ArticleNature communications2023
Ligand-specific changes in conformational flexibility mediate long-range allostery in the lac repressor.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Distinct energetic blueprints diversify function of conserved protein folds.Nature chemistry · 2026Article
- Article
- HXMS: a standardized file format for HX-MS data.Bioinformatics (Oxford, England) · 2026Article
- The Power of Protein Dynamics in Binding and Allostery.Biochemistry · 2026Review
- Bidirectional allosteric ligand regulation in a central glycolytic enzyme.bioRxiv : the preprint server for biology · 2026Article
- Site-resolved energetic information from HX-MS experiments.Nature chemical biology · 2026Article
- Loop dynamics, allostery, and function in protein tyrosine phosphatases: insights from molecular simulations.Biochemical Society transactions · 2026Review
- Computational design of dynamic biosensors for emerging synthetic opioids.Nature communications · 2026Article
- Computational design of allulose-responsive biosensor toolbox for auto-inducible protein expression and CRISPRi mediated dynamic metabolic regulation.Nature communications · 2025Article
- HDX-MS reveals pH and temperature-responsive regions on AAV capsids and the structural basis for DNA release.Gene therapy · 2025Article
- Global comparative structural analysis of responses to protein phosphorylation.Nature communications · 2025Article
- HXMS: a standardized file format for HX/MS data.bioRxiv : the preprint server for biology · 2025Article
- The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.Journal of molecular biology · 2025Review
- Molecular Insights into the Temperature-Dependent Binding and Conformational Dynamics of Noraucuparin with Bovine Serum Albumin: A Microsecond-Scale MD Simulation Study.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Computational design of dynamic biosensors for emerging synthetic opioids.bioRxiv : the preprint server for biology · 2025Article
- Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS.Protein science : a publication of the Protein Society · 2024Article
- Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis.Nature communications · 2024Article
- Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry.International journal of mass spectrometry · 2024Article
- Structural dynamics of NaCommunications biology · 2024Article
- Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes.Biophysical chemistry · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Biological regulation ubiquitously depends on protein allostery, but the regulatory mechanisms are incompletely understood, especially in proteins that undergo ligand-induced allostery with few structural changes. Here we used hydrogen-deuterium exchange with mass spectrometry (HDX/MS) to map allosteric effects in a paradigm ligand-responsive transcription factor, the lac repressor (LacI), in different functional states (apo, or bound to inducer, anti-inducer, and/or DNA). Although X-ray crystal structures of the LacI core domain in these states are nearly indistinguishable, HDX/MS experiments reveal widespread differences in flexibility. We integrate these results with modeling of protein-ligand-solvent interactions to propose a revised model for allostery in LacI, where ligand binding allosterically shifts the conformational ensemble as a result of distinct changes in the rigidity of secondary structures in the different states. Our model provides a mechanistic basis for the altered function of distal mutations. More generally, our approach provides a platform for characterizing and engineering protein allostery.
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