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目的:从氨基酸的侧链大小、带电性、二硫键的形成等方面研究氨基酸的亲疏水性质对蛋白质结构的影响。方法:利用VMD软件构建由不同亲疏水性氨基酸组成的蛋白质模型，并采用分子动力学方法对体系进行模拟。结果:体系键伸缩能与键弯曲能的大小仅与氨基酸的侧链原子数目有关，与氨基酸的亲疏水性质无明显相关性，但疏水型氨基酸构建的蛋白质链其范德华能低于亲水型氨基酸构建的蛋白质链。同时，氨基酸的亲疏水性质会直接影响蛋白质链的二级结构，通过对蛋白质链的均方根涨落和均方根偏差分析得到，疏水型氨基酸构建的蛋白质链能够维持稳定的α螺旋结构。结论:对氨基酸的亲疏水性质与蛋白质链能量及结构参数的关系的研究结果，可为后续进一步理解蛋白质的三级结构特征和动力学行为提供理论支持。
Abstract：Aims: This paper aims to study the effect of hydrophobicity of different amino acids, including the size of side chain, charged residue and disulfide bond, on the protein structures. Methods: The protein models with different hydrophilic or hydrophobic amino acids were constructed by VMD software; and the system was simulated by the molecular dynamics method. Results: Bond-stretching energy and bond-bending energy of the protein chain were not related to the hydrophobicity of the amino acids directly. Meanwhile, the VDW energy of the protein chains constructed by hydrophobic amino acids was lower than those constructed by hydrophilic amino acids. The hydrophobicity of amino acids could affect the secondary structure of protein chains. It was obtained by analyzing the root mean square fluctuation and root mean square deviation of the protein chain. The protein chains constructed by hydrophobic amino acids could maintain the α-helix structure during the simulations. Conclusions: The study of the relationship between the hydrophobicity of amino acids, the potential energy and the structure of proteins can provide theoretical support for the subsequent understanding of the conformation of protein and its application in biology.
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基本信息:
DOI：
中图分类号:Q51
引用信息:
[1]夏芳,冯宙,姜舟婷.分子动力学模拟研究氨基酸亲疏水性质对蛋白质结构的影响[J].中国计量大学学报,2024,35(03):415-421.
基金信息:
国家自然科学基金项目(No.21873087)