ArticleBiophysical journal2015
Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Synaptic Physiology Depends on Electrical Forces and Liquid-Liquid Phase Separation.Reviews of physiology, biochemistry and pharmacology · 2025Review
- On the possibility of the existence of orienting hydrodynamic steering effects in the kinetics of receptor-ligand association.European biophysics journal : EBJ · 2023Review
- Different electrostatic forces drive the binding kinetics of SARS-CoV, SARS-CoV-2 and MERS-CoV Envelope proteins with the PDZ2 domain of ZO1.Scientific reports · 2023Article
- Dynamic stability of salt stable cowpea chlorotic mottle virus capsid protein dimers and pentamers of dimers.Scientific reports · 2022Article
- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
- Searching for Hydrodynamic Orienting Effects in the Association of Tri-The journal of physical chemistry. B · 2021Article
- Markov State Models to Elucidate Ligand Binding Mechanism.Methods in molecular biology (Clifton, N.J.) · 2021Review
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.Biophysical journal · 2020Article
- Structural mechanism for Bruton's tyrosine kinase activation at the cell membrane.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Atomic-level characterization of protein-protein association.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.Biophysical journal · 2018Article
- The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes.The Journal of biological chemistry · 2017Article
- Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models.Biophysical journal · 2017Article
- Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1.PLoS computational biology · 2017Article
- Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.Biophysical journal · 2016Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have captured the binding of a peptide to a PDZ domain by unbiased molecular dynamics simulations. Analysis of the trajectories reveals on-pathway encounter complex formation, which is driven by electrostatic interactions between negatively charged carboxylate groups in the peptide and positively charged side chains surrounding the binding site. In contrast, the final stereospecific complex, which matches the crystal structure, features completely different interactions, namely the burial of the hydrophobic side chain of the peptide C-terminal residue and backbone hydrogen bonds. The simulations show that nonnative salt bridges stabilize kinetically the encounter complex during binding. Unbinding follows the inverse sequence of events with the same nonnative salt bridges in the encounter complex. Thus, in contrast to protein folding, which is driven by native interactions, the binding of charged peptides can be steered by nonnative interactions, which might be a general mechanism, e.g., in the recognition of histone tails by bromodomains.
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