Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.
DisProt
IDPs
biocuration
database
intrinsically disordered proteins
Journal
Current protocols
ISSN: 2691-1299
Titre abrégé: Curr Protoc
Pays: United States
ID NLM: 101773894
Informations de publication
Date de publication:
Jul 2022
Jul 2022
Historique:
entrez:
5
7
2022
pubmed:
6
7
2022
medline:
7
7
2022
Statut:
ppublish
Résumé
DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable three-dimensional structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, both using the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, the SARS-CoV-2 Nucleoprotein, characterized by the presence of unstructured N-terminal and C-terminal regions and a flexible linker. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Exploring the DisProt Ontology page Basic Protocol 3: Visualizing and interpreting DisProt entries-the SARS-CoV-2 Nucleoprotein use case.
Substances chimiques
Intrinsically Disordered Proteins
0
Nucleoproteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e484Informations de copyright
© 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
Références
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … Sherlock, G. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics, 25, 25-29. doi: 10.1038/75556
Binns, D., Dimmer, E., Huntley, R., Barrell, D., O'Donovan, C., & Apweiler, R. (2009). QuickGO: A web-based tool for gene ontology searching. Bioinformatics, 25, 3045-3046. doi: 10.1093/bioinformatics/btp536
Bugge, K., Brakti, I., Fernandes, C. B., Dreier, J. E., Lundsgaard, J. E., Olsen, J. G., … Kragelund, B. B. (2020). Interactions by disorder-a matter of context. Frontiers in Molecular Biosciences, 7, 110. doi: 10.3389/fmolb.2020.00110
Carbon, S., Ireland, A., Mungall, C. J., Shu, S., Marshall, B., Lewis, S., & AmiGO Hub, and Web Presence Working Group. (2009). AmiGO: Online access to ontology and annotation data. Bioinformatics, 25, 288-289. doi: 10.1093/bioinformatics/btn615
Cubuk, J., Alston, J. J., Incicco, J. J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., … Holehouse, A. S. (2021). The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications, 12, 1936. doi: 10.1038/s41467-021-21953-3
Cumberworth, A., Lamour, G., Babu, M. M., & Gsponer, J. (2013). Promiscuity as a functional trait: Intrinsically disordered regions as central players of interactomes. The Biochemical Journal, 454, 361-369. doi: 10.1042/BJ20130545
Davey, N. E., Babu, M. M., Blackledge, M., Bridge, A., Capella-Gutierrez, S., Dosztanyi, Z., … Tosatto, S. C. E. (2019). An intrinsically disordered proteins community for ELIXIR. F1000Research, 8, ELIXIR-1753. doi: 10.12688/f1000research.20136.1
Dogan, J., Gianni, S., & Jemth, P. (2014). The binding mechanisms of intrinsically disordered proteins. Physical Chemistry Chemical Physics: PCCP, 16, 6323-6331. doi: 10.1039/C3CP54226B
Dosztányi, Z., Chen, J., Dunker, A. K., Simon, I., & Tompa, P. (2006). Disorder and sequence repeats in hub proteins and their implications for network evolution. Journal of Proteome Research, 5, 2985-2995. doi: 10.1021/pr060171o
Dyson, H. J., & Wright, P. E. (2019). Perspective: The essential role of NMR in the discovery and characterization of intrinsically disordered proteins. Journal of Biomolecular NMR, 73, 651-659. doi: 10.1007/s10858-019-00280-2
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., … Fin, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids Research, 47, D427-D432. doi: 10.1093/nar/gky995
Gene Ontology Consortium. (2021). The Gene Ontology resource: Enriching a GOld mine. Nucleic Acids Research, 49, D325-D334. doi: 10.1093/nar/gkaa1113
Hatos, A., Hajdu-Soltész, B., Monzon, A. M., Palopoli, N., Álvarez, L., Aykac-Fas, B., … Piovesan, D. (2020). DisProt: Intrinsic protein disorder annotation in 2020. Nucleic Acids Research, 48, D269-D276.
Kragelund, B. B., & Skriver, K. (Eds.). (2020). Intrinsically disordered proteins: Methods and protocols. New York: Humana Press.
