ArticleJournal of molecular biology2011
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- PICK1 links KIBRA and AMPA receptor subunit GluA2 in coiled-coil-driven supramolecular complexes.The Journal of biological chemistry · 2025Article
- AMPA Receptors in Synaptic Plasticity, Memory Function, and Brain Diseases.Cellular and molecular neurobiology · 2025Review
- Molecular Dynamics Reveal Key Steps in BAR-Related Membrane Remodeling.Pathogens (Basel, Switzerland) · 2024Article
- Unconventional PDZ Recognition Revealed in α7 nAChR-PICK1 Complexes.ACS chemical neuroscience · 2024Article
- Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Down-regulation of diesel particulate matter-induced airway inflammation by the PDZ motif peptide of ZO-1.Journal of cellular and molecular medicine · 2020Article
- Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7.Protein science : a publication of the Protein Society · 2020Article
- Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces.Frontiers in molecular biosciences · 2020Article
- The Regulation of AMPA Receptor Endocytosis by Dynamic Protein-Protein Interactions.Frontiers in cellular neuroscience · 2018Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
- Membrane Binding and Modulation of the PDZ Domain of PICK1.Membranes · 2015Review
- Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.Structure (London, England : 1993) · 2015Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field.Journal of molecular modeling · 2015Article
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- The power of coarse graining in biomolecular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2014Article
- Membrane sculpting by F-BAR domains studied by molecular dynamics simulations.PLoS computational biology · 2013Article
- Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.Journal of chemical theory and computation · 2012Article
- Coexistence of phases in a protein heterodimer.The Journal of chemical physics · 2012Article
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4 authors.
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Abstract
A key regulator of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor traffic, PICK1 is known to interact with over 40 other proteins, including receptors, transporters and ionic channels, and to be active mostly as a homodimer. The current lack of a complete PICK1 structure determined at atomic resolution hinders the elucidation of its functional mechanisms. Here, we identify interactions between the component PDZ and BAR domains of PICK1 by calculating possible binding sites for the PDZ domain of PICK1 (PICK1-PDZ) to the homology-modeled, crescent-shaped dimer of the PICK1-BAR domain using multiplexed replica-exchange molecular dynamics (MREMD) and canonical molecular dynamics simulations with the coarse-grained UNRES force field. The MREMD results show that the preferred binding site for the single PDZ domain is the concave cavity of the BAR dimer. A second possible binding site is near the N-terminus of the BAR domain that is linked directly to the PDZ domain. Subsequent short canonical molecular dynamics simulations used to determine how the PICK1-PDZ domain moves to the preferred binding site on the BAR domain of PICK1 revealed that initial hydrophobic interactions drive the progress of the simulated binding. Thus, the concave face of the BAR dimer accommodates the PDZ domain first by weak hydrophobic interactions and then the PDZ domain slides to the center of the concave face, where more favorable hydrophobic interactions take over.
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