Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes

Abstract

In this study we consider the features of spatial-structure formation in proteins and their application in bioengineering. Methods for the quantitative assessment of the chirality of regular helical and irregular structures of proteins are presented. The features of self-assembly of phenylalanine (F) into peptide nanotubes (PNT), which form helices of different chirality, are also analyzed. A method is proposed for calculating the magnitude and sign of the chirality of helix-like peptide nanotubes using a sequence of vectors for the dipole moments of individual peptides.

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

“…In this work, using the data of the obtained pdb files, we will calculate the magnitude and sign of the chirality of these self-assembled nanotubes. This novel method is based on the values of the dipole moments of each amino acid or peptide [ 53 , 54 ]. Therefore, we need to obtain the values of the dipole moments of individual phenylalanine molecules in the coils of these nanotube helices.…”

“…A method for calculating the chirality magnitude and sign of helix-like peptide nanotubes (PNT) using the vectors of the successive dipole moments of their constituent peptide molecules was proposed and developed in works [ 53 , 54 ]. It is based on the procedure of the mixed product of three consecutive vectors in a coil of a helix-like structure.…”

“…This makes it possible to build successive vectors connecting these reference points in protein helices and then, using the mixed vector product method, calculate the magnitude and sign of the chirality of helix-like structures. In the works [ 53 , 54 ] this approach was developed and applied to the sequence of dipole moment vectors of individual phenylalanine and diphenylalanine molecules located along the helix line of such a peptide nanotube. Therefore, according to works [ 53 , 54 ], here the sum of the mixed (vector–scalar) products of the dipole moments related to the PNT’s chirality can be written as follows: …”

“…In the works [ 53 , 54 ] this approach was developed and applied to the sequence of dipole moment vectors of individual phenylalanine and diphenylalanine molecules located along the helix line of such a peptide nanotube. Therefore, according to works [ 53 , 54 ], here the sum of the mixed (vector–scalar) products of the dipole moments related to the PNT’s chirality can be written as follows: …”

“…Another important task of this work is to calculate the magnitude and sign of the chirality of the self-assembled helical structures of phenylalanine nanotubes. For this purpose, we will apply the method based on the calculation of the mixed vector–scalar product of the vectors of dipole moments of individual phenylalanine molecules located sequentially along the helix line of phenylalanine nanotubes [ 53 , 54 ]. This algorithm for chirality calculation based on dipole moment vectors is discussed in detail in the second part of this article.…”