ArticleBiophysical chemistry2017
Simulated pressure denaturation thermodynamics of ubiquitin.
Article in Biophysical chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Probing Contributions to the Volume and Isothermal Compressibility of Globular Proteins Using a Fluctuation Solution Theory Analysis of MD Simulations.The journal of physical chemistry. B · 2025Article
- Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes.Biophysical chemistry · 2024Article
- Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Applications of KBFF20.Journal of chemical theory and computation · 2021Article
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2 authors.
Funding
Abstract
Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.
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