分子动力学方法组装二苯丙氨酸肽纳米管

I. Likhachev, V. Bystrov, S. Filippov
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引用次数: 0

摘要

本文提出了一种利用分子动力学操纵器对复杂分子纳米结构的自组装过程进行分子动力学建模的方法。在此之前,这种方法被认为是用不同手性的苯丙氨酸(F)分子链的线性集合组装苯丙氨酸螺旋纳米管的例子:左手L-F和右手D-F手性L-FF和D-FF。二肽链自组装成纳米管螺旋结构的过程是对现有初始线性结构施加一定的力,以获得化学成分相同但螺旋几何形状不同的最终结构的模仿。主要软件采用PUMA-CUDA分子动力学模拟软件包。使用这个工具,人们可以从任何氨基酸的线性序列中研究螺旋结构的形成。采用视觉差分分析方法对分子动力学方法组装得到的纳米管和实验自组装得到的纳米管结构进行了对比分析。结果表明,所得数据符合分子螺旋结构手性随其组织层次复杂性的符号变化规律。
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Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods
The paper develops an approach to modeling the processes of self-assembly of complex molecular nanostructures by molecular dynamics methods using a molecular dynamics manipulator. Previously, this approach was considered using the example of assembling a phenylalanine helical nanotube from a linear set of chains of phenylalanine (F) molecules of different chirality: left-handed L-F and right-handed D-F chirality L-FF and D-FF. The process of self-assembly of dipeptide chains into helical structures of nanotubes is an imitation of applying certain forces to the existing initial linear structure in order to obtain the final structure of the same chemical composition, but with a different helical geometry. The PUMA-CUDA molecular dynamics simulation software package was used as the main software. Using this tool, one can investigate the formation of helical structures from a linear sequence of any amino acids. A comparative analysis of the structures of nanotubes obtained by assembling by molecular dynamics methods and by their experimental self-assembly was performed using the method of visual differential analysis. It has been established that the obtained data correspond to the law of the sign change of chirality of molecular helical structures with the complication of their hierarchical level of organization.
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来源期刊
Mathematical Biology and Bioinformatics
Mathematical Biology and Bioinformatics Mathematics-Applied Mathematics
CiteScore
1.10
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0.00%
发文量
13
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