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Sámano-Sánchez H, Gibson TJ, Chemes LB. Using Linear Motif Database Resources to Identify SH2 Domain Binders. Methods Mol Biol 2023; 2705:153-197. [PMID: 37668974 DOI: 10.1007/978-1-0716-3393-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The SH2-binding phosphotyrosine class of short linear motifs (SLiMs) are key conditional regulatory elements, particularly in signaling protein complexes beneath the cell's plasma membrane. In addition to transmitting cellular signaling information, they can also play roles in cellular hijack by invasive pathogens. Researchers can take advantage of bioinformatics tools and resources to predict the motifs at conserved phosphotyrosine residues in regions of intrinsically disordered protein. A candidate SH2-binding motif can be established and assigned to one or more of the SH2 domain subgroups. It is, however, not so straightforward to predict which SH2 domains are capable of binding the given candidate. This is largely due to the cooperative nature of the binding amino acids which enables poorer binding residues to be tolerated when the other residues are optimal. High-throughput peptide arrays are powerful tools used to derive SH2 domain-binding specificity, but they are unable to capture these cooperative effects and also suffer from other shortcomings. Tissue and cell type expression can help to restrict the list of available interactors: for example, some well-studied SH2 domain proteins are only present in the immune cell lineages. In this article, we provide a table of motif patterns and four bioinformatics strategies that introduce a range of tools that can be used in motif hunting in cellular and pathogen proteins. Experimental followup is essential to determine which SH2 domain/motif-containing proteins are the actual functional partners.
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Affiliation(s)
- Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
- Biomedical Sciences, Edinburgh Medical School, The University of Edinburgh, Edinburgh, UK
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lucía B Chemes
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Argentina.
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2
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Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte M, Bassot C, Chasapi A, Davey N, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon A, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis C, Palopoli N, Papaleo E, Pereira P, Pozzati G, Promponas V, Pujols J, Rocha AS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos K, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res 2022; 50:D480-D487. [PMID: 34850135 PMCID: PMC8728214 DOI: 10.1093/nar/gkab1082] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 02/03/2023] Open
Abstract
The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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Affiliation(s)
- Federica Quaglia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR-IBIOM), Bari, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Edoardo Salladini
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - András Hatos
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 Buenos Aires, Argentina
| | - Mátyás Pajkos
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnology, Brussels, Belgium
- Structural Biology Brussels (SBB), Bioengineering Sciences Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Samuel Peña-Díaz
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaime Santos
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Veronika Ács
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Nazanin Farahi
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnology, Brussels, Belgium
- Structural Biology Brussels (SBB), Bioengineering Sciences Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Erzsébet Fichó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
- Cytocast Kft., Vecsés, Hungary
| | - Maria Cristina Aspromonte
- Department of Woman and Child Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Claudio Bassot
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Solna, Sweden
| | - Anastasia Chasapi
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thermi, Thessalonica 57001, Greece
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London, UK
| | - Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11000Belgrade, Serbia
| | - Laszlo Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Solna, Sweden
| | - Gábor Erdős
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
| | - Pascale Gaudet
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Michelle Giglio
- Institute for Genome Sciences, University of Maryland School of Medicine 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 Buenos Aires, Argentina
| | - Javier Iserte
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
| | - Valentín Iglesias
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Zsófia Kálmán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Sonia Longhi
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288, Marseille, France
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Emiliano Maiani
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Julia Marchetti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | | | - Attila Mészáros
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnology, Brussels, Belgium
- Structural Biology Brussels (SBB), Bioengineering Sciences Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | | | - Suvarna Nadendla
- Institute for Genome Sciences, University of Maryland School of Medicine 670 W. Baltimore St., Baltimore, MD 21201, USA
| | - Juliet F Nilsson
- Lab. Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix Marseille University and Centre National de la Recherche Scientifique (CNRS), 163 Avenue de Luminy, Case 932, 13288, Marseille, France
| | - Marian Novotný
- Dep. of Cell Biology, Faculty of Science, Vinicna 7, 128 43, Prague, Czech Republic
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thermi, Thessalonica 57001, Greece
- Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, Department of Computer Science, Aristotle University of Thessalonica, Thessalonica 54124, Greece
| | - Nicolás Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Gabriele Pozzati
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Solna, Sweden
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Martin Salas
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Luciana Rodriguez Sawicki
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Aditi Shenoy
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Solna, Sweden
| | - Tamás Szaniszló
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
| | - Konstantinos D Tsirigos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11000Belgrade, Serbia
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnology, Brussels, Belgium
- Structural Biology Brussels (SBB), Bioengineering Sciences Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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Laura Darriba M, Castro CP, Coria LM, Bruno L, Laura Cerutti M, Otero LH, Chemes LB, Rasia RM, Klinke S, Cassataro J, Pasquevich KA. A disordered region retains the full protease inhibitor activity and the capacity to induce CD8+ T cells in vivo of the oral vaccine adjuvant U-Omp19. Comput Struct Biotechnol J 2022; 20:5098-5114. [PMID: 36187929 PMCID: PMC9486555 DOI: 10.1016/j.csbj.2022.08.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- M. Laura Darriba
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Celeste Pueblas Castro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lorena M. Coria
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Laura Bruno
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - M. Laura Cerutti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Santa Fe, Argentina and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Juliana Cassataro
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Karina A. Pasquevich
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Buenos Aires, Argentina
- Corresponding author.
