ArticleBiophysical journal2015
Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme.
Article in Biophysical journal, 2015. 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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22 citing papers in PubMed, 41 citations in OpenAlex.
- Damping amyloid-associated conformational fluctuations in a protein by an engineered diselenide bridge.Protein science : a publication of the Protein Society · 2026Article
- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins.Protein science : a publication of the Protein Society · 2024Article
- A pressure-jump EPR system to monitor millisecond conformational exchange rates of spin-labeled proteins.bioRxiv : the preprint server for biology · 2024Article
- Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme.Biochemistry · 2023Article
- Pressure, motion, and conformational entropy in molecular recognition by proteins.Biophysical reports · 2023Article
- Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR.Proteins · 2021Article
- How internal cavities destabilize a protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.The journal of physical chemistry. B · 2019Article
- Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins.Current opinion in structural biology · 2019Review
- Water-Protein Interactions Coupled with Protein Conformational Transition.Biophysical journal · 2018Article
- Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology.Methods (San Diego, Calif.) · 2018Article
- The consequences of cavity creation on the folding landscape of a repeat protein depend upon context.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Net Evolutionary Loss of Residue Polarity in Drosophilid Protein Cores Indicates Ongoing Optimization of Amino Acid Composition.Genome biology and evolution · 2017Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- Determinants of neuroglobin plasticity highlighted by joint coarse-grained simulations and high pressure crystallography.Scientific reports · 2017Article
- Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A.Biophysical journal · 2016Article
- Water Determines the Structure and Dynamics of Proteins.Chemical reviews · 2016Review
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Detecting O2 binding sites in protein cavities.Scientific reports · 2016Article
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Authors and funding
9 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins are manifested by their corresponding amino acid sequences, the natural rules for molecular design and their corresponding interplay remain obscure. In this study, we focused on the role of internal cavities of proteins in conformational dynamics. We investigated the pressure-induced responses from the cavity-enlarged L99A mutant of T4 lysozyme, using high-pressure NMR spectroscopy. The signal intensities of the methyl groups in the (1)H/(13)C heteronuclear single quantum correlation spectra, particularly those around the enlarged cavity, decreased with the increasing pressure, and disappeared at 200 MPa, without the appearance of new resonances, thus indicating the presence of heterogeneous conformations around the cavity within the ground state ensemble. Above 200 MPa, the signal intensities of >20 methyl groups gradually decreased with the increasing pressure, without the appearance of new resonances. Interestingly, these residues closely matched those sensing a large conformational change between the ground- and high-energy states, at atmospheric pressure. (13)C and (1)H NMR line-shape simulations showed that the pressure-induced loss in the peak intensity could be explained by the increase in the high-energy state population. In this high-energy state, the aromatic side chain of F114 gets flipped into the enlarged cavity. The accommodation of the phenylalanine ring into the efficiently packed cavity may decrease the partial molar volume of the high-energy state, relative to the ground state. We suggest that the enlarged cavity is involved in the conformational transition to high-energy states and in the volume fluctuation of the ground state.
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