ArticleProceedings of the National Academy of Sciences of the United States of America2013
Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Rigid and stable nitroxide spin label for high-resolution distance measurements on proteins by DEER experiments.Magnetic resonance letters · 2025Article
- Modeling of Cu(II)-based protein spin labels using rotamer libraries.Physical chemistry chemical physics : PCCP · 2024Article
- Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme.Biochemistry · 2023Article
- Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble.ACS central science · 2022Article
- Temperature artifacts in protein structures bias ligand-binding predictions.Chemical science · 2021Article
- De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.Journal of chemical information and modeling · 2019Article
- Optimal Tikhonov regularization for DEER spectroscopy.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2018Article
- Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure.Biophysical journal · 2017Article
- Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics.Chemical science · 2017Article
- Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.Scientific reports · 2017Article
- A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2016Article
- Mapping transiently formed and sparsely populated conformations on a complex energy landscape.eLife · 2016Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy.Biochemistry · 2016Article
- The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins.eLife · 2016Article
- Investigating the position of the hairpin loop in New Delhi metallo-β-lactamase, NDM-1, during catalysis and inhibitor binding.Journal of inorganic biochemistry · 2016Article
- Multiple-site mutations of phage Bp7 endolysin improves its activities against target bacteria.Virologica Sinica · 2015Article
- Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.Biophysical journal · 2015Article
- Stationary-phase EPR for exploring protein structure, conformation, and dynamics in spin-labeled proteins.Biochemistry · 2014Article
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4 authors.
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Abstract
The studies presented here explore the relationship between protein packing and molecular flexibility using ligand-binding cavity mutants of T4 lysozyme. Although previously reported crystal structures of the mutants investigated show single conformations that are similar to the WT protein, site-directed spin labeling in solution reveals additional conformational substates in equilibrium exchange with a WT-like population. Remarkably, binding of ligands, including the general anesthetic halothane shifts the population to the WT-like state, consistent with a conformational selection model of ligand binding, but structural adaptation to the ligand is also apparent in one mutant. Distance mapping with double electron-electron resonance spectroscopy and the absence of ligand binding suggest that the new substates induced by the cavity-creating mutations represent alternate packing modes in which the protein fills or partially fills the cavity with side chains, including the spin label in one case; external ligands compete with the side chains for the cavity space, stabilizing the WT conformation. The results have implications for mechanisms of anesthesia, the response of proteins to hydrostatic pressure, and protein engineering.
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