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Cruz FT, Rosa DP, Vasconcelos AVB, de Oliveira JS, Bleicher L, Santos AMC. Purification and partial physical-chemical characterization of a new bovine trypsin proteoform (zeta-trypsin). Int J Biol Macromol 2024; 268:131860. [PMID: 38670206 DOI: 10.1016/j.ijbiomac.2024.131860] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/01/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Recent advancements in enzyme research have unveiled a new proteoform of bovine trypsin, expanding our understanding of this well-characterized enzyme. While generally similar to other trypsins, this novel proteoform comprises three polypeptide chains, marking a significant difference in activity, kinetic properties, and conformational stability. Compared with the already known bovine trypsin proteoforms, the results showed a lower: activity, kcat and kcat.KM-1 and protein 'foldedness' ratio for the new proteoform. Molecular autolysis, a common feature in trypsin and chymotrypsin, has been explored through comparative physical chemistry properties with other proteoforms. This new proteoform of trypsin not only enriches the existing enzyme repertoire but also promises to shed light on the intricate physiological pathway for enzyme inactivation. Our results suggest that the new trypsin proteoform is one of the likely final pathways for enzyme inactivation in a physiological environment. This discovery opens up new avenues for further research into the functional implications of this new trypsin proteoform.
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Affiliation(s)
- Fabiano Torres Cruz
- Pos-Graduate Program of Biotechnology - Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Dayanne Pinho Rosa
- Pos-Graduate Program of Biochemistry - Federal University of Espírito Santo, Vitória, ES, Brazil
| | | | - Jamil Silvano de Oliveira
- Department of Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Pos-Graduate at Biochemistry and Immunology - Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Martins Costa Santos
- Pos-Graduate Program of Biotechnology - Federal University of Espírito Santo, Vitória, ES, Brazil; Pos-Graduate Program of Biochemistry - Federal University of Espírito Santo, Vitória, ES, Brazil.
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2
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Marques PH, Rodrigues TCV, Santos EH, Bleicher L, Aburjaile FF, Martins FS, Oliveira CJF, Azevedo V, Tiwari S, Soares S. Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches. J Biomol Struct Dyn 2023:1-16. [PMID: 38112302 DOI: 10.1080/07391102.2023.2293256] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pedro Henrique Marques
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thais Cristina Vilela Rodrigues
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Horta Santos
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo Jose Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Siomar Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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Reis DR, Santos BC, Bleicher L, Zárate LE, Nobre CN. Prediction of enzymatic function with high efficiency and a reduced number of features using genetic algorithm. Comput Biol Med 2023; 158:106799. [PMID: 37028140 DOI: 10.1016/j.compbiomed.2023.106799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 02/04/2023] [Accepted: 03/20/2023] [Indexed: 04/07/2023]
Abstract
The post-genomic era has raised a growing demand for efficient procedures to identify protein functions, which can be accomplished by applying machine learning to the characteristics set extracted from the protein. This approach is feature-based and has been the focus of several works in bioinformatics. In this work, we investigated the characteristics of proteins, representing the primary, secondary, tertiary, and quaternary structures of the protein, that improve the model's quality by applying dimensionality reduction techniques and using the Support Vector Machine classifier for predicting the enzymes' classes. During the investigation, two approaches were evaluated: feature extraction/transformation, which was performed using the statistical technique Factor Analysis, and feature selection methods. For feature selection, we proposed an approach based on a genetic algorithm to face the optimization conflict between the simplicity and reliability of an ideal representation of the characteristics of the enzymes and also compared and employed other methods for this purpose. The best result was accomplished using a feature subset generated by our implementation of a multi-objective genetic algorithm enriched with features that this work identified as relevant to represent the enzymes. This subset representation reduced the dataset by about 87% and reached 85.78% of F-measure performance, improving the overall quality of the model classification. In addition, we verified in this work a subset addressed with only 28 features out of a total of 424 that reached a performance above 80% of F-measure for four of the six evaluated classes, showing that satisfactory classification performance can be achieved with a reduced number of enzymes's characteristics. The datasets and implementations are openly available.
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Santos JC, Handa S, Fernandes LGV, Bleicher L, Gandin CA, de Oliveira-Neto M, Ghosh P, Nascimento ALTO. Structural and biochemical characterization of Leptospira interrogans Lsa45 reveals a penicillin-binding protein with esterase activity. Process Biochem 2023; 125:141-153. [PMID: 36643388 PMCID: PMC9836055 DOI: 10.1016/j.procbio.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Leptospirosis is a bacterial disease that affects humans and animals and is caused by Leptospira. The recommended treatment for leptospirosis is antibiotic therapy, which should be given early in the course of the disease. Despite the use of these antibiotics, their role during the course of the disease is still not completely clear because of the lack of effective clinical trials, particularly for severe cases of the disease. Here, we present the characterization of L. interrogans Lsa45 protein by gel filtration, protein crystallography, SAXS, fluorescence and enzymatic assays. The oligomeric studies revealed that Lsa45 is monomeric in solution. The crystal structure of Lsa45 revealed the presence of two subdomains: a large α/β subdomain and a small α-helical subdomain. The large subdomain contains the amino acids Ser122, Lys125, and Tyr217, which correspond to the catalytic triad that is essential for β-lactamase or serine hydrolase activity in similar enzymes. Additionally, we also confirmed the bifunctional promiscuity of Lsa45, in hydrolyzing both the 4-nitrophenyl acetate (p-NPA) and nitrocefin β-lactam antibiotic. Therefore, this study provides novel insights into the structure and function of enzymes from L. interrogans, which furthers our understanding of this bacterium and the development of new therapies for the prevention and treatment of leptospirosis.
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Affiliation(s)
- Jademilson C. Santos
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
- Instituto Federal da Bahia – IFBA - Rodovia BR-367, R. José Fontana, 1, 45810-000, Porto Seguro - BA, Brazil
| | - Sumit Handa
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Luis G. V. Fernandes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - César A. Gandin
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Dep. de Física e Biofísica, Botucatu, SP, Brazil
| | - Mario de Oliveira-Neto
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Dep. de Física e Biofísica, Botucatu, SP, Brazil
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Ana Lucia T. O. Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
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Mendoza Rengifo E, Stelmastchuk Benassi Fontolan L, Ribamar Ferreira-Junior J, Bleicher L, Penner-Hahn J, Charles Garratt R. UNEXPECTED PLASTICITY OF THE QUATERNARY STRUCTURE OF IRON-MANGANESE SUPEROXIDE DISMUTASES. J Struct Biol 2022; 214:107855. [PMID: 35390463 DOI: 10.1016/j.jsb.2022.107855] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Protein 3D structure can be remarkably robust to the accumulation of mutations during evolution. On the other hand, sometimes a single amino acid substitution can be sufficient to generate dramatic and completely unpredictable structural consequences. In an attempt to rationally alter the preferences for the metal ion at the active site of a member of the Iron/Manganese superoxide dismutase family, two examples of the latter phenomenon were identified. Site directed mutants of SOD from Trichoderma reesei were generated and studied crystallographically together with the wild type enzyme. Despite being chosen for their potential impact on the redox potential of the metal, two of the mutations (D150G and G73A) in fact resulted in significant alterations to the protein quaternary structure. The D150G mutant presented alternative inter-subunit contacts leading to a loss of symmetry of the wild type tetramer, whereas the G73A mutation transformed the tetramer into an octamer despite not participating directly in any of the inter-subunit interfaces. We conclude that there is considerable intrinsic plasticity in the Fe/MnSOD fold that can be unpredictably affected by single amino acid substitutions. In much the same way as phenotypic defects at the organism level can reveal much about normal function, so too can such mutations teach us much about the subtleties of protein structure.
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Affiliation(s)
- Emerita Mendoza Rengifo
- Laboratory of Structural Biology, Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Sao Paulo, Brazil
| | | | - Jose Ribamar Ferreira-Junior
- Laboratory of Biotechnology, School of Arts, Sciences and Humanities, University of Sao Paulo, Sao Paulo, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - James Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States
| | - Richard Charles Garratt
- Laboratory of Structural Biology, Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Sao Paulo, Brazil.
