Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

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.

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes

“…For a large number of realizations, not all monomers of chirality D yield left-handed helices, but L-monomers yield right-handed ones. The list of received spirals is given in Table 1 [ 21 ].…”

“…One of the authors is a developer of this package. It is the ability to easily make changes to the software package that makes the molecular dynamics simulation program an MD manipulator [ 21 , 55 , 56 ]. We can also change the parameters of the force field during the MD experiment in the interactive mode.…”

“…All work of this program is carried out interactively. In this case, two programs are used on a personal computer: the PUMA-CUDA program directly conducts the simulation itself, and the additional Trajectory Analyzer of Molecular Dynamics (TAMD) program [ 21 , 57 , 58 ] connects to the PUMA-CUDA program using client–server technology and visualizes the current state of the system in real time. In this mode, it is convenient to set various force actions [ 59 ] in the course of a numerical experiment (for example, set or change the stiffness of springs) and then observe how this affects the system.…”

“…As an example, in this work, to demonstrate the process of self-organization and self-assembly of complex biomolecular structures using the developed algorithm of the MD manipulator, the formation of a helix-like structure of the peptide nanotube (PNT) type based on linear chains of phenylalanine amino acids (F or Phe) of different chirality (left L-Phe and right D-Phe) [ 12 , 17 , 21 ] is shown.…”

“…In this paper, we consider modeling the self-organization of a helical structure such as a peptide nanotube based on phenylalanine molecules. To perform such self-organization on a model from a set of 48 molecules of phenylalanine, (Phe) 48 (or F 48 ), into a spiral tubular structure (F PNT), an algorithm for assembling a phenylalanine nanotube uses one of the approaches of the molecular dynamics method—the MD manipulator [ 21 ]. The MD manipulator method is a controlled MDS self-assembly process that makes it possible to obtain a new structure having the same chemical composition but different geometry and topology by applying special forces to the existing original structure.…”