. We name "Parodi limit" the maximum distance on the same glycoprotein between a site of misfolding and an N-linked glycan that can be reglucosylated by monomeric UGGT in vitro, in response to recognition of misfold at that site. Based on the MD simulations, we estimate the Parodi limit as around 70-80 Å. Frequency distributions of distances between glycoprotein residues and their closest N-linked glycosylation sites in glycoprotein crystal structures suggests relevance of the Parodi limit to UGGT activity in vivo. Our data support a "one-size-fits-all adjustable spanner" UGGT substrate recognition model, with an essential role for the UGGT TRXL2 domain.
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Affiliation(s)
- Carlos P Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Roberta Ibba
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Via Muroni 23A, 07100 Sassari, SS, Italy
| | - Dominic S Alonzi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mauro N Song
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Snežana Vasiljević
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Abhinav Kumar
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anu V Chandran
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabor Tax
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH,, UK
| | - Lucia Marti
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Johan C Hill
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Andrea Lia
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH,, UK; Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Mario Hensen
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Thomas Waksman
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan Rushton
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Simone Rubichi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina.
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH,, UK.
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8
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Arcon JP, Turjanski AG, Martí MA, Forli S. Biased Docking for Protein-Ligand Pose Prediction. Methods Mol Biol 2021; 2266:39-72. [PMID: 33759120 PMCID: PMC10708986 DOI: 10.1007/978-1-0716-1209-5_3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The interaction between a protein and its ligands is one of the basic and most important processes in biological chemistry. Docking methods aim to predict the molecular 3D structure of protein-ligand complexes starting from coordinates of the protein and the ligand separately. They are widely used in both industry and academia, especially in the context of drug development projects. AutoDock4 is one of the most popular docking tools and, as for any docking method, its performance is highly system dependent. Knowledge about specific protein-ligand interactions on a particular target can be used to successfully overcome this limitation. Here, we describe how to apply the AutoDock Bias protocol, a simple and elegant strategy that allows users to incorporate target-specific information through a modified scoring function that biases the ligand structure towards those poses (or conformations) that establish selected interactions. We discuss two examples using different bias sources. In the first, we show how to steer dockings towards interactions derived from crystal structures of the receptor with different ligands; in the second example, we define and apply hydrophobic biases derived from Molecular Dynamics simulations in mixed solvents. Finally, we discuss general concepts of biased docking, its performance in pose prediction, and virtual screening campaigns as well as other potential applications.
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Affiliation(s)
- Juan Pablo Arcon
- Departamento de Química Biológica e IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Adrián G Turjanski
- Departamento de Química Biológica e IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica e IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
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9
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Buda G, Valdez RM, Biagioli G, Olivieri FA, Affranchino N, Bouso C, Lotersztein V, Bogunovic D, Bustamante J, Martí MA. Inflammatory cutaneous lesions and pulmonary manifestations in a new patient with autosomal recessive ISG15 deficiency case report. Allergy Asthma Clin Immunol 2020; 16:77. [PMID: 32944031 PMCID: PMC7491304 DOI: 10.1186/s13223-020-00473-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/06/2020] [Indexed: 11/27/2022] Open
Abstract
Interferon-stimulated gene 15 (ISG15) was the first ubiquitin-like modifier protein identified that acts by protein conjugation (ISGylation) and is thought to modulate IFN-induced inflammation. Here, we report a new patient from a non-consanguineous Argentinian family, who was followed for recurrent ulcerative skin lesions, cerebral calcifications and lung disease. Whole Exome Sequencing (WES) revealed two novel compound heterozygous variants (c.285del and c.299_312del, NM_005101.4 GRCh37(hg19), both classified as pathogenic according to ACMG criteria) in the ISG15 gene, resulting in a complete deficiency due to disruption of the second ubiquitin domain of the corresponding protein. The clinical phenotype of this patient is unique given the presence of recurrent pulmonary manifestations and the absence of mycobacterial infections, thus resulting in a phenotype distinct from that previously described in patients with biallelic loss-of-function (LOF) ISG15 variants. This case highlights the role of ISG15 as an immunomodulating factor whose LOF variants result in heterogeneous clinical presentations.
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Affiliation(s)
- Guadalupe Buda
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Buenos Aires, Argentina.,Bitgenia, Buenos Aires, Argentina
| | - Rita María Valdez
- Hospital Militar Central, Servicio de Genética, Buenos Aires, Argentina
| | - German Biagioli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Buenos Aires, Argentina.,Bitgenia, Buenos Aires, Argentina
| | - Federico A Olivieri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Buenos Aires, Argentina
| | | | - Carolina Bouso
- Hospital Juan P. Garrahan, Servicio de Inmunología y Reumatología, Buenos Aires, Argentina
| | | | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Paris, France.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, University of Paris, Imagine Institute, Paris, EU France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, USA.,Study Center of Immunodeficiencies, Necker Hospital for Sick Children, Paris, EU France
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Buenos Aires, Argentina
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10
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Álvarez L, Suárez SA, González PJ, Brondino CD, Doctorovich F, Martí MA. The Underlying Mechanism of HNO Production by the Myoglobin-Mediated Oxidation of Hydroxylamine. Inorg Chem 2020; 59:7939-7952. [DOI: 10.1021/acs.inorgchem.9b02750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucía Álvarez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Sebastián A. Suárez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Pablo J. González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral y CONICET, S3000ZAA Santa Fe, Argentina
| | - Carlos D. Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral y CONICET, S3000ZAA Santa Fe, Argentina
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- INQUIMAE-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- IQUIBICEN-CONICET, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
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11
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Vishnopolska SA, Braslavsky D, Keselman AC, Bergada I, Marino RM, Ramirez PC, Natalia PG, Ciaccio M, Palma MID, Belgorosky A, Miras M, Nicola JP, Mortensen AH, Martí MA, Camper SA, Kitzman J, Perez Millán MI. MON-717 Novel GLI2 Mutations Identified in Pediatric Patients with Combined Pituitary Hormone Deficiency: One Gene, Various Genotypes. J Endocr Soc 2020. [PMCID: PMC7208733 DOI: 10.1210/jendso/bvaa046.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Combined pituitary hormone deficiency (CPHD) is an important clinical problem caused by mutations in more than 30 different genes. Six genes in the Sonic Hedgehog (SHH) signalling pathway are reported to cause CPHD. SHH signaling is essential to induce pituitary cell identity in cells of Rathke’s pouch by stimulating expression of the transcription factors Lhx3 and Lhx4. In the absence of SHH signaling, a repressive isoform of the transcription factor GLI2 (Gli-Kruppel family member 2) suppresses gene expression. In the presence of SHH signaling, the activating form of GLI2 gains access to the nucleus and induces expression of downstream target genes. Heterozygous GLI2 loss of function mutations are found in patients with holoprosencephaly (HPE), HPE-like phenotypes associated with pituitary anomalies, and combined pituitary hormone deficiency with or without other extra-pituitary findings. We sought to identify the cause of CPHD in 171 unrelated patients diagnosed with or without extra-pituitary manifestations that were recruited from several Argentinean medical centers. We conducted panel sequencing, and identified GLI2 heterozygous variants that were rare and predicted to be deleterious in two unrelated patients, (p.L761P and p.1404Lfs) and a single, heterozygous, rare, likely deleterious GLI2 variant identified by exome sequencing (p.A203T). p.L761P and p.A203T variants were previously reported as candidates for HPE/CPHD, no functional studies were carried out to determine the effect of the variants on the gene function. We performed functional analysis of these variants using a mammalian cell line (NIH/3T3-CG) previously engineered to be a sensor for SHH signaling. It was stably transfected with a reporter gene that expresses GFP in response to GLI2 activation by a SHH agonist. We modified this cell line to assay GLI2 variants. We created a homozygous knock out of both endogenous Gli2 genes using CRISPR-Cas9 editing, and individual cell clones were selected for loss of GFP expression in response to SHH agonist treatment by FACS. We verified that transfecting the knockout cells with wild type Gli2 restored SHH responsive GFP expression. We assayed the ability of three patient GLI2 variants to rescue GFP expression and SHH agonist responsiveness and found that all three failed to fully rescue to wild type levels. This supports the hypothesis that the GLI2 variants in three CPHD patients are likely pathogenic. Thus, we identified three likely pathogenic GLI2 mutations in CPHD patients from Argentina. The variable phenotype of patients with GLI2 mutations worldwide could be caused by variation in other genes, environmental exposures, maternal effects, and/or epigenetic factors.
