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. 2021 Sep 16;11(9):2415.
doi: 10.3390/nano11092415.

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

Vladimir Bystrov  1 , Alla Sidorova  2 , Aleksey Lutsenko  2 , Denis Shpigun  2 , Ekaterina Malyshko  2 , Alla Nuraeva  3 , Pavel Zelenovskiy  3   4 , Svitlana Kopyl  4 , Andrei Kholkin  3   4   5
Affiliations

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

Vladimir Bystrov et al. Nanomaterials (Basel). .

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.

Keywords: chirality; dipeptides; diphenylalanine; dipole moments; helical structures; molecular modeling; peptide nanotubes; polarization; self-assembly.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Images of molecular crystals composed of: (a) L-FF PNTs (space group P61), and (b) D-FF PNTs (space group P65). Hexagonal unit cells are marked with green, red, and white lines. The individual PNTs in crystal are highlighted by yellow circles. Atom colors: oxygen—red, nitrogen—blue, carbon—grey, and hydrogen—white.
Figure 2
Figure 2
Two coils of FF PNT in HyperChem workspace based on experimental crystallographic data [31,38]: (a) L-FF in the Z-plane, (b) L-FF in the Y-plane, (c) D-FF in the Z-plane, and (d) D-FF in the Y-plane.
Figure 3
Figure 3
Images of helix-like FF PNTs based on experimental crystallographic data [31,38]: (a) L-FF and (b) D-FF. L-FF PNT shows right-handed twist, whereas D-FF shows left-handed.
Figure 4
Figure 4
Graphical representation of vectors between neighboring Cα atoms in a helical protein used for calculating a scalar triple product.
Figure 5
Figure 5
Schematic presentation of dipole moments Di in two coils of (a,b) L-FF and (c,d) D-FF PNTs: (a,c) Z-plane projection, (b,d) Y-plane projection. For L-FF PNT dipole moments form a right-hand helix, whereas for D-FF PNT form a left-hand helix. Red arrows show the directions of the total dipole moments of the coil Dcoil.
Figure 6
Figure 6
A coil of L-FF PNT with vectors rD1 and rD4 pointing the centers of mass of individual FF molecules with dipole moments D1 and D4, correspondingly.
See this image and copyright information in PMC

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