تقرير
Density Functional Theory for Protein Transfer Free Energy
| العنوان: | Density Functional Theory for Protein Transfer Free Energy |
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| المؤلفون: | Mills, Eric A, Plotkin, Steven S |
| سنة النشر: | 2013 |
| المجموعة: | Condensed Matter Physics (Other) Quantitative Biology |
| مصطلحات موضوعية: | Quantitative Biology - Biomolecules, Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics |
| الوصف: | We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible surface area, and temperature-dependence of the transfer free energy all emerge naturally within this formalism, and may be compared with simplified "back of the envelope" models, which are also developed here. Depletion contributions to osmolyte induced stability range from 5-$10\kB T$ for typical protein lengths. The general DFT transfer theory developed here may be simplified to reproduce a Langmuir isotherm condensation mechanism on the protein surface in the limits of short-ranged interactions, and dilute solute. Extending the equation of state to higher solute densities results in non-monotonic behavior of the free energy driving protein or polymer collapse. Effective interaction potentials between protein backbone or sidechains and TMAO are obtained, assuming a simple backbone/sidechain 2-bead model for the protein with an effective 6-12 potential with the osmolyte. The transfer free energy $\delta g$ shows significant entropy: $d(\delta g)/dT \approx 20 \kB$ for a 100 residue protein. The application of DFT to effective solvent forces for use in implicit-solvent molecular dynamics is also developed. The simplest DFT expressions for implicit-solvent forces contain both depletion interactions and an "impeded-solvation" repulsive force at larger distances. Comment: 41 pages, 5 figures, 3 tables |
| نوع الوثيقة: | Working Paper |
| DOI: | 10.1021/jp403600q |
| URL الوصول: | http://arxiv.org/abs/1310.1126 |
| رقم الأكسشن: | edsarx.1310.1126 |
| قاعدة البيانات: | arXiv |
| DOI: | 10.1021/jp403600q |
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