ArticleThe Journal of biological chemistry2010
Role of interfacial water molecules in proline-rich ligand recognition by the Src homology 3 domain of Abl.
Article in The Journal of biological chemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 34 citations in OpenAlex.
- DyME: An MD-based engine exploiting HTP mutagenesis for protein engineering and recognition mimicry.PLoS computational biology · 2026Article
- Understanding domain swapping in the c-Src SH3 domain through hinge-loop mutagenesis.Acta crystallographica. Section D, Structural biology · 2025Article
- Exploring the druggability of the UEV domain of human TSG101 in search for broad-spectrum antivirals.Protein science : a publication of the Protein Society · 2025Article
- A Systematic Compilation of Human SH3 Domains: A Versatile Superfamily in Cellular Signaling.Cells · 2023Review
- Entropy Hotspots for the Binding of Intrinsically Disordered Ligands to a Receptor Domain.Biophysical journal · 2020Article
- Rapid Quantification of Protein-Ligand Binding viaBiophysical journal · 2020Article
- Binding site plasticity in viral PPxY Late domain recognition by the third WW domain of human NEDD4.Scientific reports · 2019Article
- The role of water molecules in the binding of class I and II peptides to the SH3 domain of the Fyn tyrosine kinase.Acta crystallographica. Section F, Structural biology communications · 2016Article
- Binding Mechanism of the N-Terminal SH3 Domain of CrkII and Proline-Rich Motifs in cAbl.Biophysical journal · 2016Article
- From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.PLoS computational biology · 2016Article
- Molecular origin of the binding of WWOX tumor suppressor to ErbB4 receptor tyrosine kinase.Biochemistry · 2013Article
- Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations.Journal of chemical information and modeling · 2013Article
- Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms.Journal of molecular recognition : JMRArticle
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interaction of Abl-Src homology 3 domain (SH3) with the high affinity peptide p41 is the most notable example of the inconsistency existing between the currently accepted description of SH3 complexes and their binding thermodynamic signature. We had previously hypothesized that the presence of interfacial water molecules is partially responsible for this thermodynamic behavior. We present here a thermodynamic, structural, and molecular dynamics simulation study of the interaction of p41 with Abl-SH3 and a set of mutants designed to alter the water-mediated interaction network. Our results provide a detailed description of the dynamic properties of the interfacial water molecules and a molecular interpretation of the thermodynamic effects elicited by the mutations in terms of the modulation of the water-mediated hydrogen bond network. In the light of these results, a new dual binding mechanism is proposed that provides a better description of proline-rich ligand recognition by Abl-SH3 and that has important implications for rational design.
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