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Afonso MQL, da Fonseca Júnior NJ, Miranda TG, Bleicher L. Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams. Front Bioinform 2022; 2:774417. [PMID: 36304314 PMCID: PMC9580940 DOI: 10.3389/fbinf.2022.774417] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons and other excitable cells. For a given organism there are often multiple, specialized sodium channels found in different tissues, whose mutations can cause deleterious effects observed in numerous diseases. Consequently, there is high medical and pharmacological interest in these proteins. Scientific literature often uses membrane diagrams to depict important patterns in these channels including the six transmembrane segments (S1–S6) present in four different homologous domains (D1–D4), the S4 voltage sensors, the pore-lining residue segments and the ion selectivity filter residues, glycosylation and phosphorylation residues, toxin binding sites and the inactivation loop, among others. Most of these diagrams are illustrated either digitally or by hand and programs specifically dedicated to the interactive and data-friendly generation of such visualizations are scarce or non-existing. This paper describes Naview, an open-source javascript visualization compatible with modern web browsers for the dynamic drawing and annotation of voltage-gated sodium channels membrane diagrams based on the D3.js library. By using a graphical user interface and combining user-defined annotations with optional UniProt code as inputs, Naview allows the creation and customization of membrane diagrams. In this interface, a user can also map and display important sodium channel properties, residues, regions and their relationships through symbols, colors, and edge connections. Such features can facilitate data exploration and provide fast, high-quality publication-ready graphics for this highly active area of research.
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Affiliation(s)
- Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Néli José da Fonseca Júnior
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thainá Godinho Miranda
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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7
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Santos NP, Santos LH, Torquato Quezado de Magalhães M, Lei J, Hilgenfeld R, Salgado Ferreira R, Bleicher L. Characterization of an Allosteric Pocket in Zika Virus NS2B-NS3 Protease. J Chem Inf Model 2022; 62:945-957. [DOI: 10.1021/acs.jcim.1c01326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Naiá Porã Santos
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Lucianna Helene Santos
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mariana Torquato Quezado de Magalhães
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck 23562, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck 23562, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck 23562, Germany
| | - Rafaela Salgado Ferreira
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Lucas Bleicher
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais (UFMG), Avenida Antônio Carlos 6627, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Paulela JA, Gomes F, Camandona VDL, Alegria TGP, Netto LES, Bleicher L, Barros MH, Ferreira-Junior JR. Coq3p relevant residues for protein activity and stability. FEMS Yeast Res 2021; 21:6424906. [PMID: 34755843 DOI: 10.1093/femsyr/foab055] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/03/2021] [Indexed: 11/14/2022] Open
Abstract
Coenzyme Q (CoQ) is an essential molecule that consists of a highly substituted benzene ring attached to a polyprenyl tail anchored in the inner mitochondrial membrane. CoQ transfers electrons from NADH dehydrogenase and succinate dehydrogenase complexes toward ubiquinol-cytochrome c reductase, and that allows aerobic growth of cells. In Saccharomyces cerevisiae, the synthesis of CoQ depends on fourteen proteins Coq1p-Co11p, Yah1p, Arh1p, and Hfd1p. Some of these proteins are components of CoQ synthome. Using ab initio molecular modeling and site-directed mutagenesis, we identified the functional residues of the O-methyltransferase Coq3p, which depends on S-adenosylmethionine for catalysis and is necessary for two O-methylation steps required for CoQ maturation. Conserved residues as well as those that coevolved in the protein structure were found to have important roles in respiratory growth, CoQ biosynthesis, and also in the stability of CoQ synthome proteins. Finally, a multiple sequence alignment showed that S. cerevisiae Coq3p has a 45 amino acid residues insertion that is poorly conserved or absent in oleaginous yeast, cells that can store up to 20% of their dry weight as lipids. These results point to the Coq3p structural determinants of its biological and catalytic function and could contribute to the development of lipid-producing yeast for biotechnology.
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Affiliation(s)
- Janaina A Paulela
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374 - Butantã - São Paulo-SP - CEP 05508-000, Brazil
| | - Fernando Gomes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, travessa 14, número 321, Cidade Universitária, São Paulo-SP, CEP 05508-090, Brazil
| | - Vittoria de Lima Camandona
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Rua Arlindo Bettio, 1000 - Vila Guaraciaba - São Paulo-SP - CEP 03828-000, Brazil
| | - Thiago G P Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, travessa 14, número 321, Cidade Universitária, São Paulo-SP, CEP 05508-090, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, travessa 14, número 321, Cidade Universitária, São Paulo-SP, CEP 05508-090, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia - Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 - Campus Pampulha - Belo Horizonte-MG CEP 31270-901, Brazil
| | - Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374 - Butantã - São Paulo-SP - CEP 05508-000, Brazil
| | - Jose Ribamar Ferreira-Junior
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, Rua Arlindo Bettio, 1000 - Vila Guaraciaba - São Paulo-SP - CEP 03828-000, Brazil
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Fonseca NJ, Afonso MQL, Carrijo L, Bleicher L. CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis. Bioinformatics 2021; 37:1026-1028. [PMID: 32780795 DOI: 10.1093/bioinformatics/btaa713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY CONAN is a web application developed to detect specificity determinants and function-related sites by amino acids co-variation networks analysis, emphasizing local coevolutionary constraints. The software allows the characterization of structurally and functionally relevant groups of residues and their relationship with subsets of sequences by automatic cross-referencing with GO terms, UniprotKb annotations and INTERPRO. AVAILABILITY AND IMPLEMENTATION CONAN is free and open-source, being distributed in the terms of the GPLV3 license. The software is available as a web application and python script versions and can be accessed at http://bioinfo.icb.ufmg.br/conan. We also provide running instructions, the source code and a user guide.
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Affiliation(s)
- N J Fonseca
- Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - M Q L Afonso
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - L Carrijo
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - L Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
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Carrijo de Oliveira L, Figueiredo Costa MA, Gonçalves Pedersolli N, Heleno Batista FA, Migliorini Figueira AC, Salgado Ferreira R, Alves Pinto Nagem R, Alves Nahum L, Bleicher L. Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies. J Mol Evol 2021; 89:370-383. [PMID: 33956179 DOI: 10.1007/s00239-021-10010-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Transthyretin was discovered in the 1940s, named after its ability to bind thyroid hormones and retinol. In the genomic era, transthyretins were found to be part of a larger family with homologs of no obvious function, then called transthyretin-related proteins. Thus, it was proposed that the transthyretin gene could be the result of gene duplication of an ancestral of this newly identified homolog, later found out to be an enzyme involved in uric acid degradation, then named HIUase (5-hydroxy-isourate hydrolase). Here, we sought to re-enact the evolutionary history of this protein family by reconstructing, from a phylogeny inferred from 123 vertebrate sequences, three ancestors corresponding to key moments in their evolution-before duplication; the common transthyretin ancestor after gene duplication and the common ancestor of Eutheria transthyretins. Experimental and computational characterization showed the reconstructed ancestor before duplication was unable to bind thyroxine and likely presented the modern HIUase reaction mechanism, while the substitutions after duplication prevented that activity and were enough to provide stable thyroxine binding, as confirmed by calorimetry and x-ray diffraction. The Eutheria transthyretin ancestor was less prone to characterization, but limited data suggested thyroxine binding as expected. Sequence/structure analysis suggests an early ability to bind the Retinol Binding Protein. We solved the X-ray structures from the two first ancestors, the first at 1.46 resolution, the second at 1.55 resolution with well-defined electron density for thyroxine, providing a useful tool for the understanding of structural adaptation from enzyme to hormone distributor.
