Large-scale de novo DNA synthesis: technologies and applications

S Kosuri, GM Church - Nature methods, 2014 - nature.com
For over 60 years, the synthetic production of new DNA sequences has helped researchers
understand and engineer biology. Here we summarize methods and caveats for the de novo …

Modulating protein–protein interactions: the potential of peptides

L Nevola, E Giralt - Chemical Communications, 2015 - pubs.rsc.org
Protein–protein interactions (PPIs) have emerged as important and challenging targets in
chemical biology and medicinal chemistry. The main difficulty encountered in the discovery …

ELM 2016—data update and new functionality of the eukaryotic linear motif resource

H Dinkel, K Van Roey, S Michael, M Kumar… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Eukaryotic Linear Motif (ELM) resource (http://elm. eu. org) is a manually
curated database of short linear motifs (SLiMs). In this update, we present the latest …

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 …

Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson's disease

S Nim, DM O'Hara, C Corbi-Verge… - Nature …, 2023 - nature.com
Accumulation of α-synuclein into toxic oligomers or fibrils is implicated in dopaminergic
neurodegeneration in Parkinson's disease. Here we performed a high-throughput, proteome …

Short linear motifs – ex nihilo evolution of protein regulation

NE Davey, MS Cyert, AM Moses - Cell Communication and Signaling, 2015 - Springer
Short sequence motifs are ubiquitous across the three major types of biomolecules:
hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs …

[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 …

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 …

Scribble: A master scaffold in polarity, adhesion, synaptogenesis, and proliferation

TT Bonello, M Peifer - Journal of Cell Biology, 2019 - rupress.org
Key events ranging from cell polarity to proliferation regulation to neuronal signaling rely on
the assembly of multiprotein adhesion or signaling complexes at particular subcellular sites …

[HTML][HTML] On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins

K Lindorff-Larsen, BB Kragelund - Journal of Molecular Biology, 2021 - Elsevier
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and
many diverging properties. IDPs—and intrinsically disordered regions (IDRs) interspersed …