ArticleThe journal of physical chemistry. B2014
Infinitely dilute partial molar properties of proteins from computer simulation.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 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
- Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations.Physical chemistry chemical physics : PCCP · 2021Article
- Influence of pH and Salts on Partial Molar Volume of Lysozyme and Bovine Serum Albumin in Aqueous Solutions.Chemical engineering & technology · 2018Article
- Simulated pressure denaturation thermodynamics of ubiquitin.Biophysical chemistry · 2017Article
- Particle and Energy Pair and Triplet Correlations in Liquids and Liquid Mixtures from Experiment and Simulation.The journal of physical chemistry. B · 2015Article
- Determination of partial molar volumes from free energy perturbation theory.Physical chemistry chemical physics : PCCP · 2015Article
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Authors and funding
2 authors.
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Abstract
A detailed understanding of temperature and pressure effects on an infinitely dilute protein's conformational equilibrium requires knowledge of the corresponding infinitely dilute partial molar properties. Established molecular dynamics methodologies generally have not provided a way to calculate these properties without either a loss of thermodynamic rigor, the introduction of nonunique parameters, or a loss of information about which solute conformations specifically contributed to the output values. Here we implement a simple method that is thermodynamically rigorous and possesses none of the above disadvantages, and we report on the method's feasibility and computational demands. We calculate infinitely dilute partial molar properties for two proteins and attempt to distinguish the thermodynamic differences between a native and a denatured conformation of a designed miniprotein. We conclude that simple ensemble average properties can be calculated with very reasonable amounts of computational power. In contrast, properties corresponding to fluctuating quantities are computationally demanding to calculate precisely, although they can be obtained more easily by following the temperature and/or pressure dependence of the corresponding ensemble averages.
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