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Affiliation(s)
| | | | | | | | | | | | | | - Laila Alves Nahum
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Lucas Bleicher
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Mariano D, Pantuza N, Santos LH, Rocha REO, de Lima LHF, Bleicher L, de Melo-Minardi RC. Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases. BMC Mol Cell Biol 2020; 21:50. [PMID: 32611314 PMCID: PMC7329481 DOI: 10.1186/s12860-020-00293-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 11/22/2022] Open
Abstract
Β-glucosidases are key enzymes used in second-generation biofuel production. They act in the last step of the lignocellulose saccharification, converting cellobiose in glucose. However, most of the β-glucosidases are inhibited by high glucose concentrations, which turns it a limiting step for industrial production. Thus, β-glucosidases have been targeted by several studies aiming to understand the mechanism of glucose tolerance, pH and thermal resistance for constructing more efficient enzymes. In this paper, we present a database of β-glucosidase structures, called Glutantβase. Our database includes 3842 GH1 β-glucosidase sequences collected from UniProt. We modeled the sequences by comparison and predicted important features in the 3D-structure of each enzyme. Glutantβase provides information about catalytic and conserved amino acids, residues of the coevolution network, protein secondary structure, and residues located in the channel that guides to the active site. We also analyzed the impact of beneficial mutations reported in the literature, predicted in analogous positions, for similar enzymes. We suggested these mutations based on six previously described mutants that showed high catalytic activity, glucose tolerance, or thermostability (A404V, E96K, H184F, H228T, L441F, and V174C). Then, we used molecular docking to verify the impact of the suggested mutations in the affinity of protein and ligands (substrate and product). Our results suggest that only mutations based on the H228T mutant can reduce the affinity for glucose (product) and increase affinity for cellobiose (substrate), which indicates an increment in the resistance to product inhibition and agrees with computational and experimental results previously reported in the literature. More resistant β-glucosidases are essential to saccharification in industrial applications. However, thermostable and glucose-tolerant β-glucosidases are rare, and their glucose tolerance mechanisms appear to be related to multiple and complex factors. We gather here, a set of information, and made predictions aiming to provide a tool for supporting the rational design of more efficient β-glucosidases. We hope that Glutantβase can help improve second-generation biofuel production. Glutantβase is available at http://bioinfo.dcc.ufmg.br/glutantbase .
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Affiliation(s)
- Diego Mariano
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Naiara Pantuza
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Lucianna H Santos
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rafael E O Rocha
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Leonardo H F de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Universidade Federal de São João Del-Rei, Campus Sete Lagoas, Sete Lagoas, 35701-970, Brazil
| | - Lucas Bleicher
- Protein Computational Biology Laboratory, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems. Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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Querino Lima Afonso M, da Fonseca NJ, de Oliveira LC, Lobo FP, Bleicher L. Coevolved Positions Represent Key Functional Properties in the Trypsin-Like Serine Proteases Protein Family. J Chem Inf Model 2020; 60:1060-1068. [DOI: 10.1021/acs.jcim.9b00903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Neli J. da Fonseca
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Lucas Carrijo de Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Francisco Pereira Lobo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627 - Pampulha, Belo Horizonte, Minas Gerais, Brazil 31270-901
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Coitinho JB, Costa MAF, Melo EM, Morais EA, de Andrade LGA, da Rocha AM, de Magalhães MTQ, Favaro DC, Bleicher L, Pedroso ERP, Goes AM, Nagem RAP. Structural and immunological characterization of a new nucleotidyltransferase-like antigen from Paracoccidioides brasiliensis. Mol Immunol 2019; 112:151-162. [PMID: 31108423 DOI: 10.1016/j.molimm.2019.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Pb27 antigen is an interesting alternative to immunological diagnosis of Paracoccidioidomycosis (PCM) and has demonstrated to be protective in experimental PCM. Its tertiary structure and possible function remained unknown till now. To study Pb27 at the atomic level, the recombinant protein was expressed in Escherichia coli BL21(DE3), purified, and its three-dimensional structure was solved by X-ray crystallography. Based on this structure, we performed a residue correlation analysis and in silico ligand search assays to address a possible biological function to Pb27. We identified Pb27 as a member of the extensive nucleotidyltransferase superfamily. The protein has an αβαβαβ topology with two domains (N- and C-terminal domains) and adopts a monomeric form as its biological unit in solution. Structural comparisons with similar members of the superfamily clearly indicate Pb27 C-terminal domain is singular and may play an important role in its biological function. Bioinformatics analysis suggested that Pb27 might bind to ATP and CTP. This suggestion is corroborated by the fact that a magnesium cation is coordinated by two aspartic acid residues present at the active site (between N- and C-terminal domains), as evidenced by X-ray diffraction data. Besides, NMR assays (1H-15N HSQC spectra) confirmed the binding of CTP to Pb27, demonstrating for the first time an interaction between a nucleotide and this protein. Moreover, we evaluated the reactivity of sera from patients with Paracoccidioides brasiliensis infection against the recombinant form of Pb27 and showed that it was recognized by sera from infected and treated patients. Predicted B and T cell epitopes were synthesized and further evaluated against sera of PCM patients, providing information of the most reactive peptides in Pb27 primary structure which interact with specific Pb27 antibodies.
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Affiliation(s)
- Juliana B Coitinho
- Departamento de Ciências Fisiológicas, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitória, ES 29043-900, Brazil
| | - Mariana A F Costa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Eliza M Melo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Elis A Morais
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Lorena G A de Andrade
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Aline M da Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana T Q de Magalhães
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Denize C Favaro
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Enio R P Pedroso
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Alfredo M Goes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil; Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ronaldo A P Nagem
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
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Fernandes JRC, Bleicher L, Beirão PSL. Closed- and open-state models of human skeletal muscle sodium channel. Biochem Biophys Res Commun 2018; 506:826-832. [PMID: 30389137 DOI: 10.1016/j.bbrc.2018.10.110] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
Abstract
Voltage-gated sodium channels play important roles in human physiology. However, their complexity hinders the understanding of their physiology and pathology at atomic level. We took advantage of the structural reports of similar channels obtained by cryo-EM (EeNav1.4, and NavPaS), and constructed models of human Nav1.4 channels at closed and open states. The open-state model is very similar to the recently published cryo-EM structure of hNav1.4. The comparison of both models shows shifts of the voltage sensors (VS) of DIII and DIV. The activated position of VS-DII in the closed model was demonstrated by Ts1 docking, thereby confirming the requirement that VS-DI, VS-DII and VS-DIII must be activated for the channel to open. The interactions observed with VS-DIII suggest a stepwise, yet fast, transition from resting to activated state. These models provide structural insights on the closed-open transition of the channel.
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Affiliation(s)
- João R C Fernandes
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil
| | - Paulo S L Beirão
- Department of Biochemistry and Immunology - ICB, Universidade Federal de Minas Gerais - UFMG, Av. Antonio Carlos, 6627, 31270-901, Belo Horizonte, MG, Brazil.
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da Fonseca NJ, Afonso MQL, de Oliveira LC, Bleicher L. A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection. Bioinformatics 2018; 35:1478-1485. [DOI: 10.1093/bioinformatics/bty846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/11/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Néli José da Fonseca
- Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil
| | - Marcelo Querino Lima Afonso
- Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil
| | - Lucas Carrijo de Oliveira
- Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil
| | - Lucas Bleicher
- Departmento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte – MG, Brazil
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16
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Gomes-Lima CJ, Maciel AAFL, Andrade MDO, Cunha VSD, Mazzeu JF, Bleicher L, Neves FDAR, Lofrano-Porto A. Thyroxine-binding globulin deficiency due to a novel SERPINA7 mutation: Clinical characterization, analysis of X-chromosome inactivation pattern and protein structural modeling. Gene 2018; 666:58-63. [PMID: 29733970 DOI: 10.1016/j.gene.2018.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/18/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Thyroxine-binding globulin (TBG) is the major human thyroid hormone transport protein, encoded by the SERPINA7 gene (Xq22.2). We aim to investigate the molecular basis of partial TBG deficiency (TBG-PD) in a female, by evaluating the X-chromosome inactivation pattern as well as the mutant protein structural modeling. DESIGN AND METHODS Sequencing of the coding region of the SERPINA7 gene was performed in a female with a TBG-PD phenotype and her first-degree relatives. The proband presented with low serum levels of total T3 (TT3) and total T4 (TT4), serum TSH level of 5.4 μUI/mL (normal range, 0.35-5.5), and serum TBG level of 5.5 mg/L (normal range, 13.6-27.2). X-chromosome inactivation pattern was evaluated by methylation analysis of the androgen receptor gene (Xq11.2). Structural analysis of the SERPIN family was performed using Pymol and Areaimol, and PFSTATS for conservation analysis and family-wide investigation of equivalent positions in human homologs. Modeller was used for point mutation structural modeling. RESULTS A novel missense SERPINA7 mutation (p.R35W; c.163C > T) was found in heterozygosity in the proband, and in hemizygosity in her affected siblings. The proband X-chromosome inactivation ratio was 20:80. The substitution of an arginine by a tryptophan is predicted to disrupt the protein surface and main electrostatic interactions. Tryptophans are extremely rare (0.1%) in this position. CONCLUSIONS We report a new SERPINA7 variant associated with TBG-PD in three siblings. We named this variant TBG-Brasilia. The X-chromosome inactivation pattern may have accounted for the rare phenotypic expression in a female. The hydrophobic nature of the mutant is predicted to create an apolar patch at the surface, which results in protein aggregation and/or misfolding, potentially responsible for thyroid hormone transport defect.