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Affiliation(s)
- Sebastian A Vishnopolska
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Debora Braslavsky
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Ana Claudia Keselman
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Ignacio Bergada
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | | | | | | | - Marta Ciaccio
- Hospital de Pediatría Garrahan, Buenos Aires, Argentina
| | | | | | - Mirta Miras
- Hospital de Niños de la Santisima Trinidad Cordoba, Cordoba, Argentina
| | | | | | - Marcelo A Martí
- Departamento de Quimica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Jacob Kitzman
- University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maria I Perez Millán
- Departamento de Fisiología Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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12
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Fago A, Natarajan C, Pettinati M, Hoffmann FG, Wang T, Weber RE, Drusin SI, Issoglio F, Martí MA, Estrin D, Storz JF. Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO 2. Am J Physiol Regul Integr Comp Physiol 2020; 318:R657-R667. [PMID: 32022587 DOI: 10.1152/ajpregu.00342.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hemoglobins (Hbs) of crocodilians are reportedly characterized by unique mechanisms of allosteric regulatory control, but there are conflicting reports regarding the importance of different effectors, such as chloride ions, organic phosphates, and CO2. Progress in understanding the unusual properties of crocodilian Hbs has also been hindered by a dearth of structural information. Here, we present the first comparative analysis of blood properties and Hb structure and function in a phylogenetically diverse set of crocodilian species. We examine mechanisms of allosteric regulation in the Hbs of 13 crocodilian species belonging to the families Crocodylidae and Alligatoridae. We also report new amino acid sequences for the α- and β-globins of these taxa, which, in combination with structural analyses, provide insights into molecular mechanisms of allosteric regulation. All crocodilian Hbs exhibited a remarkably strong sensitivity to CO2, which would permit effective O2 unloading to tissues in response to an increase in metabolism during intense activity and diving. Although the Hbs of all crocodilians exhibit similar intrinsic O2-affinities, there is considerable variation in sensitivity to Cl- ions and ATP, which appears to be at least partly attributable to variation in the extent of NH2-terminal acetylation. Whereas chloride appears to be a potent allosteric effector of all crocodile Hbs, ATP has a strong, chloride-independent effect on Hb-O2 affinity only in caimans. Modeling suggests that allosteric ATP binding has a somewhat different structural basis in crocodilian and mammalian Hbs.
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Affiliation(s)
- Angela Fago
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Martín Pettinati
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi.,Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Starkville, Mississippi
| | - Tobias Wang
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Roy E Weber
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Salvador I Drusin
- Departmento de Química Biolόgica/IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Issoglio
- Departmento de Química Biolόgica/IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departmento de Química Biolόgica/IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska
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13
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Modenutti CP, Capurro JIB, Di Lella S, Martí MA. The Structural Biology of Galectin-Ligand Recognition: Current Advances in Modeling Tools, Protein Engineering, and Inhibitor Design. Front Chem 2019; 7:823. [PMID: 31850312 PMCID: PMC6902271 DOI: 10.3389/fchem.2019.00823] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 07/28/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022] Open
Abstract
Galectins (formerly known as “S-type lectins”) are a subfamily of soluble proteins that typically bind β-galactoside carbohydrates with high specificity. They are present in many forms of life, from nematodes and fungi to animals, where they perform a wide range of functions. Particularly in humans, different types of galectins have been described differing not only in their tissue expression but also in their cellular location, oligomerization, fold architecture and carbohydrate-binding affinity. This distinct yet sometimes overlapping distributions and physicochemical attributes make them responsible for a wide variety of both intra- and extracellular functions, including tremendous importance in immunity and disease. In this review, we aim to provide a general description of galectins most important structural features, with a special focus on the molecular determinants of their carbohydrate-recognition ability. For that purpose, we structurally compare the human galectins, in light of recent mutagenesis studies and novel X-ray structures. We also offer a detailed description on how to use the solvent structure surrounding the protein as a tool to get better predictions of galectin-carbohydrate complexes, with a potential application to the rational design of glycomimetic inhibitory compounds. Finally, using Gal-1 and Gal-3 as paramount examples, we review a series of recent advances in the development of engineered galectins and galectin inhibitors, aiming to dissect the structure-activity relationship through the description of their interaction at the molecular level.
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Affiliation(s)
- Carlos P Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Buenos Aires, Argentina
| | - Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Buenos Aires, Argentina
| | - Santiago Di Lella
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Buenos Aires, Argentina
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14
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Blanco Capurro JI, Di Paola M, Gamarra MD, Martí MA, Modenutti CP. An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein-monosaccharide complexes. Glycobiology 2019; 29:124-136. [PMID: 30407518 DOI: 10.1093/glycob/cwy102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/06/2018] [Indexed: 01/13/2023] Open
Abstract
Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and ligand conformational diversity. In the last decade several strategies, such as the inclusion of glycan conformation specific scoring functions or our developed solvent-site biased method, have improved carbohydrate docking performance but significant challenges remain, in particular, those related to receptor conformational diversity. In the present work we have analyzed conventional and solvent-site biased autodock4 performance concerning receptor conformational diversity as derived from different crystal structures (apo and holo), Molecular Dynamics snapshots and Homology-based models, for 14 different lectin-monosaccharide complexes. Our results show that both conventional and biased docking yield accurate lectin-monosaccharide complexes, starting from either apo or homology-based structures, even when only moderate (45%) sequence identity templates are available. An essential element for success is a proper combination of a middle-sized (10-100 structures) conformational ensemble, derived either from Molecular dynamics or multiple homology model building. Consistent with our previous works, results show that solvent-site biased methods improve overall performance, but that results are still highly system dependent. Finally, our results also show that docking can select the correct receptor structure within the ensemble, underscoring the relevance of joint evaluation of both ligand pose and receptor conformation.
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Affiliation(s)
- Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Matias Di Paola
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Daniel Gamarra
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos P Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria, Intendente Guiraldes 2160, Ciudad Autónoma de Buenos Aires, Argentina
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15
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Galizia J, Martí MA. Reactive nitrogen and oxygen species: Friend or foe in the tuberculosis fight. Tuberculosis (Edinb) 2018; 113:175-176. [DOI: 10.1016/j.tube.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 11/27/2022]
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16
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Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez Garcia D, Barril X, Turjanski AG, Martí MA. Correction to Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking and Allows Accurate Binding Free Energy Predictions. J Chem Inf Model 2018; 58:1312. [DOI: 10.1021/acs.jcim.8b00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Galizia J, Acosta MP, Urdániz E, Martí MA, Piuri M. Evaluation of nitroxyl donors' effect on mycobacteria. Tuberculosis (Edinb) 2018; 109:35-40. [DOI: 10.1016/j.tube.2018.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/26/2017] [Accepted: 01/30/2018] [Indexed: 10/18/2022]
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18
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Radusky L, Ruiz-Carmona S, Modenutti C, Barril X, Turjanski AG, Martí MA. LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening. J Chem Inf Model 2017; 57:1741-1746. [PMID: 28700230 DOI: 10.1021/acs.jcim.7b00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compounds is directly proportional to the cost, and thus, the best possible set of ligands is the one with the highest number of true binders, for the smallest possible compound set size. Therefore, methods that are able to trim down large universal data sets enriching them in potential binders are highly appreciated. Here we present LigQ, a free webserver that is able to (i) determine best structure and ligand binding pocket for a desired protein, (ii) find known binders, as well as potential ligands known to bind to similar protein domains, (iii) most importantly, select a small set of commercial compounds enriched in potential binders, and (iv) prepare them for virtual screening. LigQ was tested with several proteins, showing an impressive capacity to retrieve true ligands from large data sets, achieving enrichment factors of over 10%. LigQ is available at http://ligq.qb.fcen.uba.ar/ .
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Affiliation(s)
- Leandro Radusky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Sergio Ruiz-Carmona
- Department of Physical Chemistry, Faculty of Pharmacy and Institute of Biomedicine (IBUB), University of Barcelona , Avgda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Xavier Barril
- Department of Physical Chemistry, Faculty of Pharmacy and Institute of Biomedicine (IBUB), University of Barcelona , Avgda. Diagonal 643, Barcelona 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
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19
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Bartesaghi S, Herrera D, Martinez DM, Petruk A, Demicheli V, Trujillo M, Martí MA, Estrín DA, Radi R. Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation. Arch Biochem Biophys 2017; 622:9-25. [PMID: 28412156 DOI: 10.1016/j.abb.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 11/29/2016] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022]
Abstract
Tyrosine nitration is an oxidative post-translational modification that can occur in proteins associated to hydrophobic bio-structures such as membranes and lipoproteins. In this work, we have studied tyrosine nitration in membranes using a model system consisting of phosphatidylcholine liposomes with pre-incorporated tyrosine-containing 23 amino acid transmembrane peptides. Tyrosine residues were located at positions 4, 8 or 12 of the amino terminal, resulting in different depths in the bilayer. Tyrosine nitration was accomplished by exposure to peroxynitrite and a peroxyl radical donor or hemin in the presence of nitrite. In egg yolk phosphatidylcholine liposomes, nitration was highest for the peptide with tyrosine at position 8 and dramatically increased as a function of oxygen levels. Molecular dynamics studies support that the proximity of the tyrosine phenolic ring to the linoleic acid peroxyl radicals contributes to the efficiency of tyrosine oxidation. In turn, α-tocopherol inhibited both lipid peroxidation and tyrosine nitration. The mechanism of tyrosine nitration involves a "connecting reaction" by which lipid peroxyl radicals oxidize tyrosine to tyrosyl radical and was fully recapitulated by computer-assisted kinetic simulations. Altogether, this work underscores unique characteristics of the tyrosine oxidation and nitration process in lipid-rich milieu that is fueled via the lipid peroxidation process.
