metadata
language: en
license: cc-by-4.0
size_categories: …
pretty_name: Systematic Intracellular Motif-Binding Analysis
tags:
- chemistry
- biology
- DMS
- growth assay
- competitive growth
dataset_summary: >-
' Transient protein-protein interactions play key roles in controlling dynamic
cellular responses. Many examples involve globular protein domains that bind
to peptide sequences known as short linear motifs (SLiMs), which are enriched
in intrinsically disordered regions of proteins. Here we describe a novel
functional assay for measuring SLiM binding, called systematic intracellular
motif-binding analysis (SIMBA). In this method, binding of a foreign globular
domain to its cognate SLiM peptide allows yeast cells to proliferate by
blocking a growth arrest signal. A high-throughput application of the SIMBA
method involving competitive growth and deep sequencing provides rapid
quantification of the relative binding strength for thousands of SLiM sequence
variants and a comprehensive interrogation of SLiM sequence features that
control their recognition and potency. We show that multiple distinct classes
of SLiM-binding domains can be analyzed by this method and that the relative
binding strength of peptides in vivo correlates with their biochemical
affinities measured in vitro. Deep mutational scanning provides
high-resolution definitions of motif recognition determinants and reveals how
sequence variations at noncore positions can modulate binding strength.
Furthermore, mutational scanning of multiple parent peptides that bind human
tankyrase ARC or YAP WW domains identifies distinct binding modes and uncovers
context effects in which the preferred residues at one position depend on
residues elsewhere. The findings establish SIMBA as a fast and incisive
approach for interrogating SLiM recognition via massively parallel
quantification of protein-peptide binding strength in vivo. '
dataset_description: Deep Mutational Scanning data for short linear motifs
repo: https://data.mendeley.com/datasets/nghf59hf4s/2
citation_bibtex: >-
'@article{subbannaQuantitativeIntracellularPeptidebinding2025, title = {A
Quantitative Intracellular Peptide-Binding Assay Reveals Recognition
Determinants and Context Dependence of Short Linear Motifs}, author =
{Subbanna, Mythili S. and Winters, Matthew J. and {\"O}rd, Mihkel and Davey,
Norman E. and Pryciak, Peter M.}, year = 2025, month = mar, journal = {The
Journal of Biological Chemistry}, volume = {301}, number = {3}, pages =
{108225}, issn = {1083-351X}, doi = {10.1016/j.jbc.2025.108225}, abstract =
{Transient protein-protein interactions play key roles in controlling dynamic
cellular responses. Many examples involve globular protein domains that bind
to peptide sequences known as short linear motifs (SLiMs), which are enriched
in intrinsically disordered regions of proteins. Here we describe a novel
functional assay for measuring SLiM binding, called systematic intracellular
motif-binding analysis (SIMBA). In this method, binding of a foreign globular
domain to its cognate SLiM peptide allows yeast cells to proliferate by
blocking a growth arrest signal. A high-throughput application of the SIMBA
method involving competitive growth and deep sequencing provides rapid
quantification of the relative binding strength for thousands of SLiM sequence
variants and a comprehensive interrogation of SLiM sequence features that
control their recognition and potency. We show that multiple distinct classes
of SLiM-binding domains can be analyzed by this method and that the relative
binding strength of peptides in~vivo correlates with their biochemical
affinities measured in~vitro. Deep mutational scanning provides
high-resolution definitions of motif recognition determinants and reveals how
sequence variations at noncore positions can modulate binding strength.
Furthermore, mutational scanning of multiple parent peptides that bind human
tankyrase ARC or YAP WW domains identifies distinct binding modes and uncovers
context effects in which the preferred residues at one position depend on
residues elsewhere. The findings establish SIMBA as a fast and incisive
approach for interrogating SLiM recognition via massively parallel
quantification of protein-peptide binding strength in~vivo.}, langid =
{english}, pmcid = {PMC11879687}, pmid = {39864625}, keywords = {Amino Acid
Motifs,cyclin-dependent kinase (CDK),high-throughput screening
(HTS),Humans,intrinsically disordered protein,ligand-binding
protein,mutagenesis,peptides,Peptides,phosphorylation,Protein Binding,protein
motif,protein-protein interaction,Saccharomyces cerevisiae,Saccharomyces
cerevisiae Proteins,yeast} }'
citation_apa: >-
'Subbanna, M. S., Winters, M. J., Örd, M., Davey, N. E., & Pryciak, P. M.
(2025). A quantitative intracellular peptide-binding assay reveals recognition
determinants and context dependence of short linear motifs. The Journal of
biological chemistry, 301(3), 108225.
https://doi.org/10.1016/j.jbc.2025.108225'