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Affiliation(s)
- Cristiane Jeyce Gomes-Lima
- Molecular Pharmacology Laboratory, Faculty of Health Sciences, University of Brasília, Brasília, DF, Brazil; Endocrinology Unit, Hospital de Base do Distrito Federal, Brasília, DF, Brazil
| | | | | | - Vinicius Santos da Cunha
- Molecular Pharmacology Laboratory, Faculty of Health Sciences, University of Brasília, Brasília, DF, Brazil
| | - Juliana Forte Mazzeu
- Medical Genetics Laboratory, Faculty of Medicine, University of Brasília, Brasília, DF, Brazil
| | - Lucas Bleicher
- Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Adriana Lofrano-Porto
- Molecular Pharmacology Laboratory, Faculty of Health Sciences, University of Brasília, Brasília, DF, Brazil; Endocrinology Unit, University Hospital of Brasília, University of Brasília, Brasília, DF, Brazil.
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Affiliation(s)
- Néli J. Fonseca-Júnior
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Marcelo Q.L. Afonso
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Lucas C. Oliveira
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Lucas Bleicher
- Departamento de Bioquimica e Imunologia, Instituto de Ciências Biologicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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18
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Oliveira A, Bleicher L, Schrago CG, Silva Junior FP. Conservation analysis and decomposition of residue correlation networks in the phospholipase A2 superfamily (PLA2s): Insights into the structure-function relationships of snake venom toxins. Toxicon 2018; 146:50-60. [DOI: 10.1016/j.toxicon.2018.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/02/2018] [Accepted: 03/28/2018] [Indexed: 01/27/2023]
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Guedes-Monteiro RF, Ferreira-Junior JR, Bleicher L, Nóbrega FG, Barrientos A, Barros MH. Mitochondrial ribosome bL34 mutants present diminished translation of cytochrome c oxidase subunits. Cell Biol Int 2017; 42:630-642. [PMID: 29160602 DOI: 10.1002/cbin.10913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/01/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022]
Abstract
Saccharomyces cerevisiae mitoribosomes are specialized in the translation of a few number of highly hydrophobic membrane proteins, components of the oxidative phosphorylation system. Mitochondrial characteristics, such as the membrane system and its redox state driven mitoribosomes evolution through great diversion from their bacterial and cytosolic counterparts. Therefore, mitoribosome presents a considerable number of mitochondrial-specific proteins, as well as new protein extensions. In this work we characterize temperature sensitive mutants of the subunit bL34 present in the 54S large subunit. Although bL34 has bacterial homologs, in yeast it has a long 65 aminoacids mitochondrial N-terminal addressing sequence, here we demonstrate that it can be replaced by the mitochondrial addressing sequence of Neurospora crassa ATP9 gene. The bL34 temperature sensitive mutants present lowered translation of mitochondrial COX1 and COX3, which resulted in reduced cytochrome c oxidase activity and respiratory growth deficiency. The sedimentation properties of bL34 in sucrose gradients suggest that similarly to its bacterial homolog, bL34 is also a later participant in the process of mitoribosome biogenesis.
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Affiliation(s)
| | | | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia - Instituto de Ciências Biológicas - Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mario H Barros
- Departamento de Microbiologia, Universidade de São Paulo, São Paulo, Brazil
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Suhadolnik MLS, Salgado APC, Scholte LLS, Bleicher L, Costa PS, Reis MP, Dias MF, Ávila MP, Barbosa FAR, Chartone-Souza E, Nascimento AMA. Novel arsenic-transforming bacteria and the diversity of their arsenic-related genes and enzymes arising from arsenic-polluted freshwater sediment. Sci Rep 2017; 7:11231. [PMID: 28894204 PMCID: PMC5593903 DOI: 10.1038/s41598-017-11548-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 04/06/2017] [Accepted: 08/25/2017] [Indexed: 02/01/2023] Open
Abstract
Bacteria are essential in arsenic cycling. However, few studies have addressed 16S rRNA and arsenic-related functional gene diversity in long-term arsenic-contaminated tropical sediment. Here, using culture-based, metagenomic and computational approaches, we describe the diversity of bacteria, genes and enzymes involved in AsIII and AsV transformation in freshwater sediment and in anaerobic AsIII- and AsV-enrichment cultures (ECs). The taxonomic profile reveals significant differences among the communities. Arcobacter, Dechloromonas, Sedimentibacter and Clostridium thermopalmarium were exclusively found in ECs, whereas Anaerobacillus was restricted to AsV-EC. Novel taxa that are both AsV-reducers and AsIII-oxidizers were identified: Dechloromonas, Acidovorax facilis, A. delafieldii, Aquabacterium, Shewanella, C. thermopalmarium and Macellibacteroides fermentans. Phylogenic discrepancies were revealed among the aioA, arsC and arrA genes and those of other species, indicating horizontal gene transfer. ArsC and AioA have sets of amino acids that can be used to assess their functional and structural integrity and familial subgroups. The positions required for AsV reduction are conserved, suggesting strong selective pressure for maintaining the functionality of ArsC. Altogether, these findings highlight the role of freshwater sediment bacteria in arsenic mobility, and the untapped diversity of dissimilatory arsenate-reducing and arsenate-resistant bacteria, which might contribute to arsenic toxicity in aquatic environments.
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Affiliation(s)
- Maria L S Suhadolnik
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana P C Salgado
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa L S Scholte
- Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcela F Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edmar Chartone-Souza
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Rios-Anjos RM, Camandona VDL, Bleicher L, Ferreira-Junior JR. Structural and functional mapping of Rtg2p determinants involved in retrograde signaling and aging of Saccharomyces cerevisiae. PLoS One 2017; 12:e0177090. [PMID: 28472157 PMCID: PMC5417653 DOI: 10.1371/journal.pone.0177090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 04/21/2017] [Indexed: 01/27/2023] Open
Abstract
In Saccharomyces cerevisiae mitochondrial dysfunction induces retrograde signaling, a pathway of communication from mitochondria to the nucleus that promotes a metabolic remodeling to ensure sufficient biosynthetic precursors for replication. Rtg2p is a positive modulator of this pathway that is also required for cellular longevity. This protein belongs to the ASKHA superfamily, and contains a putative N-terminal ATP-binding domain, but there is no detailed structural and functional map of the residues in this domain that accounts for their contribution to retrograde signaling and aging. Here we use Decomposition of Residue Correlation Networks and site-directed mutagenesis to identify Rtg2p structural determinants of retrograde signaling and longevity. We found that most of the residues involved in retrograde signaling surround the ATP-binding loops, and that Rtg2p N-terminus is divided in three regions whose mutants have different aging phenotypes. We also identified E137, D158 and S163 as possible residues involved in stabilization of ATP at the active site. The mutants shown here may be used to map other Rtg2p activities that crosstalk to other pathways of the cell related to genomic stability and aging.