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Affiliation(s)
- Silvina Bartesaghi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Departamento de Educación Médica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay.
| | - Daniel Herrera
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Débora M Martinez
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Ariel Petruk
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Cuidad Universitaria, Pab 2, C1428EHA, Buenos Aires, Argentina
| | - Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Madia Trujillo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Marcelo A Martí
- Departamento de Química Biológica and IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Cuidad Universitaria, Pab 2, C1428EHA, Buenos Aires, Argentina
| | - Darío A Estrín
- Departamento de Química Inorgánica, Analítica y Química-Física and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Cuidad Universitaria, Pab 2, C1428EHA, Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Avda. Gral. Flores 2125, Montevideo 11800, Uruguay.
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20
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Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez-Garcia D, Barril X, Turjanski AG, Martí MA. Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. J Chem Inf Model 2017; 57:846-863. [DOI: 10.1021/acs.jcim.6b00678] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan Pablo Arcon
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lucas A. Defelipe
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Carlos P. Modenutti
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Elias D. López
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | | | - Xavier Barril
- Institut
de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat
de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Adrián G. Turjanski
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
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21
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Demicheli V, Moreno DM, Jara GE, Lima A, Carballal S, Ríos N, Batthyany C, Ferrer-Sueta G, Quijano C, Estrı́n DA, Martí MA, Radi R. Mechanism of the Reaction of Human Manganese Superoxide Dismutase with Peroxynitrite: Nitration of Critical Tyrosine 34. Biochemistry 2016; 55:3403-17. [PMID: 27227512 DOI: 10.1021/acs.biochem.6b00045] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human Mn-containing superoxide dismutase (hMnSOD) is a mitochondrial enzyme that metabolizes superoxide radical (O2(•-)). O2(•-) reacts at diffusional rates with nitric oxide to yield a potent nitrating species, peroxynitrite anion (ONOO(-)). MnSOD is nitrated and inactivated in vivo, with active site Tyr34 as the key oxidatively modified residue. We previously reported a k of ∼1.0 × 10(5) M(-1) s(-1) for the reaction of hMnSOD with ONOO(-) by direct stopped-flow spectroscopy and the critical role of Mn in the nitration process. In this study, we further established the mechanism of the reaction of hMnSOD with ONOO(-), including the necessary re-examination of the second-order rate constant by an independent method and the delineation of the microscopic steps that lead to the regio-specific nitration of Tyr34. The redetermination of k was performed by competition kinetics utilizing coumarin boronic acid, which reacts with ONOO(-) at a rate of ∼1 × 10(6) M(-1) s(-1) to yield the fluorescence product, 7-hydroxycoumarin. Time-resolved fluorescence studies in the presence of increasing concentrations of hMnSOD provided a k of ∼1.0 × 10(5) M(-1) s(-1), fully consistent with the direct method. Proteomic analysis indicated that ONOO(-), but not other nitrating agents, mediates the selective modification of active site Tyr34. Hybrid quantum-classical (quantum mechanics/molecular mechanics) simulations supported a series of steps that involve the initial reaction of ONOO(-) with Mn(III) to yield Mn(IV) and intermediates that ultimately culminate in 3-nitroTyr34. The data reported herein provide a kinetic and mechanistic basis for rationalizing how MnSOD constitutes an intramitochondrial target for ONOO(-) and the microscopic events, with atomic level resolution, that lead to selective and efficient nitration of critical Tyr34.
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Affiliation(s)
- Verónica Demicheli
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Diego M Moreno
- Instituto de Química de Rosario (IQUIR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , Suipacha 531, S2002LRK Rosario, Argentina
| | - Gabriel E Jara
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Analía Lima
- Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Sebastián Carballal
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Natalia Ríos
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Departamento de Química Orgánica, Facultad de Química, Universidad de la República , Avda. General Flores 2124, Montevideo, Uruguay
| | - Carlos Batthyany
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Unidad Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Gerardo Ferrer-Sueta
- Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la Repúbica , Igua 4225, Montevideo, Uruguay
| | - Celia Quijano
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
| | - Darío A Estrı́n
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Güiraldes 2160, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay.,Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República , Avda. General Flores 2125, Montevideo, Uruguay
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22
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Urdániz E, Rondón L, Martí MA, Hatfull GF, Piuri M. Rapid Whole-Cell Assay of Antitubercular Drugs Using Second-Generation Fluoromycobacteriophages. Antimicrob Agents Chemother 2016; 60:3253-6. [PMID: 26976860 PMCID: PMC4862496 DOI: 10.1128/aac.03016-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Estefanía Urdániz
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Liliana Rondón
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
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Bustamante JP, Szretter ME, Sued M, Martí MA, Estrin DA, Boechi L. A quantitative model for oxygen uptake and release in a family of hemeproteins. Bioinformatics 2016; 32:1805-13. [PMID: 27153569 DOI: 10.1093/bioinformatics/btw083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/30/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hemeproteins have many diverse functions that largely depend on the rate at which they uptake or release small ligands, like oxygen. These proteins have been extensively studied using either simulations or experiments, albeit only qualitatively and one or two proteins at a time. RESULTS We present a physical-chemical model, which uses data obtained exclusively from computer simulations, to describe the uptake and release of oxygen in a family of hemeproteins, called truncated hemoglobins (trHbs). Through a rigorous statistical analysis we demonstrate that our model successfully recaptures all the reported experimental oxygen association and dissociation kinetic rate constants, thus allowing us to establish the key factors that determine the rates at which these hemeproteins uptake and release oxygen. We found that internal tunnels as well as the distal site water molecules control ligand uptake, whereas oxygen stabilization by distal site residues controls ligand release. Because these rates largely determine the functions of these hemeproteins, these approaches will also be important tools in characterizing the trHbs members with unknown functions. CONTACT lboechi@ic.fcen.uba.ar SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan P Bustamante
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - María E Szretter
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires Departamento De Matemática, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Mariela Sued
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Marcelo A Martí
- Departamento De Química Biológica E Instituto De Química Biológica De La Facultad De Ciencias Exactas Y Naturales (IQUIBICEN), Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Darío A Estrin
- Departamento de Química Inorgánica, Analítica Y Química Física, INQUIMAE-CONICET, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
| | - Leonardo Boechi
- Instituto De Cálculo, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires
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24
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Bustamante JP, Radusky L, Boechi L, Estrin DA, ten Have A, Martí MA. Evolutionary and Functional Relationships in the Truncated Hemoglobin Family. PLoS Comput Biol 2016; 12:e1004701. [PMID: 26788940 PMCID: PMC4720485 DOI: 10.1371/journal.pcbi.1004701] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
Predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. If function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members. Their functions are tightly related to O2 affinity and reactivity, as determined by the association and dissociation rate constants, both of which can be predicted and analyzed using in-silico based tools. In the present work we have applied a strategy, which combines homology modeling with molecular based energy calculations, to predict and analyze function of all known truncated hemoglobins in an evolutionary context. Our results show that truncated hemoglobins present conserved family features, but that its structure is flexible enough to allow the switch from high to low affinity in a few evolutionary steps. Most proteins display moderate to high oxygen affinities and multiple ligand migration paths, which, besides some minor trends, show heterogeneous distributions throughout the phylogenetic tree, again suggesting fast functional adaptation. Our data not only deepens our comprehension of the structural basis governing ligand affinity, but they also highlight some interesting functional evolutionary trends.
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Affiliation(s)
- Juan P. Bustamante
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Radusky
- Departamento de Química Biológica e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leonardo Boechi
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Arjen ten Have
- Instituto de Investigación Biológica, CONICET, Universidad Nacional de Mar del Plata. Buenos Aires, Argentina
| | - Marcelo A. Martí
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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25
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Ramírez CL, Zeida A, Jara GE, Roitberg AE, Martí MA. Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm. J Chem Theory Comput 2015; 10:4609-17. [PMID: 26588154 DOI: 10.1021/ct500672d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski's Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes.
