利用沃羅諾伊單元分佈建立胺基酸水溶液熵組態

藍長風

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利用沃羅諾伊單元分佈建立胺基酸水溶液熵組態

Entropy configuration of amino acid solvent system with Voronoi cell distribution

藍長風 , Masters　　Advisor：廖明淵　　Co-advisor ：李豐穎

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沃羅諾伊鑲嵌；德勞奈單元；統計熵；結構熵；胺基酸；蛋白質摺疊；蛋白質變性； Voronoi tessellation ； Delaunay simplex ； statistical entropy ； conformation entropy ； amino acid ； folding of protein ； denature

Abstract │ Reference (13) │ Altmetrics

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To understand the physical behavior of solvent system in microscopic structure, such as amino acids in aqueous solution, the Voronoi tessellation method was employed to analyze space distribution of solvent surrounding the solute. The Voronoi polyhedra can be constructed through Delaunay simplexes. In our analysis, each non-hydrogen atom is treated as an independent element and a space-dependent factor is introduced for every element. In an equilibrium homogenous system, each Voronoi polyhedron is not identical but should have same average factor which is treated as the standard by definition. Compared with the standard factor of the homogenous system, i.e., pure water system, the factor on the solute surface should give out the information of interaction between the solvent and the solute.  Therefore, this space-dependent factor must include the locally abnormal distribution with statistical significance.  We then constructed the statistical entropy based on this factor to interpret thermodynamic behavior of amino acids, peptides and even proteins.  Through analyzing the solvation differences between 20 standard amino acids, we quantify contribution of the different side-chain toward solvation of the solute surfaces in terms of statistical entropy.

Reference ( 13 ) 〈TOP〉

1. Dill, K. A.; MacCallum, J. L., The protein-folding problem, 50 years on. Science 2012, 338 (6110), 1042-1046.
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2. Dobson, C. M., Protein folding and misfolding. Nature 2003, 426 (6968), 884-890.
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3. Yang, C.; Jang, S.; Pak, Y., A fully atomistic computer simulation study of cold denaturation of a β-hairpin. Nature communications 2014, 5.
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4. Creamer, T. P., Side‐chain conformational entropy in protein unfolded states. Proteins: Structure, Function, and Bioinformatics 2000, 40 (3), 443-450.
連結：
5. Doig, A. J.; Sternberg, M. J., Side‐chain conformational entropy in protein folding. Protein Science 1995, 4 (11), 2247-2251.
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