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Affiliation(s)
| | | | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Paiva MC, Reis MP, Costa PS, Dias MF, Bleicher L, Scholte LLS, Nardi RMD, Nascimento AMA. Identification of new bacteria harboring qnrS and aac(6')-Ib/cr and mutations possibly involved in fluoroquinolone resistance in raw sewage and activated sludge samples from a full-scale WWTP. Water Res 2017; 110:27-37. [PMID: 27984803 DOI: 10.1016/j.watres.2016.11.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Wastewater treatment plants (WWTPs) harbor bacteria and antimicrobial resistance genes, favoring gene exchange events and resistance dissemination. Here, a culture-based and metagenomic survey of qnrA, qnrB, qnrS, and aac(6')-Ib genes from raw sewage (RS) and activated sludge (AS) of a full-scale municipal WWTP was performed. A total of 96 bacterial isolates were recovered from nalidixic acid-enrichment cultures. Bacteria harboring the aac(6')-Ib gene predominated in RS, whereas qnrS-positive isolates were specific to AS. Novel qnrS- and aac(6')-Ib-cr positive species were identified: Morganella morganii, Providencia rettgeri, and Pseudomonas guangdongensis (qnrS), and Alcaligenes faecalis and P. rettgeri (aac(6')-Ib-cr). Analysis of qnrS and aac(6')-Ib sequences from isolates and clone libraries suggested that the diversity of qnrS is wider than that of aac(6')-Ib. A large number of amino acid mutations were observed in the QnrS and AAC(6')-Ib proteins at previously undetected positions, whose structural implications are not clear. An accumulation of mutations at the C72, Q73, L74, A75 and M76 positions of QnrS, and D181 of AAC(6')-Ib might be important for resistance. These findings add significant information on bacteria harboring qnrS and aac(6')-Ib genes, and the presence of novel mutations that may eventually emerge in clinical isolates.
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Affiliation(s)
- Magna C Paiva
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Campus Dona Lindu, Universidade Federal de São João del Rei, Divinópolis, Minas Gerais, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia S Costa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcela F Dias
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Larissa L S Scholte
- Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | - Regina M D Nardi
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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da Fonseca NJ, Lima Afonso MQ, Pedersolli NG, de Oliveira LC, Andrade DS, Bleicher L. Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains. Biochem Biophys Res Commun 2017; 492:565-571. [PMID: 28087275 DOI: 10.1016/j.bbrc.2017.01.041] [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: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
Abstract
Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed.
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Affiliation(s)
- Néli José da Fonseca
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Marcelo Querino Lima Afonso
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Natan Gonçalves Pedersolli
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Carrijo de Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Dhiego Souto Andrade
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
| | - Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Av. Antônio Carlos, 6627, Belo Horizonte, 31270-901, Brazil.
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Busso C, Ferreira-Júnior JR, Paulela JA, Bleicher L, Demasi M, Barros MH. Coq7p relevant residues for protein activity and stability. Biochimie 2015; 119:92-102. [DOI: 10.1016/j.biochi.2015.10.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 10/19/2015] [Indexed: 11/27/2022]
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Ferreira-Júnior JR, Bleicher L, Barros MH. Her2p molecular modeling, mutant analysis and intramitochondrial localization. Fungal Genet Biol 2013; 60:133-9. [DOI: 10.1016/j.fgb.2013.06.006] [Citation(s) in RCA: 5] [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: 03/04/2013] [Revised: 06/07/2013] [Accepted: 06/22/2013] [Indexed: 02/05/2023]
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Afonso MQL, de Lima LHF, Bleicher L. Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box. BMC Genomics 2013; 14 Suppl 6:S1. [PMID: 24564869 PMCID: PMC3908500 DOI: 10.1186/1471-2164-14-s6-s1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Nuclear receptors (NRs) are transcription factors which bind small hormones, whose evolutionary history and the presence of different functional surfaces makes them an interesting target for a correlation based analysis. Results Correlation analysis of ligand binding domains shows that correlated residue subsets arise from the differences between functional sites in different nuclear receptor subfamilies. For the DNA binding domain, particularly, the analysis shows that the main source of correlation comes from residues that regulate hormone response element specificity, and one of the conserved residue sub-sets arises due to the presence of an unusual sequence for the DNA binding motif known as P-box in nematodes, suggesting the existence of different DBD-DNA specificities in nuclear receptors. Conclusions We conclude that DNA specificity and functional surface specialization has independently driven nuclear receptor evolution, and suggest possible binding modes for the class of divergent nuclear receptors in nematodes.
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Bleicher L, Lemke N, Garratt RC. Using amino acid correlation and community detection algorithms to identify functional determinants in protein families. PLoS One 2011; 6:e27786. [PMID: 22205928 PMCID: PMC3243672 DOI: 10.1371/journal.pone.0027786] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [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: 02/25/2011] [Accepted: 10/25/2011] [Indexed: 11/21/2022] Open
Abstract
Correlated mutation analysis has a long history of interesting applications, mostly in the detection of contact pairs in protein structures. Based on previous observations that, if properly assessed, amino acid correlation data can also provide insights about functional sub-classes in a protein family, we provide a complete framework devoted to this purpose. An amino acid specific correlation measure is proposed, which can be used to build networks summarizing all correlation and anti-correlation patterns in a protein family. These networks can be submitted to community structure detection algorithms, resulting in subsets of correlated amino acids which can be further assessed by specific parameters and procedures that provide insight into the relationship between different communities, the individual importance of community members and the adherence of a given amino acid sequence to a given community. By applying this framework to three protein families with contrasting characteristics (the Fe/Mn-superoxide dismutases, the peroxidase-catalase family and the C-type lysozyme/α-lactalbumin family), we show how our method and the proposed parameters and procedures are related to biological characteristics observed in these protein families, highlighting their potential use in protein characterization and gene annotation.
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Affiliation(s)
- Lucas Bleicher
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Bleicher L, Prates ET, Gomes TCF, Silveira RL, Nascimento AS, Rojas AL, Golubev A, Martínez L, Skaf MS, Polikarpov I. Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations. J Phys Chem B 2011; 115:7940-9. [DOI: 10.1021/jp200330z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [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)
- Lucas Bleicher
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Erica T. Prates
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Thiago C. F. Gomes
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Alessandro S. Nascimento
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Adriana L. Rojas
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
- Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alexander Golubev
- Petersburg Nuclear Physics Institute, Gatchina, St. Petersburg, 188300, Russia
| | - Leandro Martínez
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas − UNICAMP, Cx.P. 6154, Campinas, SP 13084-862, Brazil
| | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, Avenida Trabalhador São-Carlense, 400, CEP 13560-970 São Carlos, SP, Brazil
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29
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Bachega JFR, Bleicher L, Horjales ER, Santiago PS, Garratt RC, Tabak M. Crystallization and preliminary structural analysis of the giant haemoglobin from Glossoscolex paulistus at 3.2 Å. J Synchrotron Radiat 2011; 18:24-8. [PMID: 21169685 PMCID: PMC3004248 DOI: 10.1107/s090904951002772x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/13/2010] [Indexed: 05/30/2023]
Abstract
Glossoscolex paulistus is a free-living earthworm encountered in south-east Brazil. Its oxygen transport requirements are undertaken by a giant extracellular haemoglobin, or erythrocruorin (HbGp), which has an approximate molecular mass of 3.6 MDa and, by analogy with its homologue from Lumbricus terrestris (HbLt), is believed to be composed of a total of 180 polypeptide chains. In the present work the full 3.6 MDa particle in its cyanomet state was purified and crystallized using sodium citrate or PEG8000 as precipitant. The crystals contain one-quarter of the full particle in the asymmetric unit of the I222 cell and have parameters of a = 270.8 Å, b = 320.3 Å and c = 332.4 Å. Diffraction data were collected to 3.15 Å using synchrotron radiation on beamline X29A at the Brookhaven National Laboratory and represent the highest resolution data described to date for similar erythrocruorins. The structure was solved by molecular replacement using a search model corresponding to one-twelfth of its homologue from HbLt. This revealed that HbGp belongs to the type I class of erythrocruorins and provided an interpretable initial electron density map in which many features including the haem groups and disulfide bonds could be identified.