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Affiliation(s)
- Claudia L Ramírez
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Ari Zeida
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Gabriel E Jara
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
| | - Adrián E Roitberg
- Quantum Theory Project and Department of Chemistry, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Marcelo A Martí
- Instituto de Química Física de los Materiales, Medio Ambiente Y Energía (INQUIMAE), UBA-CONICET , Buenos Aires C1428EGA, Argentina
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26
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Lombardi LE, Martí MA, Capece L. CG2AA: backmapping protein coarse-grained structures. Bioinformatics 2015; 32:1235-7. [DOI: 10.1093/bioinformatics/btv740] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 12/12/2015] [Indexed: 01/24/2023] Open
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Suarez SA, Neuman NI, Muñoz M, Álvarez L, Bikiel DE, Brondino CD, Ivanović-Burmazović I, Miljkovic JL, Filipovic MR, Martí MA, Doctorovich F. Nitric Oxide Is Reduced to HNO by Proton-Coupled Nucleophilic Attack by Ascorbate, Tyrosine, and Other Alcohols. A New Route to HNO in Biological Media? J Am Chem Soc 2015; 137:4720-7. [DOI: 10.1021/ja512343w] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Sebastián A. Suarez
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
| | - Nicolás I. Neuman
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
- Departamento
de Física, Facultad de Bioquímica y Ciencias Biológicas,
Universidad Nacional del Litoral, Ciudad Universitaria, Paraje
El Pozo, Santa Fe 3000, Argentina
| | - Martina Muñoz
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
| | - Lucı́a Álvarez
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
| | - Damián E. Bikiel
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
| | - Carlos D. Brondino
- Departamento
de Física, Facultad de Bioquímica y Ciencias Biológicas,
Universidad Nacional del Litoral, Ciudad Universitaria, Paraje
El Pozo, Santa Fe 3000, Argentina
| | - Ivana Ivanović-Burmazović
- Department
of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Jan Lj. Miljkovic
- Department
of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Milos R. Filipovic
- Department
of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Marcelo A. Martí
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
- Departamento
de Química Biológica, Facultad de Ciencias Exactas y
Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, (C1428EGA) Buenos Aires, Argentina
| | - Fabio Doctorovich
- Departamento
de Química Inorgánica, Analítica y Química
Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INQUIMAE-CONICET, Ciudad Universitaria, (C1428EGA) Buenos Aires, Argentina
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Abstract
Understanding the effects of coupling protein protonation and conformational states is critical to the development of drugs targeting pH sensors and to the rational engineering of pH switches. In this work, we address this issue by performing a comprehensive study of the pH-regulated switch from the closed to the open conformation in nitrophorin 4 (NP4) that determines its pH-dependent activity. Our calculations show that D30 is the only amino acid that has two significantly different pKas in the open and closed conformations, confirming its critical role in regulating pH-dependent behavior. In addition, we describe the free-energy landscape of the conformational change as a function of pH, obtaining accurate estimations of free-energy barriers and equilibrium constants using different methods. The underlying thermodynamic model of the switch workings suggests the possibility of tuning the observed pKa only through the conformational equilibria, keeping the same conformation-specific pKas, as evidenced by the proposed K125L mutant. Moreover, coupling between the protonation and conformational equilibria results in efficient regulation and pH-sensing around physiological pH values only for some combinations of protonation and conformational equilibrium constants, placing constraints on their possible values and leaving a narrow space for protein molecular evolution. The calculations and analysis presented here are of general applicability and provide a guide as to how more complex systems can be studied, offering insight into how pH-regulated allostery works of great value for designing drugs that target pH sensors and for rational engineering of pH switches beyond the common histidine trigger.
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Affiliation(s)
- Natali V Di Russo
- Quantum Theory Project and Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
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Doctorovich F, Bikiel DE, Pellegrino J, Suárez SA, Martí MA. Reactions of HNO with metal porphyrins: underscoring the biological relevance of HNO. Acc Chem Res 2014; 47:2907-16. [PMID: 25238532 DOI: 10.1021/ar500153c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Azanone ((1)HNO, nitroxyl) shows interesting yet poorly understood chemical and biological effects. HNO has some overlapping properties with nitric oxide (NO), sharing its biological reactivity toward heme proteins, thiols, and oxygen. Despite this similarity, HNO and NO show significantly different pharmacological effects. The high reactivity of HNO means that studies must rely on the use of donor molecules such as trioxodinitrate (Angeli's salt). It has been suggested that azanone could be an intermediate in several reactions and that it may be an enzymatically produced signaling molecule. The inherent difficulty in detecting its presence unequivocally prevents evidence from yielding definite answers. On the other hand, metalloporphyrins are widely used as chemical models of heme proteins, providing us with invaluable tools for the study of the coordination chemistry of small molecules, like NO, CO, and O2. Studies with transition metal porphyrins have shown diverse mechanistic, kinetic, structural, and reactive aspects related to the formation of nitrosyl complexes. Porphyrins are also widely used in technical applications, especially when coupled to a surface, where they can be used as electrochemical gas sensors. Given their versatility, they have not escaped their role as key players in chemical studies involving HNO. This Account presents the research performed during the last 10 years in our group concerning azanone reactions with iron, manganese, and cobalt porphyrins. We begin by describing their HNO trapping capabilities, which result in formation of the corresponding nitrosyl complexes. Kinetic and mechanistic studies of these reactions show two alternative operating mechanisms: reaction of the metal center with HNO or with the donor. Moreover, we have also shown that azanone can be stabilized by coordination to iron porphyrins using electron-attracting substituents attached to the porphyrin ring, which balance the negatively charged NO¯. Second, we describe an electrochemical HNO sensing device based on the covalent attachment of a cobalt porphyrin to gold. A surface effect affects the redox potentials and allows discrimination between HNO and NO. The reaction with the former is fast, efficient, and selective, lacking spurious signals due to the presence of reactive nitrogen and oxygen species. The sensor is both biologically compatible and highly sensitive (nanomolar). This time-resolved detection allows kinetic analysis of reactions producing HNO. The sensor thus offers excellent opportunities to be used in experiments looking for HNO. As examples, we present studies concerning (a) HNO donation capabilities of new HNO donors as assessed by the sensor, (b) HNO detection as an intermediate in O atom abstraction to nitrite by phosphines, and (c) NO to HNO interconversion mediated by alcohols and thiols. Finally, we briefly discuss the key experiments required to demonstrate endogenous HNO formation to be done in the near future, involving the in vivo use of the HNO sensing device.
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Affiliation(s)
- Fabio Doctorovich
- Departamento de Química Inorgánica,
Analítica
y Química Física/INQUIMAE-CONICET and †Departamento de Química
Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
| | - Damian E. Bikiel
- Departamento de Química Inorgánica,
Analítica
y Química Física/INQUIMAE-CONICET and †Departamento de Química
Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
| | - Juan Pellegrino
- Departamento de Química Inorgánica,
Analítica
y Química Física/INQUIMAE-CONICET and †Departamento de Química
Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
| | - Sebastián A. Suárez
- Departamento de Química Inorgánica,
Analítica
y Química Física/INQUIMAE-CONICET and †Departamento de Química
Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica,
Analítica
y Química Física/INQUIMAE-CONICET and †Departamento de Química
Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
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Eberhardt M, Dux M, Namer B, Miljkovic J, Cordasic N, Will C, Kichko TI, de la Roche J, Fischer M, Suárez SA, Bikiel D, Dorsch K, Leffler A, Babes A, Lampert A, Lennerz JK, Jacobi J, Martí MA, Doctorovich F, Högestätt ED, Zygmunt PM, Ivanovic-Burmazovic I, Messlinger K, Reeh P, Filipovic MR. H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway. Nat Commun 2014; 5:4381. [PMID: 25023795 PMCID: PMC4104458 DOI: 10.1038/ncomms5381] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/12/2014] [Indexed: 02/08/2023] Open
Abstract
Nitroxyl (HNO) is a redox sibling of nitric oxide (NO) that targets distinct signalling pathways with pharmacological endpoints of high significance in the treatment of heart failure. Beneficial HNO effects depend, in part, on its ability to release calcitonin gene-related peptide (CGRP) through an unidentified mechanism. Here we propose that HNO is generated as a result of the reaction of the two gasotransmitters NO and H2S. We show that H2S and NO production colocalizes with transient receptor potential channel A1 (TRPA1), and that HNO activates the sensory chemoreceptor channel TRPA1 via formation of amino-terminal disulphide bonds, which results in sustained calcium influx. As a consequence, CGRP is released, which induces local and systemic vasodilation. H2S-evoked vasodilatatory effects largely depend on NO production and activation of HNO–TRPA1–CGRP pathway. We propose that this neuroendocrine HNO–TRPA1–CGRP signalling pathway constitutes an essential element for the control of vascular tone throughout the cardiovascular system. Nitric oxide (NO) and hydrogen sulphide (H2S) are two gaseous signalling molecules produced in tissues. Here the authors propose that NO and H2S react with each other to form nitroxyl (HNO), which activates the TRPA1 channel in nerve cells and triggers the release of the vasoactive peptide CGRP.
