ArticleThe Journal of biological chemistry2009
Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.
Article in The Journal of biological chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 49 citations in OpenAlex.
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- A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs.bioRxiv : the preprint server for biology · 2024Article
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- Activation of caspase-9 on the apoptosome as studied by methyl-TROSY NMR.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Dynamic remodeling of actin networks by cyclase-associated protein and CAP-Abp1 complexes.Current biology : CB · 2023Article
- Exploiting conformational dynamics to modulate the function of designed proteins.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- How a highly acidic SH3 domain folds in the absence of its charged peptide target.Protein science : a publication of the Protein Society · 2023Article
- Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning.PLoS computational biology · 2022Article
- Protein context shapes the specificity of SH3 domain-mediated interactions in vivo.Nature communications · 2021Article
- An Unbound Proline-Rich Signaling Peptide Frequently SamplesFrontiers in molecular biosciences · 2021Article
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres.Nature microbiology · 2019Article
- A multi-column plate adapter provides an economical and versatile high-throughput protein purification system.Protein expression and purification · 2018Article
- Article
- Exhaustive search of linear information encoding protein-peptide recognition.PLoS computational biology · 2017Article
- Article
- A semi-automated method for purification of milligram quantities of proteins on the QIAcube.Protein expression and purification · 2014Article
- Article
- PakB binds to the SH3 domain of Dictyostelium Abp1 and regulates its effects on cell polarity and early development.Molecular biology of the cell · 2013Article
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7 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite K(d) values for these peptides ranging from 0.3 to 6 mum. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell.
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