Mathematical Biology & Bioinformatics | Volume 18 Issue 1 Year 2023

Assembly of a Diphenylalanine Peptide Nanotube by Molecular Dynamics Methods

Likhachev I.V., Bystrov V.S., Filippov S.V.

In:Institute of Mathematical Problems of Biology RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia

Abstract. 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.

Key words: molecular dynamics method, MD manipulator, steered molecular dynamics, self-assembly of nanostructures, diphenylalanine, chirality, visual differential analysis.