ArticleScientific reports2016
Detecting O2 binding sites in protein cavities.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- A Perspective on the Applications of Triphasic Gas Storage in Electrochemical Systems.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- Hidden route of protein damage through oxygen-confined photooxidation.Nature communications · 2024Article
- How internal cavities destabilize a protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.Biophysical journal · 2019Article
- On identifying collective displacements in apo-proteins that reveal eventual binding pathways.PLoS computational biology · 2019Article
- Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme.PLoS computational biology · 2018Article
- Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.Biophysical journal · 2018Article
- Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities.Protein science : a publication of the Protein Society · 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
- Analysis of OBiophysical journal · 2017Article
- Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.Biophysical journal · 2016Article
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5 authors.
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Abstract
Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in (1)H, (15)N, and (13)C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.
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