Lewis, T. E., Sillitoe, I., Dawson, N., Lam, S. D., Clarke, T., Lee, D., … Lees, J. (2018). Gene3D: Extensive prediction of globular domains in proteins. Nucleic Acids Research, 46, D1282. doi: 10.1093/nar/gkx1187
Nadendla, S., Jackson, R., Munro, J., Quaglia, F., Mészáros, B., Olley, D., … Giglio, M. G. (2022). ECO: The Evidence and Conclusion Ontology, an update for 2022. Nucleic Acids Research, 50, D1515-D1521. doi: 10.1093/nar/gkab1025
Oldfield, C. J., Meng, J., Yang, J. Y., Yang, M. Q., Uversky, V. N., & Dunker, A. K. (2008). Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics, 9, (Suppl 1), S1. doi: 10.1186/1471-2164-9-S1-S1
Perdikari, T. M., Murthy, A. C., Ryan, V. H., Watters, S., Naik, M. T., & Fawzi, N. L. (2020). SARS-CoV-2 nucleocapsid protein phase-separates with RNA and with human hnRNPs. The EMBO Journal, 39, e106478. doi: 10.15252/embj.2020106478
Piovesan, D., Tabaro, F., Mičetić, I., Necci, M., Quaglia, F., Oldfield, C. J., … Tosatto, S. C. E. (2017). DisProt 7.0: A major update of the database of disordered proteins. Nucleic Acids Research, 45, D219-D227. doi: 10.1093/nar/gkw1056
Piovesan, D., Tabaro, F., Paladin, L., Necci, M., Micetic, I., Camilloni, C., … Tosatto, S. C. E. (2018). MobiDB 3.0: More annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Research, 46, D471-D476. doi: 10.1093/nar/gkx1071
Quaglia, F., Mészáros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L. B., … Piovesan, D. (2022a). DisProt in 2022: Improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Research, 50, D480-D487. doi: 10.1093/nar/gkab1082
Quaglia, F., Salladini, E., Carraro, M., Minervini, G., Tosatto, S. C. E., & Le Mercier, P. (2022b). SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. The FEBS Journal, 50(D1), D480-D487. doi: 10.1111/febs.16379
Schiavina, M., Pontoriero, L., Uversky, V. N., Felli, I. C., & Pierattelli, R. (2021). The highly flexible disordered regions of the SARS-CoV-2 nucleocapsid N protein within the 1-248 residue construct: Sequence-specific resonance assignments through NMR. Biomolecular NMR Assignments, 15, 219-227. doi: 10.1007/s12104-021-10009-8
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & UniProt Consortium. (2015). UniRef clusters: A comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics, 31, 926-932. doi: 10.1093/bioinformatics/btu739
Tompa, P. (2010). Structure and function of intrinsically disordered proteins. Boca Raton: Chapman & Hall/CRC Press.
Tompa, P. (2005). The interplay between structure and function in intrinsically unstructured proteins. FEBS Letters, 579, 3346-3354. doi: 10.1016/j.febslet.2005.03.072
UniProt Consortium. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47, D506-D515. doi: 10.1093/nar/gky1049
Uversky, V. N., & Dunker, A. K. (2010). Understanding protein non-folding. Biochimica Et Biophysica Acta, 1804, 1231-1264. doi: 10.1016/j.bbapap.2010.01.017
van der Lee, R., Buljan, M., Lang, B., Weatheritt, R. J., Daughdrill, G. W., Dunker, A. K., … Babu, M. M. (2014). Classification of intrinsically disordered regions and proteins. Chemical Reviews, 114, 6589-6631. doi: 10.1021/cr400525m
Wright, P. E., & Dyson, H. J. (2015). Intrinsically disordered proteins in cellular signalling and regulation. Nature Reviews Molecular Cell Biology, 16, 18-29. doi: 10.1038/nrm3920
Wu, C., Qavi, A. J., Hachim, A., Kavian, N., Cole, A. R., Moyle, A. B., … Leung, D. W. (2021). Characterization of SARS-CoV-2 nucleocapsid protein reveals multiple functional consequences of the C-terminal domain. iScience, 24, 102681. doi: 10.1016/j.isci.2021.102681