ArticleProtein science : a publication of the Protein Society2010
Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 40 citations in OpenAlex.
- Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics.Annual review of biophysics · 2023Review
- 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
- Mutagenic Activation of Glutathione Peroxidase-4: Approaches toward Rational Design of Allosteric Drugs.ACS omega · 2022Article
- Article
- Allosterism in the PDZ Family.International journal of molecular sciences · 2022Review
- Phosphorylation of SNX27 by MAPK11/14 links cellular stress-signaling pathways with endocytic recycling.The Journal of cell biology · 2021Article
- Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage.The protein journal · 2020Article
- "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations.Scientific reports · 2018Article
- Seeking allosteric networks in PDZ domains.Protein engineering, design & selection : PEDS · 2018Review
- Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling.Journal of biosciences · 2018Review
- Hidden electrostatic basis of dynamic allostery in a PDZ domain.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.Journal of molecular evolution · 2017Article
- Investigating Dynamic Interdomain Allostery in Pin1.Biophysical reviews · 2015Article
- Ligand-induced dynamic changes in extended PDZ domains from NHERF1.Journal of molecular biology · 2013Article
- Plasticity of PDZ domains in ligand recognition and signaling.FEBS letters · 2012Review
- Beyond the binding site: the role of the β₂-β₃ loop and extra-domain structures in PDZ domains.PLoS computational biology · 2012Article
- Combining NMR and molecular dynamics studies for insights into the allostery of small GTPase-protein interactions.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning.PLoS computational biology · 2011Review
- Sequence-specific long range networks in PSD-95/discs large/ZO-1 (PDZ) domains tune their binding selectivity.The Journal of biological chemistry · 2011Article
- Protein binding specificity versus promiscuity.Current opinion in structural biology · 2011Review
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2 authors at 1 institution in 1 country.
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Abstract
Single-domain allostery has been postulated to occur through intramolecular pathways of signaling within a protein structure. We had previously investigated these pathways by introducing a local thermal perturbation and analyzed the anisotropic propagation of structural changes throughout the protein. Here, we develop an improved approach, the Rotamerically Induced Perturbation (RIP), that identifies strong couplings between residues by analyzing the pathways of heat-flow resulting from thermal excitation of rotameric rotations at individual residues. To explore the nature of these couplings, we calculate the complete coupling maps of 5 different PDZ domains. Although the PDZ domain is a well conserved structural fold that serves as a scaffold in many protein-protein complexes, different PDZ domains display unique patterns of conformational flexibility in response to ligand binding: some show a significant shift in a set of alpha-helices, while others do not. Analysis of the coupling maps suggests a simple relationship between the computed couplings and observed conformational flexibility. In domains where the alpha-helices are rigid, we find couplings of the alpha-helices to the body of the protein, whereas in domains having ligand-responsive alpha-helices, no couplings are found. This leads to a model where the alpha-helices are intrinsically dynamic but can be damped if sidechains interact at key tertiary contacts. These tertiary contacts correlate to high covariation contacts as identified by the statistical coupling analysis method. As these dynamic modules are exploited by various allosteric mechanisms, these tertiary contacts have been conserved by evolution.
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