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Affiliation(s)
- J. F. R. Bachega
- Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
| | - L. Bleicher
- Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
| | - E. R. Horjales
- Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
| | - P. S. Santiago
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
| | - R. C. Garratt
- Centro de Biotecnologia Molecular Estrutural, Instituto de Fisica de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
| | - M. Tabak
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos – SP, CEP 13566-590, Brazil
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de C. Palmieri L, Lima LMTR, Freire JBB, Bleicher L, Polikarpov I, Almeida FCL, Foguel D. Novel Zn2+-binding sites in human transthyretin: implications for amyloidogenesis and retinol-binding protein recognition. J Biol Chem 2010; 285:31731-41. [PMID: 20659897 PMCID: PMC2951245 DOI: 10.1074/jbc.m110.157206] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Indexed: 11/06/2022] Open
Abstract
Human transthyretin (TTR) is a homotetrameric protein involved in several amyloidoses. Zn(2+) enhances TTR aggregation in vitro, and is a component of ex vivo TTR amyloid fibrils. We report the first crystal structure of human TTR in complex with Zn(2+) at pH 4.6-7.5. All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. Zn(2+) binding perturbs loop E-α-helix-loop F, the region involved in holo-retinol-binding protein (holo-RBP) recognition, mainly at acidic pH; TTR affinity for holo-RBP decreases ∼5-fold in the presence of Zn(2+). Interestingly, this same region is disrupted in the crystal structure of the amyloidogenic intermediate of TTR formed at acidic pH in the absence of Zn(2+). HNCO and HNCA experiments performed in solution at pH 7.5 revealed that upon Zn(2+) binding, although the α-helix persists, there are perturbations in the resonances of the residues that flank this region, suggesting an increase in structural flexibility. While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). These data highlight structural and functional roles of Zn(2+) in TTR-related amyloidoses, as well as in holo-RBP recognition and vitamin A homeostasis.
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Affiliation(s)
| | | | | | - Lucas Bleicher
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Igor Polikarpov
- the Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo 13560-970, Brazil
| | - Fabio C. L. Almeida
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil and
| | - Debora Foguel
- From the Instituto de Bioquimica Medica, Programa de Biologia Estrutural
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Busso C, Bleicher L, Ferreira-Júnior JR, Barros MH. Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding. FEBS Lett 2010; 584:1609-14. [DOI: 10.1016/j.febslet.2010.03.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/08/2010] [Accepted: 03/15/2010] [Indexed: 11/30/2022]
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Trivella DBB, Bleicher L, Palmieri LDC, Wiggers HJ, Montanari CA, Kelly JW, Lima LMTR, Foguel D, Polikarpov I. Conformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: implications to tetramer stability and ligand-binding. J Struct Biol 2010; 170:522-31. [PMID: 20211733 DOI: 10.1016/j.jsb.2010.03.002] [Citation(s) in RCA: 34] [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] [Received: 11/18/2009] [Revised: 02/27/2010] [Accepted: 03/02/2010] [Indexed: 11/26/2022]
Abstract
Transthyretin (TTR) is a tetrameric beta-sheet-rich transporter protein directly involved in human amyloid diseases. It was recently found that the isoflavone genistein (GEN) potently inhibits TTR amyloid fibril formation (Green et al., 2005) and is therefore a promising candidate for TTR amyloidosis treatment. Here we used structural and biophysical approaches to characterize genistein binding to the wild type (TTRwt) and to its most frequent amyloidogenic variant, the V30M mutant. In a dose-dependent manner, genistein elicited considerable increases in both mutant and TTRwt stability as demonstrated by high hydrostatic pressure (HHP) and acid-mediated dissociation/denaturation assays. TTR:GEN crystal complexes and isothermal titration calorimetry (ITC) experiments showed that the binding mechanisms of genistein to the TTRwt and to V30M are different and are dependent on apoTTR structure conformations. Furthermore, we could also identify potential allosteric movements caused by genistein binding to the wild type TTR that explains, at least in part, the frequently observed negatively cooperative process between the two sites of TTRwt when binding ligands. These findings show that TTR mutants may present different ligand recognition and therefore are of value in ligand design for inhibiting TTR amyloidosis.
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Affiliation(s)
- Daniela B B Trivella
- Instituto de Física de São Carlos, Universidade de São Paulo, P.O. Box 369, 13560-970 São Carlos, SP, Brazil
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Watanabe L, de Moura PR, Bleicher L, Nascimento AS, Zamorano LS, Calvete JJ, Sanz L, Pérez A, Bursakov S, Roig MG, Shnyrov VL, Polikarpov I. Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia). J Struct Biol 2009; 169:226-42. [PMID: 19854274 DOI: 10.1016/j.jsb.2009.10.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [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: 07/18/2009] [Revised: 10/10/2009] [Accepted: 10/16/2009] [Indexed: 11/15/2022]
Abstract
Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85A. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP.
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Affiliation(s)
- Leandra Watanabe
- Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP, Brazil
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Bachega JFR, Navarro MVAS, Bleicher L, Bortoleto-Bugs RK, Dive D, Hoffmann P, Viscogliosi E, Garratt RC. Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity. Proteins 2009; 77:26-37. [DOI: 10.1002/prot.22412] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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de Moura PR, Watanabe L, Bleicher L, Colau D, Dumoutier L, Lemaire MM, Renauld JC, Polikarpov I. Crystal structure of a soluble decoy receptor IL-22BP bound to interleukin-22. FEBS Lett 2009; 583:1072-7. [PMID: 19285080 DOI: 10.1016/j.febslet.2009.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [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: 01/20/2009] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 12/19/2022]
Abstract
Interleukin-22 (IL-22) plays an important role in the regulation of immune and inflammatory responses in mammals. The IL-22 binding protein (IL-22BP), a soluble receptor that specifically binds IL-22, prevents the IL-22/interleukin-22 receptor 1 (IL-22R1)/interleukin-10 receptor 2 (IL-10R2) complex assembly and blocks IL-22 biological activity. Here we present the crystal structure of the IL-22/IL-22BP complex at 2.75 A resolution. The structure reveals IL-22BP residues critical for IL-22 binding, which were confirmed by site-directed mutagenesis and functional studies. Comparison of IL-22/IL-22BP and IL-22/IL-22R1 crystal structures shows that both receptors display an overlapping IL-22 binding surface, which is consistent with the inhibitory role played by IL-22 binding protein.
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36
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Golubev A, Rojas A, Nascimento A, Bleicher L, Kulminskaya A, Eneyskaya E, Polikarpov I. Crystallization and Preliminary Crystallographic Analysis of Laminarinase from Rhodothermus marinus: A Case of Pseudomerohedral Twinning. Protein Pept Lett 2008; 15:1142-4. [DOI: 10.2174/092986608786071139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bleicher L, de Moura PR, Watanabe L, Colau D, Dumoutier L, Renauld JC, Polikarpov I. Crystal structure of the IL-22/IL-22R1 complex and its implications for the IL-22 signaling mechanism. FEBS Lett 2008; 582:2985-92. [PMID: 18675809 DOI: 10.1016/j.febslet.2008.07.046] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [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: 06/13/2008] [Revised: 07/02/2008] [Accepted: 07/06/2008] [Indexed: 12/18/2022]
Abstract
Interleukin-22 (IL-22) is a member of the interleukin-10 cytokine family, which is involved in anti-microbial defenses, tissue damage protection and repair, and acute phase responses. Its signaling mechanism involves the sequential binding of IL-22 to interleukin-22 receptor 1 (IL-22R1), and of this dimer to interleukin-10 receptor 2 (IL-10R2) extracellular domain. We report a 1.9A crystal structure of the IL-22/IL-22R1 complex, revealing crucial interacting residues at the IL-22/IL-22R1 interface. Functional importance of key residues was confirmed by site-directed mutagenesis and functional studies. Based on the X-ray structure of the binary complex, we discuss a molecular basis of the IL-22/IL-22R1 recognition by IL-10R2.
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Affiliation(s)
- Lucas Bleicher
- Instituto de Física de São Carlos, Universidade de São Paulo, CEP 13560-970 São Carlos, SP, Brazil
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Kuser P, Cupri F, Bleicher L, Polikarpov I. Crystal structure of yeast hexokinase PI in complex with glucose: A classical "induced fit" example revised. Proteins 2008; 72:731-40. [PMID: 18260108 DOI: 10.1002/prot.21956] [Citation(s) in RCA: 28] [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: 11/07/2022]
Abstract
Hexokinase is the first enzyme in the glycolytic pathway that catalyzes the transfer of a phosphoryl group from ATP to glucose to form glucose-6-phosphate and ADP. Two yeast hexokinase isozymes are known, namely PI and PII. Here we redetermined the crystal structure of yeast hexokinase PI from Saccharomyces cerevisiae as a complex with its substrate, glucose, and refined it at 2.95 A resolution. Comparison of the holo-PI yeast hexokinase and apo-hexokinase structures shows in detail the rigid body domain closure and specific loop movements as glucose binds and sheds more light on structural basis of the "induced fit" mechanism of reaction in the HK enzymatic action. We also performed statistical coupling analysis of the hexokinase family, which reveals two co-evolved continuous clusters of amino acid residues and shows that the evolutionary coupled amino acid residues are mostly confined to the active site and the hinge region, further supporting the importance of these parts of the protein for the enzymatic catalysis.
