ArticleBiophysical journal2006
Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- A Perspective on Interdicting in Protein Misfolding for Therapeutic Drug Design: Modulating the Formation of Nonlocal Contacts in α-Synuclein as a Strategy against Parkinson's Disease.The journal of physical chemistry. B · 2024Review
- Turn-On Protein Switches for Controlling Actin Binding in Cells.bioRxiv : the preprint server for biology · 2023Article
- Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules.Journal of the American Chemical Society · 2020Article
- Two-site recognition of Staphylococcus aureus peptidoglycan by lysostaphin SH3b.Nature chemical biology · 2020Article
- Dynamic structure of the full-length scaffolding protein NHERF1 influences signaling complex assembly.The Journal of biological chemistry · 2019Article
- Optimal Affinity Enhancement by a Conserved Flexible Linker Controls p53 Mimicry in MdmX.Biophysical journal · 2017Article
- The light chains of kinesin-1 are autoinhibited.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Imaging and manipulating proteins in live cells through covalent labeling.Nature chemical biology · 2015Article
- A semi-automated method for purification of milligram quantities of proteins on the QIAcube.Protein expression and purification · 2014Article
- Identification of minimally interacting modules in an intrinsically disordered protein.Biophysical journal · 2012Article
- Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex.PLoS computational biology · 2011Article
- Tuning protein autoinhibition by domain destabilization.Nature structural & molecular biology · 2011Article
- Affinity, avidity, and kinetics of target sequence binding to LC8 dynein light chain isoforms.The Journal of biological chemistry · 2010Article
- Theory of free energy and entropy in noncovalent binding.Chemical reviews · 2009Review
- Internal regulatory interactions determine DNA binding specificity by a Hox transcription factor.Journal of molecular biology · 2009Article
- Receptor-associated protein (RAP) has two high-affinity binding sites for the low-density lipoprotein receptor-related protein (LRP): consequences for the chaperone functions of RAP.The Biochemical journal · 2009Article
- Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins.Biophysical journal · 2009Article
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1 author.
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Abstract
Flexible linkers are often found to tether binding sequence motifs or connect protein domains. Here we analyze three usages of flexible linkers: 1), intramolecular binding of proline-rich peptides (PRPs) to SH3 domains for kinase regulation; 2), intramolecular binding of PRP for increasing the folding stability of SH3 domains; and 3), covalent linking of PRPs and other ligands for high-affinity bivalent binding. The basis of these analyses is a quantitative relation between intermolecular and intramolecular binding constants. This relation has the form K(i) = K(e0)p for intramolecular binding and K(e) = K(e01)K(e02)p for bivalent binding. The effective concentration p depends on the length of the linker and the distance between the linker attachment points in the bound state. Several applications illustrate the usefulness of the quantitative relation. These include intramolecular binding to the Itk SH3 domain by an internal PRP and to a circular permutant of the alpha-spectrin SH3 domain by a designed PRP, and bivalent binding to the two SH3 domains of Grb2 by two linked PRPs. These and other examples suggest that flexible linkers and sequence motifs tethered to them, like folded protein domains, are also subject to tight control during evolution.
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