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23 results on '"Pandurangan, Arun P."'

4. SARS-CoV-2 Omicron subvariant spike N405 unlikely to rapidly deamidate

Author

Beaudoin, Christopher A., primary, Petsolari, Emmanouela, additional, Hamaia, Samir W., additional, Hala, Sharif, additional, Alofi, Fadwa S., additional, Pandurangan, Arun P., additional, Blundell, Tom L., additional, Chaitanya Vedithi, Sundeep, additional, Huang, Christopher L.-H., additional, and Jackson, Antony P., additional

Published
2023
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5. InterPro in 2022

Author

Paysan-Lafosse, Typhaine, primary, Blum, Matthias, additional, Chuguransky, Sara, additional, Grego, Tiago, additional, Pinto, Beatriz Lázaro, additional, Salazar, Gustavo A, additional, Bileschi, Maxwell L, additional, Bork, Peer, additional, Bridge, Alan, additional, Colwell, Lucy, additional, Gough, Julian, additional, Haft, Daniel H, additional, Letunić, Ivica, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Orengo, Christine A, additional, Pandurangan, Arun P, additional, Rivoire, Catherine, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Wu, Cathy H, additional, and Bateman, Alex, additional

Published
2022
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7. InterPro in 2022.

Author

Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, and Sigrist, Christian J A

Published
2023
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8. Evolution and host-specific adaptation of Pseudomonas aeruginosa.

Author

Weimann, Aaron, Dinan, Adam M., Ruis, Christopher, Bernut, Audrey, Pont, Stéphane, Brown, Karen, Ryan, Judy, Santos, Lúcia, Ellison, Louise, Ukor, Emem, Pandurangan, Arun P., Krokowski, Sina, Blundell, Tom L., Welch, Martin, Blane, Beth, Judge, Kim, Bousfield, Rachel, Brown, Nicholas, Bryant, Josephine M., and Kukavica-Ibrulj, Irena

Published
2024
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9. The InterPro protein families and domains database: 20 years on

Author

Blum, Matthias, primary, Chang, Hsin-Yu, additional, Chuguransky, Sara, additional, Grego, Tiago, additional, Kandasaamy, Swaathi, additional, Mitchell, Alex, additional, Nuka, Gift, additional, Paysan-Lafosse, Typhaine, additional, Qureshi, Matloob, additional, Raj, Shriya, additional, Richardson, Lorna, additional, Salazar, Gustavo A, additional, Williams, Lowri, additional, Bork, Peer, additional, Bridge, Alan, additional, Gough, Julian, additional, Haft, Daniel H, additional, Letunic, Ivica, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Necci, Marco, additional, Orengo, Christine A, additional, Pandurangan, Arun P, additional, Rivoire, Catherine, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Wu, Cathy H, additional, Bateman, Alex, additional, and Finn, Robert D, additional

Published
2020
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11. Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health

Author

Jubb, Harry C., Pandurangan, Arun P., Turner, Meghan A., Ochoa-Montaño, Bernardo, Blundell, Tom L., Ascher, David B., Blundell, Tom [0000-0002-2708-8992], Ascher, David [0000-0003-2948-2413], and Apollo - University of Cambridge Repository

Subjects
Protein interaction, Biophysics, Genetic Diseases, Inborn, Proteins, Drug development, Health, Protein stability, Mutation, Humans, Molecular Targeted Therapy, Molecular Biology, Protein-protein interfaces, Mutations, Protein Binding
Abstract

Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance. The importance of these protein mutations has led to the development of many resources for understanding and predicting their effects. We propose that a better understanding of how these mutations affect the structure, function, and formation of multiprotein complexes provides novel opportunities for tackling them, including the development of small-molecule drugs targeted specifically to mutated PPIs.

Published
2017

12. InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Author

Mitchell, Alex L, primary, Attwood, Teresa K, additional, Babbitt, Patricia C, additional, Blum, Matthias, additional, Bork, Peer, additional, Bridge, Alan, additional, Brown, Shoshana D, additional, Chang, Hsin-Yu, additional, El-Gebali, Sara, additional, Fraser, Matthew I, additional, Gough, Julian, additional, Haft, David R, additional, Huang, Hongzhan, additional, Letunic, Ivica, additional, Lopez, Rodrigo, additional, Luciani, Aurélien, additional, Madeira, Fabio, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Necci, Marco, additional, Nuka, Gift, additional, Orengo, Christine, additional, Pandurangan, Arun P, additional, Paysan-Lafosse, Typhaine, additional, Pesseat, Sebastien, additional, Potter, Simon C, additional, Qureshi, Matloob A, additional, Rawlings, Neil D, additional, Redaschi, Nicole, additional, Richardson, Lorna J, additional, Rivoire, Catherine, additional, Salazar, Gustavo A, additional, Sangrador-Vegas, Amaia, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Sutton, Granger G, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Yong, Siew-Yit, additional, and Finn, Robert D, additional

Published
2018
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14. Correction: Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin

Author

Leung, Carl, primary, Dudkina, Natalya V, additional, Lukoyanova, Natalya, additional, Hodel, Adrian W, additional, Farabella, Irene, additional, Pandurangan, Arun P, additional, Jahan, Nasrin, additional, Damaso, Mafalda Pires, additional, Osmanović, Dino, additional, Reboul, Cyril F, additional, Dunstone, Michelle A, additional, Andrew, Peter W, additional, Lonnen, Rana, additional, Topf, Maya, additional, Saibil, Helen R, additional, and Hoogenboom, Bart W, additional