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Cobos ES, Sánchez IE, Chemes LB, Martinez JC, Murciano-Calles J. A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands. Biomolecules 2021; 11:biom11081071. [PMID: 34439737 PMCID: PMC8393326 DOI: 10.3390/biom11081071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/01/2023] Open
Abstract
PDZ domains are binding modules mostly involved in cell signaling and cell–cell junctions. These domains are able to recognize a wide variety of natural targets and, among the PDZ partners, viruses have been discovered to interact with their host via a PDZ domain. With such an array of relevant and diverse interactions, PDZ binding specificity has been thoroughly studied and a traditional classification has grouped PDZ domains in three major specificity classes. In this work, we have selected four human PDZ domains covering the three canonical specificity-class binding mode and a set of their corresponding binders, including host/natural, viral and designed PDZ motifs. Through calorimetric techniques, we have covered the entire cross interactions between the selected PDZ domains and partners. The results indicate a rather basic specificity in each PDZ domain, with two of the domains that bind their cognate and some non-cognate ligands and the two other domains that basically bind their cognate partners. On the other hand, the host partners mostly bind their corresponding PDZ domain and, interestingly, the viral ligands are able to bind most of the studied PDZ domains, even those not previously described. Some viruses may have evolved to use of the ability of the PDZ fold to bind multiple targets, with resulting affinities for the virus–host interactions that are, in some cases, higher than for host–host interactions.
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Affiliation(s)
- Eva S. Cobos
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, 1428 Buenos Aires, Argentina;
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, 1650 Buenos Aires, Argentina;
| | - Jose C. Martinez
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Javier Murciano-Calles
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
- Correspondence:
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Mészáros B, Sámano-Sánchez H, Alvarado-Valverde J, Čalyševa J, Martínez-Pérez E, Alves R, Shields DC, Kumar M, Rippmann F, Chemes LB, Gibson TJ. Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. Sci Signal 2021; 14:eabd0334. [PMID: 33436497 PMCID: PMC7928535 DOI: 10.1126/scisignal.abd0334] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
The first reported receptor for SARS-CoV-2 on host cells was the angiotensin-converting enzyme 2 (ACE2). However, the viral spike protein also has an RGD motif, suggesting that cell surface integrins may be co-receptors. We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif (ELM) resource and identified candidate short linear motifs (SLiMs) in their short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton, and cell signaling. These SLiM candidates are highly conserved in vertebrates and may interact with the μ2 subunit of the endocytosis-associated AP2 adaptor complex, as well as with various protein domains (namely, I-BAR, LC3, PDZ, PTB, and SH2) found in human signaling and regulatory proteins. Several motifs overlap in the tail sequences, suggesting that they may act as molecular switches, such as in response to tyrosine phosphorylation status. Candidate LC3-interacting region (LIR) motifs are present in the tails of integrin β3 and ACE2, suggesting that these proteins could directly recruit autophagy components. Our findings identify several molecular links and testable hypotheses that could uncover mechanisms of SARS-CoV-2 attachment, entry, and replication against which it may be possible to develop host-directed therapies that dampen viral infection and disease progression. Several of these SLiMs have now been validated to mediate the predicted peptide interactions.