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Affiliation(s)
- Paula Kuser
- EMBRAPA Informática Agropecuária, Av. Dr. André Tosello, s/n, Cidade Universitária Zeferino Vaz, C. P. 6041, CEP 13083-970, Campinas, São Paulo, Brazil
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Bleicher L, Aparicio R, Nunes FM, Martinez L, Gomes Dias SM, Figueira ACM, Santos MAM, Venturelli WH, da Silva R, Donate PM, Neves FA, Simeoni LA, Baxter JD, Webb P, Skaf MS, Polikarpov I. Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms. BMC Struct Biol 2008; 8:8. [PMID: 18237438 PMCID: PMC2275733 DOI: 10.1186/1472-6807-8-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Accepted: 01/31/2008] [Indexed: 12/14/2022]
Abstract
Background Thyroid receptors, TRα and TRβ, are involved in important physiological functions such as metabolism, cholesterol level and heart activities. Whereas metabolism increase and cholesterol level lowering could be achieved by TRβ isoform activation, TRα activation affects heart rates. Therefore, β-selective thyromimetics have been developed as promising drug-candidates for treatment of obesity and elevated cholesterol level. GC-1 [3,5-dimethyl-4-(4'-hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid] has ability to lower LDL cholesterol with 600- to 1400-fold more potency and approximately two- to threefold more efficacy than atorvastatin (Lipitor©) in studies in rats, mice and monkeys. Results To investigate GC-1 specificity, we solved crystal structures and performed molecular dynamics simulations of both isoforms complexed with GC-1. Crystal structures reveal that, in TRα Arg228 is observed in multiple conformations, an effect triggered by the differences in the interactions between GC-1 and Ser277 or the corresponding asparagine (Asn331) of TRβ. The corresponding Arg282 of TRβ is observed in only one single stable conformation, interacting effectively with the ligand. Molecular dynamics support this model: our simulations show that the multiple conformations can be observed for the Arg228 in TRα, in which the ligand interacts either strongly with the ligand or with the Ser277 residue. In contrast, a single stable Arg282 conformation is observed for TRβ, in which it strongly interacts with both GC-1 and the Asn331. Conclusion Our analysis suggests that the key factors for GC-1 selectivity are the presence of an oxyacetic acid ester oxygen and the absence of the amino group relative to T3. These results shed light into the β-selectivity of GC-1 and may assist the development of new compounds with potential as drug candidates to the treatment of hypercholesterolemia and obesity.
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Affiliation(s)
- Lucas Bleicher
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense, 400 CEP 13560-970 São Carlos, SP, Brazil.
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40
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Calgaro MR, Neto MDO, Figueira ACM, Santos MAM, Portugal RV, Guzzi CA, Saidemberg DM, Bleicher L, Vernal J, Fernandez P, Terenzi H, Palma MS, Polikarpov I. Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface. Protein Sci 2007; 16:1762-72. [PMID: 17600153 PMCID: PMC2203355 DOI: 10.1110/ps.062692207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells.
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MESH Headings
- Circular Dichroism
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/isolation & purification
- Dimerization
- Mass Spectrometry
- Models, Biological
- Models, Molecular
- Nuclear Receptor Subfamily 4, Group A, Member 1
- Protein Structure, Secondary
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/isolation & purification
- Receptors, Glucocorticoid/chemistry
- Receptors, Steroid/chemistry
- Receptors, Steroid/genetics
- Receptors, Steroid/isolation & purification
- Scattering, Small Angle
- Solutions
- Transcription Factors/chemistry
- Transcription Factors/genetics
- Transcription Factors/isolation & purification
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Affiliation(s)
- Marcos R Calgaro
- Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, CEP 13566-590 São Carlos, São Paulo, Brazil
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41
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Matozo HC, Santos MAM, de Oliveira Neto M, Bleicher L, Lima LMTR, Iuliano R, Fusco A, Polikarpov I. Low-resolution structure and fluorescence anisotropy analysis of protein tyrosine phosphatase eta catalytic domain. Biophys J 2007; 92:4424-32. [PMID: 17400699 PMCID: PMC1877755 DOI: 10.1529/biophysj.106.094961] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rat protein tyrosine phosphatase eta, rPTPeta, is a class I "classical" transmembrane RPTP, with an intracellular portion composed of a unique catalytic region. The rPTPeta and the human homolog DEP-1 are downregulated in rat and human neoplastic cells, respectively. However, the malignant phenotype is reverted after exogenous reconstitution of rPTPeta, suggesting that its function restoration could be an important tool for gene therapy of human cancers. Using small-angle x-ray scattering (SAXS) and biophysical techniques, we characterized the intracellular catalytic domain of rat protein tyrosine phosphatase eta (rPTPetaCD) in solution. The protein forms dimers in solution as confirmed by SAXS data analysis. The SAXS data also indicated that rPTPetaCD dimers are elongated and have an average radius of gyration of 2.65 nm and a D(max) of 8.5 nm. To further study the rPTPetaCD conformation in solution, we built rPTPetaCD homology models using as scaffolds the crystallographic structures of RPTPalpha-D1 and RPTPmicro-D1 dimers. These models were, then, superimposed onto ab initio low-resolution SAXS structures. The structural comparisons and sequence alignment analysis of the putative dimerization interfaces provide support to the notion that the rPTPetaCD dimer architecture is more closely related to the crystal structure of autoinhibitory RPTPalpha-D1 dimer than to the dimeric arrangement exemplified by RPTPmicro-D1. Finally, the characterization of rPTPetaCD by fluorescence anisotropy measurements demonstrates that the dimer dissociation is concentration dependent with a dissociation constant of 21.6 +/- 2.0 microM.
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Affiliation(s)
- Huita C Matozo
- Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, São Carlos, Brazil
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42
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Nascimento AS, Dias SMG, Nunes FM, Aparício R, Ambrosio ALB, Bleicher L, Figueira ACM, Santos MAM, de Oliveira Neto M, Fischer H, Togashi M, Craievich AF, Garratt RC, Baxter JD, Webb P, Polikarpov I. Structural Rearrangements in the Thyroid Hormone Receptor Hinge Domain and Their Putative Role in the Receptor Function. J Mol Biol 2006; 360:586-98. [PMID: 16781732 DOI: 10.1016/j.jmb.2006.05.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [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] [Received: 01/17/2006] [Revised: 04/12/2006] [Accepted: 05/03/2006] [Indexed: 11/21/2022]
Abstract
The thyroid hormone receptor (TR) D-domain links the ligand-binding domain (LBD, EF-domain) to the DNA-binding domain (DBD, C-domain), but its structure, and even its existence as a functional unit, are controversial. The D domain is poorly conserved throughout the nuclear receptor family and was originally proposed to comprise an unfolded hinge that facilitates rotation between the LBD and the DBD. Previous TR LBD structures, however, have indicated that the true unstructured region is three to six amino acid residues long and that the D-domain N terminus folds into a short amphipathic alpha-helix (H0) contiguous with the DBD and that the C terminus of the D-domain comprises H1 and H2 of the LBD. Here, we solve structures of TR-LBDs in different crystal forms and show that the N terminus of the TRalpha D-domain can adopt two structures; it can either fold into an amphipathic helix that resembles TRbeta H0 or form an unstructured loop. H0 formation requires contacts with the AF-2 coactivator-binding groove of the neighboring TR LBD, which binds H0 sequences that resemble coactivator LXXLL motifs. Structural analysis of a liganded TR LBD with small angle X-ray scattering (SAXS) suggests that AF-2/H0 interactions mediate dimerization of this protein in solution. We propose that the TR D-domain has the potential to form functionally important extensions of the DBD and LBD or unfold to permit TRs to adapt to different DNA response elements. We also show that mutations of the D domain LXXLL-like motif indeed selectively inhibit TR interactions with an inverted palindromic response element (F2) in vitro and TR activity at this response element in cell-based transfection experiments.