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Affiliation(s)
- Mirjam Eberhardt
- 1] Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany [2] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [3] Department of Anesthesiology and Intensive Care, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Maria Dux
- 1] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [2] Department of Physiology, University of Szeged, Dóm tér 10, H-6720 Szeged, Hungary
| | - Barbara Namer
- Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany
| | - Jan Miljkovic
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Nada Cordasic
- Department of Nephrology and Hypertension, University of Erlangen-Nuremberg, Krankenhausstrasse 12, 91054 Erlangen, Germany
| | - Christine Will
- Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany
| | - Tatjana I Kichko
- Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany
| | - Jeanne de la Roche
- Department of Anesthesiology and Intensive Care, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Michael Fischer
- 1] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [2] Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB1 2PD, UK
| | - Sebastián A Suárez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Damian Bikiel
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Karola Dorsch
- Institute of Pathology, University of Ulm, Albert-Einstein-Allee 23, 89070 Ulm, Germany
| | - Andreas Leffler
- Department of Anesthesiology and Intensive Care, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Alexandru Babes
- 1] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [2] Department of Anatomy, Physiology and Biophysics, Faculty of Biology, University of Bucharest, Splaiul Independentei 91-95, 050095 Bucharest, Romania
| | - Angelika Lampert
- 1] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [2]
| | - Jochen K Lennerz
- Institute of Pathology, University of Ulm, Albert-Einstein-Allee 23, 89070 Ulm, Germany
| | - Johannes Jacobi
- Department of Nephrology and Hypertension, University of Erlangen-Nuremberg, Krankenhausstrasse 12, 91054 Erlangen, Germany
| | - Marcelo A Martí
- 1] Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina [2] Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Edward D Högestätt
- Clinical Chemistry & Pharmacology, Department of Laboratory Medicine, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Peter M Zygmunt
- Clinical Chemistry & Pharmacology, Department of Laboratory Medicine, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Ivana Ivanovic-Burmazovic
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Karl Messlinger
- Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany
| | - Peter Reeh
- 1] Institute of Physiology and Pathophysiology Friedrich-Alexander University Erlangen-Nuremberg, Universitaetsstrasse 17, 91054 Erlangen, Germany [2]
| | - Milos R Filipovic
- 1] Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nuremberg, Egerlandstrasse 1, 91058 Erlangen, Germany [2]
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Alvarez L, Suarez SA, Bikiel DE, Reboucas JS, Batinić-Haberle I, Martí MA, Doctorovich F. Redox potential determines the reaction mechanism of HNO donors with Mn and Fe porphyrins: defining the better traps. Inorg Chem 2014; 53:7351-60. [PMID: 25001488 DOI: 10.1021/ic5007082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Azanone ((1)HNO, nitroxyl) is a highly reactive molecule with interesting chemical and biological properties. Like nitric oxide (NO), its main biologically related targets are oxygen, thiols, and metalloproteins, particularly heme proteins. As HNO dimerizes with a rate constant between 10(6) and 10(7) M(-1) s(-1), reactive studies are performed using donors, which are compounds that spontaneously release HNO in solution. In the present work, we studied the reaction mechanism and kinetics of two azanone donors Angelís Salt and toluene sulfohydroxamic acid (TSHA) with eight different Mn porphyrins as trapping agents. These porphyrins differ in their total peripheral charge (positively or negatively charged) and in their Mn(III)/Mn(II) reduction potential, showing for each case positive (oxidizing) and negative (reducing) values. Our results show that the reduction potential determines the azanone donor reaction mechanism. While oxidizing porphyrins accelerate decomposition of the donor, reducing porphyrins react with free HNO. Our results also shed light into the donor decomposition mechanism using ab initio methods and provide a thorough analysis of which MnP are the best candidates for azanone trapping and quantification experiments.
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Affiliation(s)
- Lucía Alvarez
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pab. II (1428), Buenos Aires, Argentina
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Singh S, Thakur N, Oliveira A, Petruk AA, Hade MD, Sethi D, Bidon-Chanal A, Martí MA, Datta H, Parkesh R, Estrin DA, Luque FJ, Dikshit KL. Mechanistic insight into the enzymatic reduction of truncated hemoglobin N of Mycobacterium tuberculosis: role of the CD loop and pre-A motif in electron cycling. J Biol Chem 2014; 289:21573-83. [PMID: 24928505 DOI: 10.1074/jbc.m114.578187] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many pathogenic microorganisms have evolved hemoglobin-mediated nitric oxide (NO) detoxification mechanisms, where a globin domain in conjunction with a partner reductase catalyzes the conversion of toxic NO to innocuous nitrate. The truncated hemoglobin HbN of Mycobacterium tuberculosis displays a potent NO dioxygenase activity despite lacking a reductase domain. The mechanism by which HbN recycles itself during NO dioxygenation and the reductase that participates in this process are currently unknown. This study demonstrates that the NADH-ferredoxin/flavodoxin system is a fairly efficient partner for electron transfer to HbN with an observed reduction rate of 6.2 μM/min(-1), which is nearly 3- and 5-fold faster than reported for Vitreoscilla hemoglobin and myoglobin, respectively. Structural docking of the HbN with Escherichia coli NADH-flavodoxin reductase (FdR) together with site-directed mutagenesis revealed that the CD loop of the HbN forms contacts with the reductase, and that Gly(48) may have a vital role. The donor to acceptor electron coupling parameters calculated using the semiempirical pathway method amounts to an average of about 6.4 10(-5) eV, which is lower than the value obtained for E. coli flavoHb (8.0 10(-4) eV), but still supports the feasibility of an efficient electron transfer. The deletion of Pre-A abrogated the heme iron reduction by FdR in the HbN, thus signifying its involvement during intermolecular interactions of the HbN and FdR. The present study, thus, unravels a novel role of the CD loop and Pre-A motif in assisting the interactions of the HbN with the reductase and the electron cycling, which may be vital for its NO-scavenging function.
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Affiliation(s)
- Sandeep Singh
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Naveen Thakur
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Ana Oliveira
- the Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació Torribera, Santa Coloma de Gramenet, Spain, and
| | - Ariel A Petruk
- the Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Mangesh Dattu Hade
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Deepti Sethi
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Axel Bidon-Chanal
- the Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació Torribera, Santa Coloma de Gramenet, Spain, and
| | - Marcelo A Martí
- the Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Himani Datta
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Raman Parkesh
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Dario A Estrin
- the Departamento de Química Inorgánica, Analítica, y Química Física/INQUIMAE CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - F Javier Luque
- the Department de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Campus de l'Alimentació Torribera, Santa Coloma de Gramenet, Spain, and
| | - Kanak L Dikshit
- From the CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India,
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Martinez A, Peluffo G, Petruk AA, Hugo M, Piñeyro D, Demicheli V, Moreno DM, Lima A, Batthyány C, Durán R, Robello C, Martí MA, Larrieux N, Buschiazzo A, Trujillo M, Radi R, Piacenza L. Structural and molecular basis of the peroxynitrite-mediated nitration and inactivation of Trypanosoma cruzi iron-superoxide dismutases (Fe-SODs) A and B: disparate susceptibilities due to the repair of Tyr35 radical by Cys83 in Fe-SODB through intramolecular electron transfer. J Biol Chem 2014; 289:12760-78. [PMID: 24616096 DOI: 10.1074/jbc.m113.545590] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, contains exclusively iron-dependent superoxide dismutases (Fe-SODs) located in different subcellular compartments. Peroxynitrite, a key cytotoxic and oxidizing effector biomolecule, reacted with T. cruzi mitochondrial (Fe-SODA) and cytosolic (Fe-SODB) SODs with second order rate constants of 4.6 ± 0.2 × 10(4) M(-1) s(-1) and 4.3 ± 0.4 × 10(4) M(-1) s(-1) at pH 7.4 and 37 °C, respectively. Both isoforms are dose-dependently nitrated and inactivated by peroxynitrite. Susceptibility of T. cruzi Fe-SODA toward peroxynitrite was similar to that reported previously for Escherichia coli Mn- and Fe-SODs and mammalian Mn-SOD, whereas Fe-SODB was exceptionally resistant to oxidant-mediated inactivation. We report mass spectrometry analysis indicating that peroxynitrite-mediated inactivation of T. cruzi Fe-SODs is due to the site-specific nitration of the critical and universally conserved Tyr(35). Searching for structural differences, the crystal structure of Fe-SODA was solved at 2.2 Å resolution. Structural analysis comparing both Fe-SOD isoforms reveals differences in key cysteines and tryptophan residues. Thiol alkylation of Fe-SODB cysteines made the enzyme more susceptible to peroxynitrite. In particular, Cys(83) mutation (C83S, absent in Fe-SODA) increased the Fe-SODB sensitivity toward peroxynitrite. Molecular dynamics, electron paramagnetic resonance, and immunospin trapping analysis revealed that Cys(83) present in Fe-SODB acts as an electron donor that repairs Tyr(35) radical via intramolecular electron transfer, preventing peroxynitrite-dependent nitration and consequent inactivation of Fe-SODB. Parasites exposed to exogenous or endogenous sources of peroxynitrite resulted in nitration and inactivation of Fe-SODA but not Fe-SODB, suggesting that these enzymes play distinctive biological roles during parasite infection of mammalian cells.