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Affiliation(s)
- Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Elizabeth Martínez-Pérez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Laboratorio de bioinformática estructural, Fundación Instituto Leloir, C1405BWE Buenos Aires, Argentina
| | - Renato Alves
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Denis C Shields
- School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Friedrich Rippmann
- Computational Chemistry & Biology, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, CP1650 San Martín, Buenos Aires, Argentina.
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
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Taboada C, Brunetti AE, Lyra ML, Fitak RR, Faigón Soverna A, Ron SR, Lagorio MG, Haddad CFB, Lopes NP, Johnsen S, Faivovich J, Chemes LB, Bari SE. Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin. Proc Natl Acad Sci U S A 2020; 117:18574-18581. [PMID: 32661155 PMCID: PMC7414155 DOI: 10.1073/pnas.2006771117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations-a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism-the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.
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Affiliation(s)
- Carlos Taboada
- Department of Biology, Duke University, Durham, NC 27708;
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
| | - Andrés E Brunetti
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
- Laboratorio de Genética Evolutiva "Claudio Juan Bidau," Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Universidad Nacional de Misiones, 3300 Posadas, Misiones, Argentina
| | - Mariana L Lyra
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, São Paulo, Brazil
| | - Robert R Fitak
- Department of Biology, Duke University, Durham, NC 27708
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816
| | - Ana Faigón Soverna
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Aptdo. 17-01-2184, Quito, Ecuador
| | - María G Lagorio
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, 13506-900 Rio Claro, São Paulo, Brazil
| | - Norberto P Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040903 Ribeirão Preto, São Paulo, Brazil
| | - Sönke Johnsen
- Department of Biology, Duke University, Durham, NC 27708
| | - Julián Faivovich
- División Herpetología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia," Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires C1405DJR, Argentina
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina
| | - Lucía B Chemes
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1405BWE, Argentina;
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Buenos Aires, Argentina
| | - Sara E Bari
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina;
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7
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Kumar M, Gouw M, Michael S, Sámano-Sánchez H, Pancsa R, Glavina J, Diakogianni A, Valverde JA, Bukirova D, Čalyševa J, Palopoli N, Davey NE, Chemes LB, Gibson TJ. ELM-the eukaryotic linear motif resource in 2020. Nucleic Acids Res 2020; 48:D296-D306. [PMID: 31680160 PMCID: PMC7145657 DOI: 10.1093/nar/gkz1030] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [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: 09/25/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins. In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs and motif mimicry by pathogenic bacterial effector proteins. The current release of the ELM database contains 289 motif classes and 3523 individual protein motif instances manually curated from 3467 scientific publications. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Rita Pancsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Athina Diakogianni
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Dayana Bukirova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Nazarbayev University, Nur-Sultan 010000, Kazakhstan
| | - Jelena Čalyševa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Nicolas Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes - CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Norman E Davey
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas (IIBio) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de San Martín. Av. 25 de Mayo y Francia, CP1650, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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8
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Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database (Oxford) 2020; 2020:baaa040. [PMID: 32507889 PMCID: PMC7276420 DOI: 10.1093/database/baaa040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/24/2020] [Accepted: 05/06/2020] [Indexed: 11/12/2022]
Abstract
Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at great expense is significantly underutilised. The protein motif biology field does not have sufficient resources to curate the corpus of motif-related literature and, to date, only a fraction of the available articles have been curated. In this study, we develop a set of tools and a web resource, 'articles.ELM', to rapidly identify the motif literature articles pertinent to a researcher's interest. At the core of the resource is a manually curated set of about 8000 motif-related articles. These articles are automatically annotated with a range of relevant biological data allowing in-depth search functionality. Machine-learning article classification is used to group articles based on their similarity to manually curated motif classes in the Eukaryotic Linear Motif resource. Articles can also be manually classified within the resource. The 'articles.ELM' resource permits the rapid and accurate discovery of relevant motif articles thereby improving the visibility of motif literature and simplifying the recovery of valuable biological insights sequestered within scientific articles. Consequently, this web resource removes a critical bottleneck in scientific productivity for the motif biology field. Database URL: http://slim.icr.ac.uk/articles/.