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Affiliation(s)
- Alessandro S Nascimento
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense, 400 CEP 13560-970 São Carlos, SP, Brazil
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Cosford ND, Bleicher L, Vernier JM, Chavez-Noriega L, Rao TS, Siegel RS, Suto C, Washburn M, Lloyd GK, McDonald IA. Recombinant human receptors and functional assays in the discovery of altinicline (SIB-1508Y), a novel acetylcholine-gated ion channel (nAChR) agonist. Pharm Acta Helv 2000; 74:125-30. [PMID: 10812948 DOI: 10.1016/s0031-6865(99)00024-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Neuronal nicotinic acetylcholine receptors (nAChRs) are a class of ion channels with significant potential as molecular targets for the design of drugs to treat a variety of CNS disorders. The discovery that neuronal nAChRs are further subdivided into multiple subtypes suggests that drugs which act selectively at specific nAChR subtypes might effectively treat Parkinson's disease (PD), Alzheimer's disease (AD), schizophrenia, ADHD, depression, anxiety or pain without the accompanying adverse side effects associated with non-selective agents such as nicotine (1) and epibatidine. Altinicline (SIB-1508Y) is a novel, small molecule designed to selectively activate neuronal nAChRs and is undergoing clinical evaluation for the treatment of PD. It was selected from a series of compounds primarily on the basis of results from functional assays, including (a) measurement of Ca2+ flux in stable cell lines expressing specific recombinant human neuronal nAChR subtypes; (b) determination of in vitro and in vivo neurotransmitter release; (c) in vivo models of PD. Biological data on both altinicline and the series of compounds from which it was selected are reported.
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Affiliation(s)
- N D Cosford
- Merck Research Laboratories San Diego, La Jolla, CA 92037, USA
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Varney MA, Cosford ND, Jachec C, Rao SP, Sacaan A, Lin FF, Bleicher L, Santori EM, Flor PJ, Allgeier H, Gasparini F, Kuhn R, Hess SD, Veliçelebi G, Johnson EC. SIB-1757 and SIB-1893: selective, noncompetitive antagonists of metabotropic glutamate receptor type 5. J Pharmacol Exp Ther 1999; 290:170-81. [PMID: 10381773] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023] Open
Abstract
Cell lines expressing the human metabotropic glutamate receptor subtype 5a (hmGluR5a) and hmGluR1b were used as targets in an automated high-throughput screening (HTS) system that measures changes in intracellular Ca2+ ([Ca2+]i) using fluorescence detection. This functional screen was used to identify the mGluR5-selective antagonist, SIB-1757 [6-methyl-2-(phenylazo)-3-pyridinol], which inhibited the glutamate-induced [Ca2+]i responses at hmGluR5 with an IC50 of 0.37 microM compared with an IC50 of >100 microM at hmGluR1. Schild analysis demonstrated a noncompetitive mechanism of inhibition. Pharmacophore mapping was used to identify an additional compound, SIB-1893 [(E)-2-methyl-6-(2-phenylethenyl)pyridine], which was also shown to block glutamate-induced increases in [Ca2+]i at hmGluR5 with an IC50 of 0.29 microM compared with an IC50 of >100 microM at hmGluR1. SIB-1757 and SIB-1893 showed little or no activity when tested for agonist and antagonist activity at the other recombinant human mGluR subtypes, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, kainate, and N-methyl-D-aspartate receptors. In rat neonatal brain slices, SIB-1757 and SIB-1893 inhibited (S)-3,5-dihydroxyphenylglycine (DHPG)-evoked inositol phosphate accumulation in hippocampus and striatum by 60% to 80%, with a potency similar to that observed on recombinant mGluR5. However, in the cerebellum, a brain region with low mGluR5 expression, SIB-1757 failed to inhibit DHPG-evoked inositol phosphate accumulation. In cultured rat cortical neurons, SIB-1757 and SIB-1893 largely inhibited DHPG-evoked [Ca2+]i signals, revealing a population of neurons that were less sensitive to SIB-1757 and SIB-1893. This is the first description of highly selective, noncompetitive mGluR5 antagonists. These compounds will be useful tools in evaluating the role of mGluR5 in normal physiology and in animal models of disease.
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Affiliation(s)
- M A Varney
- SIBIA Neurosciences, Inc., La Jolla, California, USA
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Vernier JM, El-Abdellaoui H, Holsenback H, Cosford ND, Bleicher L, Barker G, Bontempi B, Chavez-Noriega L, Menzaghi F, Rao TS, Reid R, Sacaan AI, Suto C, Washburn M, Lloyd GK, McDonald IA. 4-[[2-(1-Methyl-2-pyrrolidinyl)ethyl]thio]phenol hydrochloride (SIB-1553A): a novel cognitive enhancer with selectivity for neuronal nicotinic acetylcholine receptors. J Med Chem 1999; 42:1684-6. [PMID: 10346920 DOI: 10.1021/jm990035d] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J M Vernier
- SIBIA Neurosciences Inc., 505 Coast Boulevard South, La Jolla, California 92037, USA
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Sacaan AI, Reid RT, Santori EM, Adams P, Correa LD, Mahaffy LS, Bleicher L, Cosford ND, Stauderman KA, McDonald IA, Rao TS, Lloyd GK. Pharmacological characterization of SIB-1765F: a novel cholinergic ion channel agonist. J Pharmacol Exp Ther 1997; 280:373-83. [PMID: 8996218] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nicotine, the prototypical agonist for neuronal nicotinic acetylcholine receptors (NAChR), nonselectively activates NAChR limiting its use in elucidating the function of NAChR subtypes. SIB-1765F is a subtype selective NAChR agonist that displaces [3H]-nicotine binding with an IC50 of 4.6 nM and [3H]-cytisine binding with an IC50 of 12.2 nM which is 2000- to 6000-fold lower than its displacement of [3H]-QNB or [125I]-alpha-bungarotoxin. SIB-1765F did not inhibit human or rat cholinesterases or the uptake of [3H]-DA in synaptosomal preparations. SIB-1765F mimicked (-)-nicotine in stimulating [3H]-DA release from rat striatal and olfactory tubercle slices, with EC50 values of 99.6 and 39.6 microM, respectively. Such stimulation was sensitive to mecamylamine and DH beta E. SIB-1765F also released endogenous DA in the striatum and the nucleus accumbens as measured by in vivo microdialysis. SIB-1765F was less efficacious than (-)-nicotine at stimulating [3H]-NE release from rat hippocampal slices; in contrast, SIB-1765F increased [3H]-NE release from rat thalamic and cortical slices with efficacies approaching those of (-)-nicotine. Similar to (-)-nicotine and (+/-)-epibatidine, subcutaneous administration of SIB-1765F increased the turnover rate of dopamine ex vivo both in the striatum and olfactory tubercles in a mecamylamine-sensitive manner. Because the release of striatal DA and hippocampal NE appears to be regulated by distinct NAChR, differential effects of SIB-1765F on striatal DA and hippocampal NE release supports the NAChR subtype selectivity of SIB-1765F compared to (-)-nicotine. This is further demonstrated by observations showing that SIB-1765F has a higher affinity for h alpha 4 beta 2 NAChR relative to h alpha 4 beta 4 NAChRs in displacing [3H]-epibatidine binding and increasing cytosolic CA+2 concentration in cell lines stably expressing h alpha 4 beta 2 or h alpha 4 beta 4.
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Affiliation(s)
- A I Sacaan
- SIBIA Neurosciences, Inc., La Jolla, California, USA
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48
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Cosford ND, Bleicher L, Herbaut A, McCallum JS, Vernier JM, Dawson H, Whitten JP, Adams P, Chavez-Noriega L, Correa LD, Crona JH, Mahaffy LS, Menzaghi F, Rao TS, Reid R, Sacaan AI, Santori E, Stauderman KA, Whelan K, Lloyd GK, McDonald IA. (S)-(-)-5-ethynyl-3-(1-methyl-2-pyrrolidinyl)pyridine maleate (SIB-1508Y): a novel anti-parkinsonian agent with selectivity for neuronal nicotinic acetylcholine receptors. J Med Chem 1996; 39:3235-7. [PMID: 8765504 DOI: 10.1021/jm960328w] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- N D Cosford
- SIBIA Neurosciences Inc., La Jolla, California 92037, USA
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