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Affiliation(s)
- Alejandra Martinez
- From the Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
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Suárez SA, Bikiel DE, Wetzler DE, Martí MA, Doctorovich F. Time-Resolved Electrochemical Quantification of Azanone (HNO) at Low Nanomolar Level. Anal Chem 2013; 85:10262-9. [DOI: 10.1021/ac402134b] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sebastián A. Suárez
- Departamento
de Química Inorgánica, Analítica
y Química Física/INQUIMAE-CONICET, and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Damian E. Bikiel
- Departamento
de Química Inorgánica, Analítica
y Química Física/INQUIMAE-CONICET, and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Diana E. Wetzler
- Departamento
de Química Inorgánica, Analítica
y Química Física/INQUIMAE-CONICET, and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento
de Química Inorgánica, Analítica
y Química Física/INQUIMAE-CONICET, and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
| | - Fabio Doctorovich
- Departamento
de Química Inorgánica, Analítica
y Química Física/INQUIMAE-CONICET, and ‡Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA, Buenos Aires, Argentina
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Boechi L, Arrar M, Martí MA, Olson JS, Roitberg AE, Estrin DA. Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7. J Biol Chem 2013; 288:6754-62. [PMID: 23297402 DOI: 10.1074/jbc.m112.426056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the elucidation of the myoglobin (Mb) structure, a histidine residue on the E helix (His-E7) has been proposed to act as a gate with an open or closed conformation controlling access to the active site. Although it is believed that at low pH, the His-E7 gate is in its open conformation, the full relationship between the His-E7 protonation state, its conformation, and ligand migration in Mb is hotly debated. We used molecular dynamics simulations to first address the effect of His-E7 protonation on its conformation. We observed the expected shift from the closed to the open conformation upon protonation, but more importantly, noted a significant difference between the conformations of the two neutral histidine tautomers. We further computed free energy profiles for oxygen migration in each of the possible His-E7 states as well as in two instructive Mb mutants: Ala-E7 and Trp-E7. Our results show that even in the closed conformation, the His-E7 gate does not create a large barrier to oxygen migration and permits oxygen entry with only a small rotation of the imidazole side chain and movement of the E helix. We identify, instead, a hydrophobic site in the E7 channel that can accommodate an apolar diatomic ligand and enhances ligand uptake particularly in the open His-E7 conformation. This rate enhancement is diminished in the closed conformation. Taken together, our results provide a new conceptual framework for the histidine gate hypothesis.
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Affiliation(s)
- Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física/Inquimae-Conicet, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Pabellon 2, C1428EHA Buenos Aires, Argentina
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Ferreiro DN, Boechi L, Estrin DA, Martí MA. The key role of water in the dioxygenase function of Escherichia coli flavohemoglobin. J Inorg Biochem 2012; 119:75-84. [PMID: 23220591 DOI: 10.1016/j.jinorgbio.2012.10.015] [Citation(s) in RCA: 6] [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: 06/01/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
Flavohemoglobins (FHbs) are members of the globin superfamily, widely distributed among prokaryotes and eukaryotes that have been shown to carry out nitric oxide dioxygenase (NOD) activity. In prokaryotes, such as Escherichia coli, NOD activity is a defence mechanism against the NO release by the macrophages of the hosts' immune system during infection. Because of that, FHbs have been studied thoroughly and several drugs have been developed in an effort to fight infectious processes. Nevertheless, the protein's structural determinants involved in the NOD activity are still poorly understood. In this context, the aim of the present work is to unravel the molecular basis of FHbs structural dynamics-to-function relationship using state of the art computer simulation tools. In an effort to fulfill this goal, we studied three key processes that determine NOD activity, namely i) ligand migration into the active site ii) stabilization of the coordinated oxygen and iii) intra-protein electron transfer (ET). Our results allowed us to determine key factors related to all three processes like the presence of a long hydrophobic tunnel for ligand migration, the presence of a water mediated hydrogen bond to stabilize the coordinated oxygen and therefore achieve a high affinity, and the best possible ET paths between the FAD and the heme, where water molecules play an important role. Taken together the presented results close an important gap in our understanding of the wide and diverse globin structural-functional relationships.
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Affiliation(s)
- Dardo N Ferreiro
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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Di Russo NV, Estrin DA, Martí MA, Roitberg AE. pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4. PLoS Comput Biol 2012; 8:e1002761. [PMID: 23133364 PMCID: PMC3486867 DOI: 10.1371/journal.pcbi.1002761] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [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: 06/22/2012] [Accepted: 09/13/2012] [Indexed: 11/21/2022] Open
Abstract
The acid-base behavior of amino acids is an important subject of study due to their prominent role in enzyme catalysis, substrate binding and protein structure. Due to interactions with the protein environment, their pKas can be shifted from their solution values and, if a protein has two stable conformations, it is possible for a residue to have different “microscopic”, conformation-dependent pKa values. In those cases, interpretation of experimental measurements of the pKa is complicated by the coupling between pH, protonation state and protein conformation. We explored these issues using Nitrophorin 4 (NP4), a protein that releases NO in a pH sensitive manner. At pH 5.5 NP4 is in a closed conformation where NO is tightly bound, while at pH 7.5 Asp30 becomes deprotonated, causing the conformation to change to an open state from which NO can easily escape. Using constant pH molecular dynamics we found two distinct microscopic Asp30 pKas: 8.5 in the closed structure and 4.3 in the open structure. Using a four-state model, we then related the obtained microscopic values to the experimentally observed “apparent” pKa, obtaining a value of 6.5, in excellent agreement with experimental data. This value must be interpreted as the pH at which the closed to open population transition takes place. More generally, our results show that it is possible to relate microscopic structure dependent pKa values to experimentally observed ensemble dependent apparent pKas and that the insight gained in the relatively simple case of NP4 can be useful in several more complex cases involving a pH dependent transition, of great biochemical interest. The interaction of an amino acid with its protein environment can result in an acid-base behavior that is very different from what would be observed in solution. This environment can be greatly altered when the protein changes conformation. As a result, the amino acid will have two different “microscopic” pKa values. Nitrophorin 4 is a good case study to explore this behavior, because it undergoes a pH-dependent conformational change that is well characterized experimentally. Using computer simulation tools, we found that the key titratable Aspartic acid 30, has two very different microscopic pKas: 4.3 and 8.5, which are significantly different to the observed transition pKa in solution. However, using a simple model, we were able to understand how this causes the conformational change to take place at pH∼6.5, as measured experimentally. The insight gained in this relatively simple case can be useful in other more complex cases where the apparent pKa is also a result of the interplay of different conformations where some amino acids experience very different environments.
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Affiliation(s)
- Natali V. Di Russo
- Quantum Theory Project and Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Dario A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- * E-mail: (MAM); (AER)
| | - Adrian E. Roitberg
- Quantum Theory Project and Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (MAM); (AER)
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Gauto DF, Petruk AA, Modenutti CP, Blanco JI, Di Lella S, Martí MA. Solvent structure improves docking prediction in lectin-carbohydrate complexes. Glycobiology 2012; 23:241-58. [PMID: 23089616 DOI: 10.1093/glycob/cws147] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but particularly challenging because of their usually low binding affinity. In silico docking methods have a long-standing tradition in predicting protein-ligand complexes, and allow a potentially fast exploration of a number of possible protein-carbohydrate complex structures. However, determining which of these predicted complexes represents the correct structure is not always straightforward. In this work, we present a modification of the scoring function provided by AutoDock4, a widely used docking software, on the basis of analysis of the solvent structure adjacent to the protein surface, as derived from molecular dynamics simulations, that allows the definition and characterization of regions with higher water occupancy than the bulk solvent, called water sites. They mimic the interaction held between the carbohydrate -OH groups and the protein. We used this information for an improved docking method in relation to its capacity to correctly predict the protein-carbohydrate complexes for a number of tested proteins, whose ligands range in size from mono- to tetrasaccharide. Our results show that the presented method significantly improves the docking predictions. The resulting solvent-structure-biased docking protocol, therefore, appears as a powerful tool for the design and optimization of development of glycomimetic drugs, while providing new insights into protein-carbohydrate interactions. Moreover, the achieved improvement also underscores the relevance of the solvent structure to the protein carbohydrate recognition process.