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Affiliation(s)
- N Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Roque Saenz Peña 352, Bernal, Buenos Aires B1876BXD, Argentina
| | - J A Iserte
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina
| | - L B Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, Av. 25 de Mayo y Francia, San Martín, Buenos Aires B1650, Argentina
| | - C Marino-Buslje
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina
| | - G Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Roque Saenz Peña 352, Bernal, Buenos Aires B1876BXD, Argentina
| | - T J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - N E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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9
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Glavina J, Román EA, Espada R, de Prat-Gay G, Chemes LB, Sánchez IE. Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein. Virology 2018; 525:117-131. [PMID: 30265888 DOI: 10.1016/j.virol.2018.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 05/22/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 01/04/2023]
Abstract
E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery.
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Affiliation(s)
- Juliana Glavina
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina
| | - Ernesto A Román
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Rocío Espada
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Lucía B Chemes
- Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina; Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Ignacio E Sánchez
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas. Buenos Aires, Argentina.
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10
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Molina IG, Esperante SA, Marino-Buslje C, Chemes LB, de Prat-Gay G. Cooperative RNA Recognition by a Viral Transcription Antiterminator. J Mol Biol 2018; 430:777-792. [PMID: 29414675 DOI: 10.1016/j.jmb.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 12/05/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 01/18/2023]
Abstract
RNA transcription of mononegavirales decreases gradually from the 3' leader promoter toward the 5' end of the genome, due to a decay in polymerase processivity. In the respiratory syncytial virus and metapneumovirus, the M2-1 protein ensures transcription anti-termination. Despite being a homotetramer, respiratory syncytial virus M2-1 binds two molecules of RNA of 13mer or longer per tetramer, and temperature-sensitive secondary structure in the RNA ligand is unfolded by stoichiometric interaction with M2-1. Fine quantitative analysis shows positive cooperativity, indicative of conformational asymmetry in the tetramer. RNA binds to M2-1 through a fast bimolecular association followed by slow rearrangements corresponding to an induced-fit mechanism, providing a sequential description of the time events of cooperativity. The first binding event of half of the RNA molecule to one of the sites increases the affinity of the second binding event on the adjacent contacting protomer by 15-fold, product of increased effective concentration caused by the entropic link. This mechanism allows for high-affinity binding with an otherwise relaxed sequence specificity, and instead suggests a yet undefined structural recognition signature in the RNA for modulating gene transcription. This work provides a basis for an essential event for understanding transcription antitermination in pneumoviruses and its counterpart Ebola virus VP30.
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Affiliation(s)
- Ivana G Molina
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Sebastian A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Cristina Marino-Buslje
- Structural Bioinformatics Unit, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.
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11
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Palopoli N, González Foutel NS, Gibson TJ, Chemes LB. Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity. Protein Eng Des Sel 2018; 31:69-77. [DOI: 10.1093/protein/gzx068] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/10/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET. Roque Sáenz Peña 352. CP (B1876BXD), Bernal, Buenos Aires, Argentina
- Structural Bioinformatics Unit, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Nicolás S González Foutel
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Lucía B Chemes
- Protein Structure Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435 CP 1405, Buenos Aires, Argentina
- Instituto de Investigaciones Biotecnológicas IIB-INTECH, Universidad Nacional de San Martín. Av. 25 de Mayo y Francia CP 1650, San Martín, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
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12
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Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, Palopoli N, Roey KV, Altenberg B, Reményi A, Dinkel H, Gibson TJ. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Res 2018; 46:D428-D434. [PMID: 29136216 PMCID: PMC5753338 DOI: 10.1093/nar/gkx1077] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [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: 10/01/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research. In this database update, we present the latest additions to the database including 32 new motif classes, and new features including Uniprot and Reactome integration. Finally, to help provide cellular context, we present some biological insights about SLiMs in the cell cycle, as targets for bacterial pathogenicity and their functionality in the human kinome.
