[HTML][HTML] The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome

NE Davey, L Simonetti, Y Ivarsson - Current opinion in structural biology, 2023 - Elsevier
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 …

Identifying new substrates and functions for an old enzyme: calcineurin

J Roy, MS Cyert - Cold Spring Harbor Perspectives in …, 2020 - cshperspectives.cshlp.org
Biological processes are dynamically regulated by signaling networks composed of protein
kinases and phosphatases. Calcineurin, or PP3, is a conserved phosphoserine …

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

C Benz, M Ali, I Krystkowiak, L Simonetti… - Molecular Systems …, 2022 - embopress.org
Specific protein–protein interactions are central to all processes that underlie cell
physiology. Numerous studies have together identified hundreds of thousands of human …

Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

T Kruse, C Benz, DH Garvanska, R Lindqvist… - Nature …, 2021 - nature.com
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host
factors. However, most current large-scale methods do not identify this important class of …

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease

L Ping, SR Kundinger, DM Duong, L Yin, M Gearing… - Scientific data, 2020 - nature.com
Alzheimer's disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in
which individuals exhibit amyloid-beta (Aβ) plaque accumulation in the absence of clinically …

The structural context of posttranslational modifications at a proteome-wide scale

I Bludau, S Willems, WF Zeng, MT Strauss… - PLoS …, 2022 - journals.plos.org
The recent revolution in computational protein structure prediction provides folding models
for entire proteomes, which can now be integrated with large-scale experimental data. Mass …

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

O Avram, D Rapoport, S Portugez… - Nucleic acids …, 2019 - academic.oup.com
Large-scale mining and analysis of bacterial datasets contribute to the comprehensive
characterization of complex microbial dynamics within a microbiome and among different …

Human VAPome analysis reveals MOSPD1 and MOSPD3 as membrane contact site proteins interacting with FFAT-related FFNT motifs

B Cabukusta, I Berlin, DM van Elsland, I Forkink… - Cell Reports, 2020 - cell.com
Membrane contact sites (MCS) are intracellular regions where two organelles come closer
to exchange information and material. The majority of the endoplasmic reticulum (ER) MCS …

Systematic discovery of short linear motifs decodes calcineurin phosphatase signaling

CP Wigington, J Roy, NP Damle, VK Yadav, C Blikstad… - Molecular cell, 2020 - cell.com
Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling,
but sequence degeneracy and low binding affinities make them difficult to identify. We …

PP1 and PP2A use opposite phospho-dependencies to control distinct processes at the kinetochore

RJ Smith, MH Cordeiro, NE Davey, G Vallardi… - Cell reports, 2019 - cell.com
Summary PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve
specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases …