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Volume 16   Issue 2   Year 2021
Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

Likhachev I.V., Bystrov V.S.

Institute of Mathematical Problems of Biology RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russia
 
Abstract. Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.
 
Key words: molecular dynamics method, MD manipulator, steered molecular dynamics, self-assembly of nanostructures, phenylalanine, chirality.

 

Table of Contents Original Article
Math. Biol. Bioinf.
2021;16(2):244-255
doi: 10.17537/2021.16.244
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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