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Affiliation(s)
- Marc Gouw
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Benjamin Lang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Benoit Bely
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP 1405, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires CP 2160, Argentina
- Instituto de Investigaciones Biotecnoltógicas, Universidad Nacional de General San Martín, IIB-INTECH-CONICET, San Martín, Buenos Aires CP 1650, Argentina
| | - Norman E Davey
- UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ziqi Deng
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | | | | | | | - Nicolás Palopoli
- Department of Science and Technology, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Buenos Aires, Argentina
| | - Kim V Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Brigitte Altenberg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Attila Reményi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Holger Dinkel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Leibniz-Institute on Aging, Fritz Lipmann Institute (FLI), Jena D-07745, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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13
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Borkosky SS, Camporeale G, Chemes LB, Risso M, Noval MG, Sánchez IE, Alonso LG, de Prat Gay G. Hidden Structural Codes in Protein Intrinsic Disorder. Biochemistry 2017; 56:5560-5569. [PMID: 28952717 DOI: 10.1021/acs.biochem.7b00721] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.
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Affiliation(s)
- Silvia S Borkosky
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gabriela Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Marikena Risso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - María Gabriela Noval
- Department of Microbiology, New York University , Alexandria Center for Life Sciences, New York, New York 10016, United States
| | - Ignacio E Sánchez
- Protein Physiology Laboratory, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Leonardo G Alonso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
| | - Gonzalo de Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) CONICET , Buenos Aires, Argentina
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14
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Noval MG, Esperante SA, Molina IG, Chemes LB, Prat-Gay GD. Intrinsic Disorder to Order Transitions in the Scaffold Phosphoprotein P from the Respiratory Syncytial Virus RNA Polymerase Complex. Biochemistry 2016; 55:1441-54. [PMID: 26901160 DOI: 10.1021/acs.biochem.5b01332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsic disorder is at the center of biochemical regulation and is particularly overrepresented among the often multifunctional viral proteins. Replication and transcription of the respiratory syncytial virus (RSV) relies on a RNA polymerase complex with a phosphoprotein cofactor P as the structural scaffold, which consists of a four-helix bundle tetramerization domain flanked by two domains predicted to be intrinsically disordered. Because intrinsic disorder cannot be reduced to a defined atomic structure, we tackled the experimental dissection of the disorder-order transitions of P by a domain fragmentation approach. P remains as a tetramer above 70 °C but shows a pronounced reversible secondary structure transition between 10 and 60 °C. While the N-terminal module behaves as a random coil-like IDP in a manner independent of tetramerization, the isolated C-terminal module displays a cooperative and reversible metastable transition. When linked to the tetramerization domain, the C-terminal module becomes markedly more structured and stable, with strong ANS binding. Therefore, the tertiary structure in the C-terminal module is not compact, conferring "late" molten globule-like IDP properties, stabilized by interactions favored by tetramerization. The presence of a folded structure highly sensitive to temperature, reversibly and almost instantly formed and broken, suggests a temperature sensing activity. The marginal stability allows for exposure of protein binding sites, offering a thermodynamic and kinetic fine-tuning in order-disorder transitions, essential for the assembly and function of the RSV RNA polymerase complex.
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Affiliation(s)
- María G Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Sebastian A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Ivana G Molina
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.,CNPq, Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro, RJ, Brazil
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Pretel E, Sánchez IE, Fassolari M, Chemes LB, de Prat-Gay G. Conformational Heterogeneity Determined by Folding and Oligomer Assembly Routes of the Interferon Response Inhibitor NS1 Protein, Unique to Human Respiratory Syncytial Virus. Biochemistry 2015; 54:5136-46. [DOI: 10.1021/acs.biochem.5b00615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Esteban Pretel
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Ignacio E. Sánchez
- Protein
Physiology Laboratory, Departamento de Química Biológica,
Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marisol Fassolari
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B. Chemes
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein
Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
- Ciência
Sem Fronteiras Senior Fellow, CNPq, Laboratório de Genômica
Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Chemes LB, Camporeale G, Sánchez IE, de Prat-Gay G, Alonso LG. Cysteine-rich positions outside the structural zinc motif of human papillomavirus E7 provide conformational modulation and suggest functional redox roles. Biochemistry 2014; 53:1680-96. [PMID: 24559112 DOI: 10.1021/bi401562e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The E7 protein from high-risk human papillomavirus is essential for cell transformation in cervical, oropharyngeal, and other HPV-related cancers, mainly through the inactivation of the retinoblastoma (Rb) tumor suppressor. Its high cysteine content (~7%) and the observation that HPV-transformed cells are under oxidative stress prompted us to investigate the redox properties of the HPV16 E7 protein under biologically compatible oxidative conditions. The seven cysteines in HPV16 E7 remain reduced in conditions resembling the basal reduced state of a cell. However, under oxidative stress, a stable disulfide bridge forms between cysteines 59 and 68. Residue 59 has a protective effect on the other cysteines, and its mutation leads to an overall increase in the oxidation propensity of E7, including cysteine 24 central to the Rb binding motif. Gluthationylation of Cys 24 abolishes Rb binding, which is reversibly recovered upon reduction. Cysteines 59 and 68 are located 18.6 Å apart, and the formation of the disulfide bridge leads to a large structural rearrangement while retaining strong Zn association. These conformational and covalent changes are fully reversible upon restoration of the reductive environment. In addition, this is the first evidence of an interaction between the N-terminal intrinsically disordered and the C-terminal globular domains, known to be highly and separately conserved among human papillomaviruses. The significant conservation of such noncanonical cysteines in HPV E7 proteins leads us to propose a functional redox activity. Such an activity adds to the previously discovered chaperone activity of E7 and supports the picture of a moonlighting pathological role of this paradigmatic viral oncoprotein.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
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Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res 2013; 42:D259-66. [PMID: 24214962 PMCID: PMC3964949 DOI: 10.1093/nar/gkt1047] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [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] [Indexed: 02/05/2023] Open
Abstract
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. The current version of ELM contains ∼200 different motif classes with over 2400 experimentally validated instances manually curated from >2000 scientific publications. Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways.
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Affiliation(s)
- Holger Dinkel
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht-Karls-Universität, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co. Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland, Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina
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18
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Noval MG, Gallo M, Perrone S, Salvay AG, Chemes LB, de Prat-Gay G. Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation. PLoS One 2013; 8:e72760. [PMID: 24086265 PMCID: PMC3785498 DOI: 10.1371/journal.pone.0072760] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 04/22/2013] [Accepted: 07/14/2013] [Indexed: 12/25/2022] Open
Abstract
Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus.
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Affiliation(s)
- María G. Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Mariana Gallo
- NMR Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Sebastián Perrone
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Andres G. Salvay
- Institute of Physics of Liquids and Biological Systems, Universidad Nacional de La Plata, La Plata, Argentina
- Department of Science and Technology, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Lucía B. Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina
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19
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Chemes LB, Noval MG, Sánchez IE, de Prat-Gay G. Folding of a cyclin box: linking multitarget binding to marginal stability, oligomerization, and aggregation of the retinoblastoma tumor suppressor AB pocket domain. J Biol Chem 2013; 288:18923-38. [PMID: 23632018 DOI: 10.1074/jbc.m113.467316] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The retinoblastoma tumor suppressor (Rb) controls the proliferation, differentiation, and survival of cells in most eukaryotes with a role in the fate of stem cells. Its inactivation by mutation or oncogenic viruses is required for cellular transformation and eventually carcinogenesis. The high conservation of the Rb cyclin fold prompted us to investigate the link between conformational stability and ligand binding properties of the RbAB pocket domain. RbAB unfolding presents a three-state transition involving cooperative secondary and tertiary structure changes and a partially folded intermediate that can oligomerize. The first transition corresponds to unfolding of the metastable B subdomain containing the binding site for the LXCXE motif present in cellular and viral targets, and the second transition corresponds to the stable A subdomain. The low thermodynamic stability of RbAB translates into a propensity to rapidly oligomerize and aggregate at 37 °C (T50 = 28 min) that is suppressed by human papillomavirus E7 and E2F peptide ligands, suggesting that Rb is likely stabilized in vivo through binding to target proteins. We propose that marginal stability and associated oligomerization may be conserved for function as a "hub" protein, allowing the formation of multiprotein complexes, which could constitute a robust mechanism to retain its cell cycle regulatory role throughout evolution. Decreased stability and oligomerization are shared with the p53 tumor suppressor, suggesting a link between folding and function in these two essential cell regulators that are inactivated in most cancers and operate within multitarget signaling pathways.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Patricias Argentinas 435, 1405 Buenos Aires, Argentina
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20
