ArticleProteins2009
Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis.The journal of physical chemistry. B · 2023Article
- Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations.Protein science : a publication of the Protein Society · 2022Article
- Article
- Sparse group selection and analysis of function-related residue for protein-state recognition.Journal of computational chemistry · 2022Article
- RNPS1 inhibits excessive tumor necrosis factor/tumor necrosis factor receptor signaling to support hematopoiesis in mice.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Molecular insights into the interaction of HPV-16 E6 variants against MAGI-1 PDZ1 domain.Scientific reports · 2022Article
- Allosterism in the PDZ Family.International journal of molecular sciences · 2022Review
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Landscape of drug-resistance mutations in kinase regulatory hotspots.Briefings in bioinformatics · 2021Article
- Allosteric Pathways Originating at Cysteine Residues in Regulators of G-Protein Signaling Proteins.Biophysical journal · 2021Article
- Phosphorylation-induced changes in the PDZ domain of Dishevelled 3.Scientific reports · 2021Article
- Transmembrane Polar Relay Drives the Allosteric Regulation for ABCG5/G8 Sterol Transporter.International journal of molecular sciences · 2020Article
- Real-time observation of ligand-induced allosteric transitions in a PDZ domain.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Spectral analysis of molecular dynamics simulations on PDZ: MD sectors.Journal of biomolecular structure & dynamics · 2020Article
- Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study.Computational and structural biotechnology journal · 2020Article
- The binding affinity of PTPN13's tandem PDZ2/3 domain is allosterically modulated.BMC molecular and cell biology · 2019Article
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.PLoS computational biology · 2019Article
- Engineering Allostery into Proteins.Advances in experimental medicine and biology · 2019Review
- REDAN: Relative Entropy-Based Dynamical Allosteric Network Model.Molecular physics · 2019Article
3 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane-associated protein complexes by binding to the carboxyl termini of their partners. PDZ domains are thought also to play a signal transduction role by propagating the information that binding has occurred to remote sites. In this study, a molecular dynamics (MD) simulation-based approach, referred to as an interaction correlation analysis, is applied to the PDZ2 domain to identify the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlations between all residue pairs obtained from the MD simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N-terminal side of helix alpha1 and the adjacent C-terminus of loop beta1-beta2. The other pathway is perpendicular to the central beta-sheet and extends toward the side of PDZ2 domain opposite to the ligand binding pocket. The results complement previous studies based on multiple sequence analysis, NMR, and MD simulations. Importantly, they reveal the energetic origin of the long-range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction.
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