Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

Abstract

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

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.…”