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Chemes LB, Glavina J, Alonso LG, Marino-Buslje C, de Prat-Gay G, Sánchez IE. Sequence evolution of the intrinsically disordered and globular domains of a model viral oncoprotein. PLoS One 2012; 7:e47661. [PMID: 23118886 PMCID: PMC3485249 DOI: 10.1371/journal.pone.0047661] [Citation(s) in RCA: 21] [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: 07/21/2012] [Accepted: 09/14/2012] [Indexed: 12/11/2022] Open
Abstract
In the present work, we have used the papillomavirus E7 oncoprotein to pursue structure-function and evolutionary studies that take into account intrinsic disorder and the conformational diversity of globular domains. The intrinsically disordered (E7N) and globular (E7C) domains of E7 show similar degrees of conservation and co-evolution. We found that E7N can be described in terms of conserved and coevolving linear motifs separated by variable linkers, while sequence evolution of E7C is compatible with the known homodimeric structure yet suggests other activities for the domain. Within E7N, inter-residue relationships such as residue co-evolution and restricted intermotif distances map functional coupling and co-occurrence of linear motifs that evolve in a coordinate manner. Within E7C, additional cysteine residues proximal to the zinc-binding site may allow redox regulation of E7 function. Moreover, we describe a conserved binding site for disordered domains on the surface of E7C and suggest a putative target linear motif. Both homodimerization and peptide binding activities of E7C are also present in the distantly related host PHD domains, showing that these two proteins share not only structural homology but also functional similarities, and strengthening the view that they evolved from a common ancestor. Finally, we integrate the multiple activities and conformations of E7 into a hierarchy of structure-function relationships.
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Affiliation(s)
- Lucía B. Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Juliana Glavina
- Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Leonardo G. Alonso
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Cristina Marino-Buslje
- Structural Bioinformatics Laboratory. Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Ignacio E. Sánchez
- Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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21
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Chemes LB, Glavina J, Faivovich J, de Prat-Gay G, Sánchez IE. Evolution of linear motifs within the papillomavirus E7 oncoprotein. J Mol Biol 2012; 422:336-46. [PMID: 22683353 DOI: 10.1016/j.jmb.2012.05.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/07/2012] [Accepted: 05/30/2012] [Indexed: 12/11/2022]
Abstract
Many protein functions can be traced to linear sequence motifs of less than five residues, which are often found within intrinsically disordered domains. In spite of their prevalence, their role in protein evolution is only beginning to be understood. The study of papillomaviruses has provided many insights on the evolution of protein structure and function. We have chosen the papillomavirus E7 oncoprotein as a model system for the evolution of functional linear motifs. The multiple functions of E7 proteins from paradigmatic papillomavirus types can be explained to a large extent in terms of five linear motifs within the intrinsically disordered N-terminal domain and two linear motifs within the globular homodimeric C-terminal domain. We examined the motif inventory of E7 proteins from over 200 known papillomavirus types and found that the motifs reported for paradigmatic papillomavirus types are absent from many uncharacterized E7 proteins. Several motif pairs occur more often than expected, suggesting that linear motifs may evolve and function in a cooperative manner. The E7 linear motifs have appeared or disappeared multiple times during papillomavirus evolution, confirming the evolutionary plasticity of short functional sequences. Four of the motifs appeared several times during papillomavirus evolution, providing direct evidence for convergent evolution. Interestingly, the evolution pattern of a motif is independent of its location in a globular or disordered domain. The correlation between the presence of some motifs and virus host specificity and tissue tropism suggests that linear motifs play a role in the adaptive evolution of papillomaviruses.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Patricias Argentinas 435 (1405), Buenos Aires, Argentina
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22
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Abstract
Circular dichroism (CD) spectroscopy is a simple and powerful technique, which allows for the assessment of the conformational properties of a protein or protein domain. Intrinsically disordered proteins (IDPs), as discussed throughout this series, differ from random coil polypeptides in that different regions present specific conformational preferences, exhibiting dynamic secondary structure content [1]. These dynamic secondary structure elements can be stabilized or perturbed by different chemical (solvent, ionic strength, pH) or physical (temperature) agents, by posttranslational modifications, and by ligands. This information is important for defining ID nature. As IDPs present dynamic conformations, circular dichroism measurements (and other approaches as well) should be carried out not as single spectra performed in unique conditions, but instead changing the chemical conditions and observing the behavior, as part of the determination of the ID nature.In this chapter, we present the basic methodology for performing Far-UV CD measurements on a protein of interest and for identifying and characterizing intrinsically disordered regions, and several protocols for the analysis of residual secondary structure present in the protein under study. These techniques are straightforward to perform; they require minimal training and can be preliminary to more complex methodologies such as NMR.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure, Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas, Buenos Aires, Argentina.