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Affiliation(s)
- Diego F Gauto
- Departamento de Química Inorgánica, Analítica y Química Física, CONICET, Ciudad Universitaria, Buenos Aires, Argentina
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Doctorovich F, Bikiel D, Pellegrino J, Suárez SA, Martí MA. Stabilization and detection of nitroxyl by iron and cobalt porphyrins in solution and on surfaces. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424610002914] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nitroxyl (HNO/NO-) is a small short-lived molecule that has been suggested to be produced by nitric oxide (NO) synthases under certain conditions. As for NO , biologically relevant targets of HNO are mainly heme-proteins and therefore, it has been difficult to discriminate the physio-pathological role of each molecule conclusively. Therefore, accurate discrimination between them is still an unresolved matter. On the other hand, there is only scarce information about nitroxyl-metalloporphyrin complexes. Hence, there is growing interest in obtaining and characterizing stable heme model nitroxyl complexes. In this review we show how HNO and NO can be discriminated electrochemically by a Co porphyrin attached to a gold surface, and how nitroxyl can be stabilized by coordination to an electron-poor Fe porphyrin. The Co porphyrin with four anchors, cobalt(II)-5,10,15,20-tetrakis[3-(p-acetylthio-propoxy)phenyl]porphyrin [Co(P)] was covalently attached to gold electrodes, and its reactions with NO and HNO donors were studied electrochemically. By fixing the potential to values that oxidize CoIII(P)NO-, HNO can be selectively detected by amperometric techniques. On the other hand, the one-electron chemical reduction of FeII(TFPPBr8)NO (TFPPBr8= 2 ,3,7,8,12,13,17,18-octa-β-bromo-5,10,15,20-[tetrakis-(pentafluorophenyl)]porphyrin) with cobaltocene yields the significantly stable {FeNO}8nitroxyl anion complex, [Co(C5H5)2]+[Fe(TFPPBr8)NO]-, which was isolated and characterized by several spectroscopies and DFT calculations. This species is intermediate between FeIINO-and FeINO , which is contrasted with the predominant FeIINO-character of known non-heme {FeNO}8complexes.
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Affiliation(s)
- Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Damian Bikiel
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Juan Pellegrino
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Sebastián A. Suárez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
- Departamento de Química Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (1428), Buenos Aires, Argentina
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40
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Forti F, Boechi L, Bikiel D, Martí MA, Nardini M, Bolognesi M, Viappiani C, Estrin D, Luque FJ. Ligand Migration in Methanosarcina acetivorans Protoglobin: Effects of Ligand Binding and Dimeric Assembly. J Phys Chem B 2011; 115:13771-80. [DOI: 10.1021/jp208562b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Flavio Forti
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Damian Bikiel
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marco Nardini
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Martino Bolognesi
- Dipartimento di Scienze Biomolecolari e Biotecnologie and CIMAINA, Università degli Studi di Milano, I-20131 Milano, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica, Università degli Studi di Parma, Parma, Italy
- NEST, Istituto Nanoscienze-CNR, Italy
| | - Darío Estrin
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avinguda Diagonal 643, E-08028, Barcelona, Spain
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Guardia CMA, Gauto DF, Di Lella S, Rabinovich GA, Martí MA, Estrin DA. An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network. J Chem Inf Model 2011; 51:1918-30. [PMID: 21702482 DOI: 10.1021/ci200180h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Galectins, a family of evolutionarily conserved animal lectins, have been shown to modulate signaling processes leading to inflammation, apoptosis, immunoregulation, and angiogenesis through their ability to interact with poly-N-acetyllactosamine-enriched glycoconjugates. To date 16 human galectin carbohydrate recognition domains have been established by sequence analysis and found to be expressed in several tissues. Given the divergent functions of these lectins, it is of vital importance to understand common and differential features in order to search for specific inhibitors of individual members of the human galectin family. In this work we performed an integrated computational analysis of all individual members of the human galectin family. In the first place, we have built homology-based models for galectin-4 and -12 N-terminus, placental protein 13 (PP13) and PP13-like protein for which no experimental structural information is available. We have then performed classical molecular dynamics simulations of the whole 15 members family in free and ligand-bound states to analyze protein and protein-ligand interaction dynamics. Our results show that all galectins adopt the same fold, and the carbohydrate recognition domains are very similar with structural differences located in specific loops. These differences are reflected in the dynamics characteristics, where mobility differences translate into entropy values which significantly influence their ligand affinity. Thus, ligand selectivity appears to be modulated by subtle differences in the monosaccharide binding sites. Taken together, our results may contribute to the understanding, at a molecular level, of the structural and dynamical determinants that distinguish individual human galectins.
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Affiliation(s)
- Carlos M A Guardia
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Ciudad de Buenos Aires, Argentina
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Mañez PA, Lu C, Boechi L, Martí MA, Shepherd M, Wilson JL, Poole RK, Luque FJ, Yeh SR, Estrin DA. Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni. Biochemistry 2011; 50:3946-56. [PMID: 21476539 PMCID: PMC4535342 DOI: 10.1021/bi101137n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxygen affinity in heme-containing proteins is determined by a number of factors, such as the nature and conformation of the distal residues that stabilize the heme bound-oxygen via hydrogen-bonding interactions. The truncated hemoglobin III from Campylobacter jejuni (Ctb) contains three potential hydrogen-bond donors in the distal site: TyrB10, TrpG8, and HisE7. Previous studies suggested that Ctb exhibits an extremely slow oxygen dissociation rate due to an interlaced hydrogen-bonding network involving the three distal residues. Here we have studied the structural and kinetic properties of the G8(WF) mutant of Ctb and employed state-of-the-art computer simulation methods to investigate the properties of the O(2) adduct of the G8(WF) mutant, with respect to those of the wild-type protein and the previously studied E7(HL) and/or B10(YF) mutants. Our data indicate that the unique oxygen binding properties of Ctb are determined by the interplay of hydrogen-bonding interactions between the heme-bound ligand and the surrounding TyrB10, TrpG8, and HisE7 residues.
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Affiliation(s)
- Pau Arroyo Mañez
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Changyuan Lu
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Leonardo Boechi
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Mark Shepherd
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Jayne Louise Wilson
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Robert K. Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - F. Javier Luque
- Department de Fisicoquimica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica, y Química Fisica, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
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44
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Alvarez LD, Dansey MV, Martí MA, Bertucci PY, Di Chenna PH, Pecci A, Burton G. Biological activity and ligand binding mode to the progesterone receptor of A-homo analogues of progesterone. Bioorg Med Chem 2011; 19:1683-91. [DOI: 10.1016/j.bmc.2011.01.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/11/2011] [Accepted: 01/16/2011] [Indexed: 11/27/2022]
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45
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Gauto DF, Di Lella S, Estrin DA, Monaco HL, Martí MA. Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor. Carbohydr Res 2011; 346:939-48. [PMID: 21453906 DOI: 10.1016/j.carres.2011.02.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 02/07/2011] [Accepted: 02/16/2011] [Indexed: 11/29/2022]
Abstract
Lectins are able to recognize specific carbohydrate structures through their carbohydrate recognition domain (CRD). The lectin from the mushroom Agaricus bisporus (ABL) has the remarkable ability of selectively recognizing the TF-antigen, composed of Galβ1-3GalNAc, Ser/Thr linked to proteins, specifically exposed in neoplastic tissues. Strikingly, the recently solved crystal structure of tetrameric ABL in the presence of TF-antigen and other carbohydrates showed that each monomer has two CRDs, each being able to bind specifically to different monosaccharides that differ only in the configuration of a single hydroxyl, like N-acetyl-d-galactosamine (GalNAc) and N-acetyl-d-glucosamine (GlcNAc). Understanding how lectin CRDs bind and discriminate mono and/or (poly)-saccharides is an important issue in glycobiology, with potential impact in the design of better and selective lectin inhibitors with potential therapeutic properties. In this work, and based on the unusual monosaccharide epimeric specificity of the ABL CRDs, we have performed molecular dynamics simulations of the natural (crystallographic) and inverted (changing GalNAc for GlcNAc and vice-versa) ABL-monosaccharide complexes in order to understand the selective ligand recognition properties of each CRD. We also performed a detailed analysis of the CRD local solvent structure, using previously developed methodology, and related it with the recognition mechanism. Our results provide a detailed picture of each ABL CRD specificity, allowing a better understanding of the carbohydrate selective recognition process in this particular lectin.
