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Molecular Dynamics Simulation Research of the Stabilization Effect of Osmolytes on Protein Structure

Author: JiLuo
Tutor: DongXiaoYan
School: Tianjin University
Course: Biochemical Engineering
Keywords: Molecular dynamics simulations Model analysis Protein Structure Penetrant Molecular volume
CLC: Q51
Type: Master's thesis
Year: 2009
Downloads: 34
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Abstract


Only correctly folded protein molecules to have biological activity; protein engineering and clinical medicine, must ensure that the target protein in the appropriate conformation. Penetrant has a unique stabilizing effect on the protein structure, and it is widely used artificial stability and refolding proteins, their stability mechanism has also become a hot research in the field of biotechnology. Prior studies have found that the penetrants on the protein the ability to stabilize and inversely related to its molecular surface of the proportion of the surface area of ??the polar groups, but ignores the influence of the molecular volume is represented by the steric effect, there is a certain error. We speculate that the molecular volume are also factors affect the penetrant stable role theory before the correction and development, For to optimize experimental and production conditions, the rational design of new additives and ligands, has important guiding significance. In this study, a computer simulation of the advantages of model protein CI2 investigated by molecular dynamics simulation of typical penetrant CI2 thermal stability; research core is based on simulation data using statistical two-parameter fitting model analysis of the relationship between the molecular volume and surface area of ??the polar group ratio penetrant stable capacity and deepen the understanding of the impact factors of the penetrant ability to stabilize rational. After the model simulation results with specific data analysis means, further analysis of the polyols the penetrant and protein molecular mechanism on the reason for the unique nature of the polyols penetrant. The study found penetrants of CI2 has a different degree of stability and capacity; CI2 structure features comprehensive description of the one-dimensional parameters defined and calculated after corresponding penetrant stable capacity of CI2 defined from the quantitative point of view. Associated with the experimental results, the simulation results more credible. Mathematical model analysis and found that the introduction of molecular volume greatly improve the accuracy of the model, and prove that the penetrant size of its ability to stabilize important; due to the molecular volume and steric effect is directly related to, and therefore when the proportion of the surface area of ??the polar groups constant, the stability of the ability of the penetrant is enhanced with the increase of the molecular volume; When the molecular volume is constant, the stability of the ability of the penetrant is first decreased with the increase in the proportion of the surface area of ??the polar group, when this ratio exceeds a certain valve value, its ability to stabilize but began to rise. Polyols penetrants and other penetrants large differences found in the analysis process, so a separate analysis found that its ability to stabilize the molecular volume is directly related to several polyols penetrants; while surface area due to their polar groups generally higher proportion, and little difference from each other, so this ratio has little effect, and there is a positive correlation with the corresponding ability to stabilize phenomenon. At the level of the molecular mechanism, it is found that the steric effect caused by the larger molecular volume of the alcohols penetrants, and surface multiple hydroxyl cause intermolecular aggregation phenomena with each other, is caused a major factor on their unique nature.

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CLC: > Biological Sciences > Biochemistry > Protein
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