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Esperante SA, Chemes LB, Sánchez IE, de Prat-Gay G. The respiratory syncytial virus transcription antiterminator M(2-1) is a highly stable, zinc binding tetramer with strong pH-dependent dissociation and a monomeric unfolding intermediate. Biochemistry 2011; 50:8529-39. [PMID: 21877705 DOI: 10.1021/bi200661k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human respiratory syncytial virus M(2-1) transcription antiterminator is an essential elongation factor required by the RNA polymerase for effective transcription beyond the first two nonstructural genes. Its exclusive presence in pneumovirus among all paramyxovirus suggests a unique function within this small genus. With the aim of understanding its biochemical properties, we investigated this α-helical tetramer by making use of a biophysical approach. We found that the tetramer hydrodynamic radius is considerably extended at high ionic strengths and determined its zinc content to be one atom per monomer. Dissociation-unfolding experiments show a fully reversible and concentration-dependent cooperative transition, but secondary and tertiary structural changes are uncoupled at lower protein concentrations. We detect the presence of a monomeric intermediate, which can be classified as a "late molten globule" with substantial secondary and tertiary structure. Global fittings of experiments from three different probes at two M(2-1) concentrations provide a free energy of dissociation-unfolding of -36.8 ± 0.1 kcal mol(-1), corresponding to a tight dissociation constant of 10(-28) M(3) at pH 7.0. The tetramer affinity is strongly governed by pH, with a free energy change of 13 kcal mol(-1) when pH decreases from 7.0 to 5.0 (K(D) = 10(-18) M(3)). The drastic changes that take place within a pH range compatible with a cellular environment strongly suggest a regulatory effect of pH on M(2-1) structure and biochemical properties, likely affecting transcription and interaction with proteins and RNA.
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Affiliation(s)
- Sebastián A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBA-Conicet, Patricias Argentinas 435, 1405 Buenos Aires, Argentina
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Chemes LB, Sánchez IE, de Prat-Gay G. Kinetic Recognition of the Retinoblastoma Tumor Suppressor by a Specific Protein Target. J Mol Biol 2011; 412:267-84. [DOI: 10.1016/j.jmb.2011.07.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/04/2011] [Accepted: 07/11/2011] [Indexed: 12/25/2022]
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Chemes LB, Sánchez IE, Smal C, de Prat-Gay G. Targeting mechanism of the retinoblastoma tumor suppressor by a prototypical viral oncoprotein. Structural modularity, intrinsic disorder and phosphorylation of human papillomavirus E7. FEBS J 2010; 277:973-88. [PMID: 20088881 DOI: 10.1111/j.1742-4658.2009.07540.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA tumor viruses ensure genome amplification by hijacking the cellular replication machinery and forcing infected cells to enter the S phase. The retinoblastoma (Rb) protein controls the G1/S checkpoint, and is targeted by several viral oncoproteins, among these the E7 protein from human papillomaviruses (HPVs). A quantitative investigation of the interaction mechanism between the HPV16 E7 protein and the RbAB domain in solution revealed that 90% of the binding energy is determined by the LxCxE motif, with an additional binding determinant (1.0 kcal.mol(-1)) located in the C-terminal domain of E7, establishing a dual-contact mode. The stoichiometry and subnanomolar affinity of E7 indicated that it can bind RbAB as a monomer. The low-risk HPV11 E7 protein bound 2.0 kcal.mol(-1) more weakly than the high-risk HPV16 and HPV18 type counterparts, but the modularity and binding mode were conserved. Phosphorylation at a conserved casein kinase II site in the natively unfolded N-terminal domain of E7 affected the local conformation by increasing the polyproline II content and stabilizing an extended conformation, which allowed for a tighter interaction with the Rb protein. Thus, the E7-RbAB interaction involves multiple motifs within the N-terminal domain of E7 and at least two conserved interaction surfaces in RbAB. We discussed a mechanistic model of the interaction of the Rb protein with a viral target in solution, integrated with structural data and the analysis of other cellular and viral proteins, which provided information about the balance of interactions involving the Rb protein and how these determine the progression into either the normal cell cycle or transformation.
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Affiliation(s)
- Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
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