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Protein-solvent interactions and classical density functional theory Mills, Eric A
Abstract
We use classical density functional theory to investigate the interactions between solvents and proteins. We examine a diverse experimental literature to establish thermodynamic properties of protein-cosolute interaction, particularly the compensation between transfer entropy and transfer enthalpy. We develop a method of analysing the uncertainties in such measurements and use the method to resolve a long-standing debate over entropy-enthalpy compensation. We develop a classical density functional theory for interactions between proteins and cosolutes. The theory developed here ignores the solvent-solvent interaction but is nonetheless quite accurate. We use this approach to reproduce transfer free energies reported elsewhere, and show that the cDFT model captures the desolvation barrier and the temperature dependence of the transfer free energy. We use experimental values that we have analyzed to define the parameter space of a model density functional theory approach. We then extend the classical density functional theory to capture protein-water interactions, thus developing a new implicit solvent model. Along the way we give a proof that the free energy of a bath of particles in a finite external potential is independent of the external potential in the isothermal-isobaric ensemble. We finally discuss the challenges remaining in implementing our implicit solvent model.
Item Metadata
Title |
Protein-solvent interactions and classical density functional theory
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Creator | |
Publisher |
University of British Columbia
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Date Issued |
2015
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Description |
We use classical density functional theory to investigate the interactions between solvents and proteins. We examine a diverse experimental literature to establish thermodynamic properties of protein-cosolute interaction, particularly the compensation between transfer entropy and transfer enthalpy. We develop a method of analysing the uncertainties in such measurements and use the method to resolve a long-standing debate over entropy-enthalpy compensation. We develop a classical density functional theory for interactions between proteins and cosolutes. The theory developed here ignores the solvent-solvent interaction but is nonetheless quite accurate. We use this approach to reproduce transfer free energies reported elsewhere, and show that the cDFT model captures the desolvation barrier and the temperature dependence of the transfer free energy. We use experimental values that we have analyzed to define the parameter space of a model density functional theory approach. We then extend the classical density functional theory to capture protein-water interactions, thus developing a new implicit solvent model. Along the way we give a proof that the free energy of a bath of particles in a finite external potential is independent of the external potential in the isothermal-isobaric ensemble. We finally discuss the challenges remaining in implementing our implicit solvent model.
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Genre | |
Type | |
Language |
eng
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Date Available |
2015-12-09
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution-NonCommercial-NoDerivs 2.5 Canada
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DOI |
10.14288/1.0221256
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URI | |
Degree | |
Program | |
Affiliation | |
Degree Grantor |
University of British Columbia
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Graduation Date |
2016-02
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Campus | |
Scholarly Level |
Graduate
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Rights URI | |
Aggregated Source Repository |
DSpace
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Rights
Attribution-NonCommercial-NoDerivs 2.5 Canada