ArticleStructure (London, England : 1993)2016
Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.
Article in Structure (London, England : 1993), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Conformational Dynamics of the Active Site Loop in Dihydroorotase Highlighting the Limitations of Loop-In Structures for Inhibitor Docking.International journal of molecular sciences · 2025Article
- Metabolic profiling and antimicrobial activity ofFrontiers in pharmacology · 2025Article
- Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors.Nature communications · 2022Article
- The Non-continuum Nature of Eukaryotic Transcriptional Regulation.Advances in experimental medicine and biology · 2022Article
- A Fluorescence-Based Assay to Determine PDZ-Ligand Binding Thermodynamics.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Computational Design of PDZ-Peptide Binding.Methods in molecular biology (Clifton, N.J.) · 2021Article
- First High-Resolution Crystal Structures of the Glucocorticoid Receptor Ligand-Binding Domain-Peroxisome Proliferator-ActivatedMolecular pharmacology · 2019Article
- Conformational Dynamics and Cooperativity Drive the Specificity of a Protein-Ligand Interaction.Biophysical journal · 2019Article
- Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition.International review of cell and molecular biology · 2019Review
- Modulation of the HIV nucleocapsid dynamics finely tunes its RNA-binding properties during virion genesis.Nucleic acids research · 2018Article
- Article
- Bacillus subtilis exhibits MnmC-like tRNA modification activities.RNA biology · 2018Article
- A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.Frontiers in molecular biosciences · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.