ArticleNature communications2022
Atomic resolution protein allostery from the multi-state structure of a PDZ domain.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 31 citations in OpenAlex.
- AlloPool is a deep learning framework that infers protein allostery from molecular dynamics simulations.PLoS biology · 2026Article
- The planar cell polarity protein Vangl2 interacts with the PDZ-domains of Scribble but not with a unique PDZ-like domain in Inturned.FEBS letters · 2026Article
- Newton's cradle-like allosteric mechanism explains regulatory RsmE RNA binding.Nature communications · 2026Article
- Restraining Interproton Angular and Distance Dynamics with KEnRef.The journal of physical chemistry. B · 2026Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Dynamic networks connect the USP14 active site region with the proteasome interaction surface.Protein science : a publication of the Protein Society · 2025Article
- Biophysical and structural analyses of the interaction between the SHANK1 PDZ domain and an internal SLiM.The Biochemical journal · 2024Article
- Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR.Journal of the American Chemical Society · 2024Article
- Functional protein dynamics in a crystal.Nature communications · 2024Article
- Functional Protein Dynamics in a Crystal.bioRxiv : the preprint server for biology · 2024Article
- A Modified Tridecapeptide Probe for Imaging Cell Junction.Molecules (Basel, Switzerland) · 2024Article
- Ultrafast Fragment Screening Using Photo-Hyperpolarized (CIDNP) NMR.Journal of the American Chemical Society · 2023Article
- MDiGest: A Python package for describing allostery from molecular dynamics simulations.The Journal of chemical physics · 2023Article
- Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-Cell NMR.Angewandte Chemie (International ed. in English) · 2023Article
- Protein dynamics: The future is bright and complicated!Structural dynamics (Melville, N.Y.) · 2023Article
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Authors and funding
13 authors at 4 institutions in 5 countries.
Funding
Abstract
Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally and dynamically correlated protein sites at atomic resolution. This is demonstrated in the present work for the well-studied PDZ2 domain of protein human tyrosine phosphatase 1E for which protein allostery had been predicted. Two-state protein structures were calculated for both the free form and in complex with the RA-GEF2 peptide using the exact nuclear Overhauser effect (eNOE) method. In the apo protein, an allosteric conformational selection step comprising almost 60% of the domain was detected with an "open" ligand welcoming state and a "closed" state that obstructs the binding site by changing the distance between the β-sheet 2, α-helix 2, and sidechains of residues Lys38 and Lys72. The observed induced fit-type apo-holo structural rearrangements are in line with the previously published evolution-based analysis covering ~25% of the domain with only a partial overlap with the protein allostery of the open form. These presented structural studies highlight the presence of a dedicated highly optimized and complex dynamic interplay of the PDZ2 domain owed by the structure-dynamics landscape.
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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.