Browsing by author "Davey, Norman"
Now showing items 1-20 of 25
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A screen for novel targets casts polyphosphorylation of lysine as a common post-translational modification
Bentley-DeSousa, A; Moteshareie, H; Holinier, C; Tseng, Y-C; Bondy-Chorney, E; et al. (2018-04) -
An intrinsically disordered proteins community for ELIXIR
Davey, N; Babu, M; Blackledge, M; Bridge, A; Capella-Gutierrez, S; et al. (2019-10-15)Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments ... -
Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo.
Bandyopadhyay, S; Bhaduri, S; Örd, M; Davey, NE; Loog, M; et al. (CELL PRESS, 2020-11-16)Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking ... -
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.
Quaglia, F; Mészáros, B; Salladini, E; Hatos, A; Pancsa, R; et al. (OXFORD UNIV PRESS, 2022-01-07)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 ... -
DisProt: intrinsic protein disorder annotation in 2020.
Hatos, A; Hajdu-Soltész, B; Monzon, AM; Palopoli, N; Álvarez, L; et al. (OXFORD UNIV PRESS, 2020-01-08)The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version ... -
ELM-the eukaryotic linear motif resource in 2020.
Kumar, M; Gouw, M; Michael, S; Sámano-Sánchez, H; Pancsa, R; et al. (OXFORD UNIV PRESS, 2020-01-08)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 ... -
ELM-the Eukaryotic Linear Motif resource-2024 update.
Kumar, M; Michael, S; Alvarado-Valverde, J; Zeke, A; Lazar, T; et al. (OXFORD UNIV PRESS, 2024-01-05)Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant, especially when considering post-translational modifications. As well as ... -
ELM: the status of the 2010 eukaryotic linear motif resource.
Gould, CM; Diella, F; Via, A; Puntervoll, P; Gemünd, C; et al. (OXFORD UNIV PRESS, 2010-01-01)Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. ... -
A functional interaction between liprin-α1 and B56γ regulatory subunit of protein phosphatase 2A supports tumor cell motility.
Ripamonti, M; Lamarca, A; Davey, NE; Tonoli, D; Surini, S; et al. (NATURE PORTFOLIO, 2022-09-28)Scaffold liprin-α1 is required to assemble dynamic plasma membrane-associated platforms (PMAPs) at the front of migrating breast cancer cells, to promote protrusion and invasion. We show that the N-terminal region of ... -
Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs.
Mihalič, F; Simonetti, L; Giudice, G; Sander, MR; Lindqvist, R; et al. (NATURE PORTFOLIO, 2023-04-26)Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic ... -
Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions.
Kliche, J; Garvanska, DH; Simonetti, L; Badgujar, D; Dobritzsch, D; et al. (WILEY, 2023-07-11)Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified ... -
MobiDB: intrinsically disordered proteins in 2021.
Piovesan, D; Necci, M; Escobedo, N; Monzon, AM; Hatos, A; et al. (OXFORD UNIV PRESS, 2021-01-08)The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, ... -
The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome.
Davey, NE; Simonetti, L; Ivarsson, Y (CURRENT BIOLOGY LTD, 2023-06-01)Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have ... -
Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification.
Hein, JB; Nguyen, HT; Garvanska, DH; Nasa, I; Kruse, T; et al. (SPRINGERNATURE, 2023-12-06)Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop ... -
Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1).
Balasuriya, N; Davey, NE; Johnson, JL; Liu, H; Biggar, KK; et al. (AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2020-06-12)Protein kinase B (AKT1) is a central node in a signaling pathway that regulates cell survival. The diverse pathways regulated by AKT1 are communicated in the cell via the phosphorylation of perhaps more than 100 cellular ... -
PP1 and PP2A Use Opposite Phospho-dependencies to Control Distinct Processes at the Kinetochore.
Smith, RJ; Cordeiro, MH; Davey, NE; Vallardi, G; Ciliberto, A; et al. (CELL PRESS, 2019-08-20)PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases localize to an almost identical molecular space and ... -
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.
Benz, C; Ali, M; Krystkowiak, I; Simonetti, L; Sayadi, A; et al. (WILEY, 2022-01-01)Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many ... -
SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1.
Sebaa, R; Johnson, J; Pileggi, C; Norgren, M; Xuan, J; et al. (ELSEVIER SCIENCE BV, 2019-07-01)OBJECTIVE: Brown adipose tissue (BAT) is important for thermoregulation in many mammals. Uncoupling protein 1 (UCP1) is the critical regulator of thermogenesis in BAT. Here we aimed to investigate the deacetylation control ... -
SLiM-binding pockets: an attractive target for broad-spectrum antivirals.
Simonetti, L; Nilsson, J; McInerney, G; Ivarsson, Y; Davey, NE (CELL PRESS, 2023-01-07)Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively ... -
A structural biology community assessment of AlphaFold2 applications.
Akdel, M; Pires, DEV; Pardo, EP; Jänes, J; Zalevsky, AO; et al. (Springer Science and Business Media LLC, 2022-11-01)Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the ...