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Affiliation(s)
- Diego F Gauto
- Departamento de Química Inorgánica, Analítica, y Química Física, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Ciudad de Buenos Aires, Argentina, Argentina
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46
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Di Lella S, Caramelo JJ, Guardia CM, Martí MA, Rabinovich GA, Estrin DA. Unraveling Key Features of the Beta-Galactoside Binding Protein Galectin-1 in Interplay with Ligand Binding and Dimerization Equilibria. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.3207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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47
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Pesce A, Nardini M, Dewilde S, Capece L, Martí MA, Congia S, Salter MD, Blouin GC, Estrin DA, Ascenzi P, Moens L, Bolognesi M, Olson JS. Ligand migration in the apolar tunnel of Cerebratulus lacteus mini-hemoglobin. J Biol Chem 2010; 286:5347-58. [PMID: 21147768 DOI: 10.1074/jbc.m110.169045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The large apolar tunnel traversing the mini-hemoglobin from Cerebratulus lacteus (CerHb) has been examined by x-ray crystallography, ligand binding kinetics, and molecular dynamic simulations. The addition of 10 atm of xenon causes loss of diffraction in wild-type (wt) CerHbO(2) crystals, but Leu-86(G12)Ala CerHbO(2), which has an increased tunnel volume, stably accommodates two discrete xenon atoms: one adjacent to Leu-86(G12) and another near Ala-55(E18). Molecular dynamics simulations of ligand migration in wt CerHb show a low energy pathway through the apolar tunnel when Leu or Ala, but not Phe or Trp, is present at the 86(G12) position. The addition of 10-15 atm of xenon to solutions of wt CerHbCO and L86A CerHbCO causes 2-3-fold increases in the fraction of geminate ligand recombination, indicating that the bound xenon blocks CO escape. This idea was confirmed by L86F and L86W mutations, which cause even larger increases in the fraction of geminate CO rebinding, 2-5-fold decreases in the bimolecular rate constants for ligand entry, and large increases in the computed energy barriers for ligand movement through the apolar tunnel. Both the addition of xenon to the L86A mutant and oxidation of wt CerHb heme iron cause the appearance of an out Gln-44(E7) conformer, in which the amide side chain points out toward the solvent and appears to lower the barrier for ligand escape through the E7 gate. However, the observed kinetics suggest little entry and escape (≤ 25%) through the E7 pathway, presumably because the in Gln-44(E7) conformer is thermodynamically favored.
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Affiliation(s)
- Alessandra Pesce
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy
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48
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Howes BD, Giordano D, Boechi L, Russo R, Mucciacciaro S, Ciaccio C, Sinibaldi F, Fittipaldi M, Martí MA, Estrin DA, di Prisco G, Coletta M, Verde C, Smulevich G. The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125. J Biol Inorg Chem 2010; 16:299-311. [PMID: 21076847 DOI: 10.1007/s00775-010-0726-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [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: 09/07/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022]
Abstract
The genome of the cold-adapted bacterium Pseudoalteromonas haloplanktis TAC125 contains multiple genes encoding three distinct monomeric hemoglobins exhibiting a 2/2 α-helical fold. In the present work, one of these hemoglobins is studied by resonance Raman, electronic absorption and electronic paramagnetic resonance spectroscopies, kinetic measurements, and different bioinformatic approaches. It is the first cold-adapted bacterial hemoglobin to be characterized. The results indicate that this protein belongs to the 2/2 hemoglobin family, Group II, characterized by the presence of a tryptophanyl residue on the bottom of the heme distal pocket in position G8 and two tyrosyl residues (TyrCD1 and TyrB10). However, unlike other bacterial hemoglobins, the ferric state, in addition to the aquo hexacoordinated high-spin form, shows multiple hexacoordinated low-spin forms, where either TyrCD1 or TyrB10 can likely coordinate the iron. This is the first example in which both TyrCD1 and TyrB10 are proposed to be the residues that are alternatively involved in heme hexacoordination by endogenous ligands.
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Affiliation(s)
- Barry D Howes
- Dipartimento di Chimica, Università di Firenze, 50019, Sesto Fiorentino (FI), Italy
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49
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Presman DM, Alvarez LD, Levi V, Eduardo S, Digman MA, Martí MA, Veleiro AS, Burton G, Pecci A. Insights on glucocorticoid receptor activity modulation through the binding of rigid steroids. PLoS One 2010; 5:e13279. [PMID: 20949009 PMCID: PMC2952596 DOI: 10.1371/journal.pone.0013279] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 09/16/2010] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The glucocorticoid receptor (GR) is a transcription factor that regulates gene expression in a ligand-dependent fashion. This modular protein is one of the major pharmacological targets due to its involvement in both cause and treatment of many human diseases. Intense efforts have been made to get information about the molecular basis of GR activity. METHODOLOGY/PRINCIPAL FINDINGS Here, the behavior of four GR-ligand complexes with different glucocorticoid and antiglucocorticoid properties were evaluated. The ability of GR-ligand complexes to oligomerize in vivo was analyzed by performing the novel Number and Brightness assay. Results showed that most of GR molecules form homodimers inside the nucleus upon ligand binding. Additionally, in vitro GR-DNA binding analyses suggest that ligand structure modulates GR-DNA interaction dynamics rather than the receptor's ability to bind DNA. On the other hand, by coimmunoprecipitation studies we evaluated the in vivo interaction between the transcriptional intermediary factor 2 (TIF2) coactivator and different GR-ligand complexes. No correlation was found between GR intranuclear distribution, cofactor recruitment and the homodimerization process. Finally, Molecular determinants that support the observed experimental GR LBD-ligand/TIF2 interaction were found by Molecular Dynamics simulation. CONCLUSIONS/SIGNIFICANCE The data presented here sustain the idea that in vivo GR homodimerization inside the nucleus can be achieved in a DNA-independent fashion, without ruling out a dependent pathway as well. Moreover, since at least one GR-ligand complex is able to induce homodimer formation while preventing TIF2 coactivator interaction, results suggest that these two events might be independent from each other. Finally, 21-hydroxy-6,19-epoxyprogesterone arises as a selective glucocorticoid with potential pharmacological interest. Taking into account that GR homodimerization and cofactor recruitment are considered essential steps in the receptor activation pathway, results presented here contribute to understand how specific ligands influence GR behavior.
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Affiliation(s)
- Diego M. Presman
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lautaro D. Alvarez
- Departamento de Química Orgánica/UMYMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Valeria Levi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvina Eduardo
- Departamento de Química Orgánica/UMYMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Michelle A. Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering and Developmental Biology Center Optical Biology Core Facility, University of California Irvine, Irvine, California, United States of America
| | - Marcelo A. Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adriana S. Veleiro
- Departamento de Química Orgánica/UMYMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gerardo Burton
- Departamento de Química Orgánica/UMYMFOR-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adali Pecci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- IFIBYNE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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50
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Di Lella S, Martí MA, Croci DO, Guardia CMA, Díaz-Ricci JC, Rabinovich GA, Caramelo JJ, Estrin DA. Linking the structure and thermal stability of beta-galactoside-binding protein galectin-1 to ligand binding and dimerization equilibria. Biochemistry 2010; 49:7652-8. [PMID: 20666428 DOI: 10.1021/bi100356g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The stability of proteins involves a critical balance of interactions of different orders of magnitude. In this work, we present experimental evidence of an increased thermal stability of galectin-1, a multifunctional beta-galactoside-binding protein, upon binding to the disaccharide lactose. Analysis of structural changes occurring upon binding of lectin to its specific glycans and thermal denaturation of the protein and the complex were analyzed by circular dichroism. On the other hand, we studied dimerization as another factor that may induce structural and thermal stability changes. The results were then complemented with molecular dynamics simulations followed by a detailed computation of thermodynamic properties, including the internal energy, solvation free energy, and conformational entropy. In addition, an energetic profile of the binding and dimerization processes is also presented. Whereas binding and cross-linking of lactose do not alter galectin-1 structure, this interaction leads to substantial changes in the flexibility and internal energy of the protein which confers increased thermal stability to this endogenous lectin. Given that an improved understanding of the physicochemical properties of galectin-glycan lattices may contribute to the dissection of their biological functions and prediction of their therapeutic applications, our study suggests that galectin binding to specific disaccharide ligands may increase the thermal stability of this glycan-binding protein, an effect that could influence its critical biological functions.
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Affiliation(s)
- Santiago Di Lella
- Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
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