Published
2015
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15. Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin

Author

Leung, Carl, primary, Dudkina, Natalya V, additional, Lukoyanova, Natalya, additional, Hodel, Adrian W, additional, Farabella, Irene, additional, Pandurangan, Arun P, additional, Jahan, Nasrin, additional, Pires Damaso, Mafalda, additional, Osmanović, Dino, additional, Reboul, Cyril F, additional, Dunstone, Michelle A, additional, Andrew, Peter W, additional, Lonnen, Rana, additional, Topf, Maya, additional, Saibil, Helen R, additional, and Hoogenboom, Bart W, additional

Published
2014
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16. Author response: Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin

Author

Leung, Carl, primary, Dudkina, Natalya V, additional, Lukoyanova, Natalya, additional, Hodel, Adrian W, additional, Farabella, Irene, additional, Pandurangan, Arun P, additional, Jahan, Nasrin, additional, Pires Damaso, Mafalda, additional, Osmanović, Dino, additional, Reboul, Cyril F, additional, Dunstone, Michelle A, additional, Andrew, Peter W, additional, Lonnen, Rana, additional, Topf, Maya, additional, Saibil, Helen R, additional, and Hoogenboom, Bart W, additional

Published
2014
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17. Photo-antagonism of the GABAA receptor

Author

Mortensen, Martin, primary, Iqbal, Favaad, additional, Pandurangan, Arun P., additional, Hannan, Saad, additional, Huckvale, Rosemary, additional, Topf, Maya, additional, Baker, James R., additional, and Smart, Trevor G., additional

Published
2014
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20. InterPro: the protein sequence classification resource in 2025.

Author

Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, and Bateman A

Abstract

InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences into families and predict the presence of domains and significant sites. The InterPro database provides annotations for over 200 million sequences, ensuring extensive coverage of UniProtKB, the standard repository of protein sequences, and includes mappings to several other major resources, such as Gene Ontology (GO), Protein Data Bank in Europe (PDBe) and the AlphaFold Protein Structure Database. In this publication, we report on the status of InterPro (version 101.0), detailing new developments in the database, associated web interface and software. Notable updates include the increased integration of structures predicted by AlphaFold and the enhanced description of protein families using artificial intelligence. Over the past two years, more than 5000 new InterPro entries have been created. The InterPro website now offers access to 85 000 protein families and domains from its member databases and serves as a long-term archive for retired databases. InterPro data, software and tools are freely available., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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21. The InterPro protein families and domains database: 20 years on.

Author

Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, and Finn RD

Subjects
Amino Acid Sequence, COVID-19 metabolism, Internet, Molecular Sequence Annotation, Protein Domains, Protein Interaction Maps, SARS-CoV-2 metabolism, Sequence Alignment, Databases, Protein, Proteins chemistry
Abstract

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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22. Optopharmacology reveals a differential contribution of native GABA A receptors to dendritic and somatic inhibition using azogabazine.

Author

Mortensen M, Huckvale R, Pandurangan AP, Baker JR, and Smart TG

Subjects
Animals, Animals, Newborn, Cells, Cultured, Cerebellum drug effects, Cerebellum metabolism, Dendrites drug effects, Dose-Response Relationship, Drug, GABA-A Receptor Antagonists pharmacology, HEK293 Cells, Humans, Inhibitory Postsynaptic Potentials drug effects, Inhibitory Postsynaptic Potentials physiology, Protein Binding physiology, Rats, Rats, Sprague-Dawley, Dendrites metabolism, GABA-A Receptor Antagonists chemistry, GABA-A Receptor Antagonists metabolism, Optogenetics methods, Receptors, GABA-A chemistry, Receptors, GABA-A metabolism
Abstract

γ-aminobutyric acid type-A receptors (GABA A Rs) are inhibitory ligand-gated ion channels in the brain that are crucial for controlling neuronal excitation. To explore their physiological roles in cellular and neural network activity, it is important to understand why specific GABA A R isoforms are distributed not only to various brain regions and cell types, but also to specific areas of the membrane in individual neurons. To address this aim we have developed a novel photosensitive compound, azogabazine, that targets and reversibly inhibits GABA A Rs. The receptor selectivity of the compound is based on the competitive antagonist, gabazine, and photosensitivity is conferred by a photoisomerisable azobenzene group. Azogabazine can exist in either cis or trans conformations that are controlled by UV and blue light respectively, to affect receptor inhibition. We report that the trans-isomer preferentially binds and inhibits GABA A R function, whilst promotion of the cis-isomer caused unbinding of azogabazine from GABA A Rs. Using cultured cerebellar granule cells, azogabazine in conjunction with UV light applied to defined membrane domains, revealed higher densities of GABA A Rs at somatic inhibitory synapses compared to those populating proximal dendritic zones, even though the latter displayed a higher number of synapses per unit area of membrane. Azogabazine also revealed more pronounced GABA-mediated inhibition of action potential firing in proximal dendrites compared to the soma. Overall, azogabazine is a valuable addition to the photochemical toolkit that can be used to interrogate GABA A R function and inhibition., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2020
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23. InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Author

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, and Finn RD

Subjects
Animals, Databases, Genetic, Gene Ontology, Humans, Internet, Multigene Family, Protein Domains genetics, Sequence Homology, Amino Acid, Software, User-Computer Interface, Databases, Protein, Molecular Sequence Annotation
Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

Published
2019
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