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目的:研究蛋白质二级结构中α螺旋的比例对蛋白质三级结构的影响。方法:构建不同的蛋白质链模型，以α螺旋结构占比的不同对体系进行区分并采用分子动力学模拟的方法进行研究。结果:以不同比例α螺旋结构的蛋白质链作为样本，研究其结构的稳定性以及体系的能量。结果表明，体系的键伸缩能和键弯曲能几乎不随蛋白质链中α螺旋结构比例的变化而变化，范德华能受α螺旋结构占比的影响较大，α螺旋占比大的蛋白质链其体系范德华能减小。同时我们发现在该温度(400 K)下，α螺旋结构占比低的蛋白质链中，容易发生α螺旋结构解旋现象，而α螺旋结构占比高的蛋白质链中，部分连接处的非α螺旋结构反而会转变成α螺旋结构。通过分析组成蛋白质链的氨基酸残基的均方根偏差和均方根涨落值可以发现蛋白质链中含α螺旋结构的比例越高，其结构稳定性越强，柔性减弱。结论:这些研究成果呈现α螺旋对蛋白质整体结构的影响，也为其结构转变的动力学行为研究提供理论依据。
Abstract：Aims: This paper aims to study the effect of α-helix of the secondary structure level of the protein on its 3D structure. Methods: We constructed protein models with different proportions of α-helical structure simulated by the molecular dynamics method. Results: The energy and structural stability of protein samples at 400 K were analyzed. The results showed that the bond stretching energy and bond bending energy of the system did not change with the proportion of the α-helical structure. But the van der Waals energy was greatly affected by the proportion of the α-helical structure, i.e., it gradually decreased with the increase ratio of the α-helical proportion. We also concluded that the α-helical structure was easily destroyed when the proportion of residues that formed as α-helix was lower than 50%. Once the proportion of residues composed of α-helical structure was high enough, some part of the protein chain, especially that at the junctions of α-helix would be transformed from random coils or turn to α-helical structures. The root mean square deviation and root mean square fluctuation of the residues of protein chains showed that the higher proportion of α-helix on the secondary structures, the stronger structural stability and the weaker flexibility of the protein. Conclusions: These results provide the effect of α-helix on the secondary structure level of the protein on its structural stability, and give a theoretical basis for the study of dynamic transformation of proteins.
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基本信息:
DOI：
中图分类号:Q518.2
引用信息:
[1]金承昊,冯宙,姜舟婷.α螺旋结构影响蛋白质稳定性的模拟研究[J].中国计量大学学报,2023,34(02):265-270.
基金信息:
国家自然科学基金资助项目(No.21873087)