ArticleProceedings of the National Academy of Sciences of the United States of America2015
Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Hydraulic Activation of the AsLOV2 Photoreceptor.bioRxiv : the preprint server for biology · 2025Article
- Capturing protein dynamics across timescales with site-directed spin labeling electron paramagnetic resonance spectroscopy.Current opinion in structural biology · 2025Review
- 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
- High-Pressure ESR Spectroscopy: On the Rotational Motion of Spin Probes in Pressurized Ionic Liquids.The journal of physical chemistry. B · 2022Article
- Energy penalties enhance flexible receptor docking in a model cavity.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- DEER Analysis of GPCR Conformational Heterogeneity.Biomolecules · 2021Review
- Oriented Soft DNA Curtains for Single-Molecule Imaging.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles.PLoS computational biology · 2021Article
- Viewing rare conformations of the βProceedings of the National Academy of Sciences of the United States of America · 2020Article
- How internal cavities destabilize a protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Void distributions reveal structural link between jammed packings and protein cores.Physical review. E · 2019Article
- Optimal Tikhonov regularization for DEER spectroscopy.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2018Article
- High-pressure EPR spectroscopy studies of theApplied magnetic resonance · 2017Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- 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
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6 authors.
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Abstract
Application of hydrostatic pressure shifts protein conformational equilibria in a direction to reduce the volume of the system. A current view is that the volume reduction is dominated by elimination of voids or cavities in the protein interior via cavity hydration, although an alternative mechanism wherein cavities are filled with protein side chains resulting from a structure relaxation has been suggested [López CJ, Yang Z, Altenbach C, Hubbell WL (2013) Proc Natl Acad Sci USA 110(46):E4306-E4315]. In the present study, mechanisms for elimination of cavities under high pressure are investigated in the L99A cavity mutant of T4 lysozyme and derivatives thereof using site-directed spin labeling, pressure-resolved double electron-electron resonance, and high-pressure circular dichroism spectroscopy. In the L99A mutant, the ground state is in equilibrium with an excited state of only ∼ 3% of the population in which the cavity is filled by a protein side chain [Bouvignies et al. (2011) Nature 477(7362):111-114]. The results of the present study show that in L99A the native ground state is the dominant conformation to pressures of 3 kbar, with cavity hydration apparently taking place in the range of 2-3 kbar. However, in the presence of additional mutations that lower the free energy of the excited state, pressure strongly populates the excited state, thereby eliminating the cavity with a native side chain rather than solvent. Thus, both cavity hydration and structure relaxation are mechanisms for cavity elimination under pressure, and which is dominant is determined by details of the energy landscape.
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