Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties

Abstract

The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (–1.014 eV) then for D-FF (–0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (–6.18 eV) and for D-FF (–6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2–3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis

“…Note that optimizing L-FF PNTs with water is concerned with difficulties since these structures are less stable as compared to D-FF PNTs. This also agrees with previously obtained data: D-FF nanotubes have a denser and stronger deep packing than L-FF PNTs [ 25 , 28 , 29 ]; L-FF PNTs have larger cavity sizes, with looser and less uniform surface of the internal cavity compared to D-FF PNTs [ 28 , 30 ]. It was necessary to vary some parameters and methods of the optimization procedure in VASP to obtain the most stable and suitable optimized structure.…”

“…As results, many of these structures have piezoelectric and ferroelectric properties [ 19 , 20 , 21 , 22 , 23 , 24 ]. This has been shown and investigated in detail in our previous works [ 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. Self-assembly of such PNTs occurs in aqueous media rather quickly and under certain conditions that affect the rate of their growth and the shape of self-organizing structures [ 31 , 32 ].…”

“…We do not yet insist directly on the occurrence of ferroelectricity of water and ice structures inside peptide nanotubes, since reliable phase transitions between the polar (ferroelectric) and nonpolar (paraelectric) phases, which have pronounced changes in the dielectric constant according to the well-known Curie-Weiss law [ 19 ], have not yet been detected. Meanwhile, ferroelectricity was observed by Bdikin I., Bystrov V., Kopyl S., et al in [ 63 ], though in other β-sheet FF PNT structure [ 17 , 24 ], not in α-helix, as is studied now [ 25 , 26 , 27 , 28 , 29 ]. Besides, water was not known to occur in the internal cavity of such PNT.…”

“…A similar initial structure is also used and for L-FF PNT. During the optimization process (using the VASP program, as described above), the structure of water clusters changes—there is a displacement of water molecules inside the cavity under the influence of an electric field inside the cavity (arisen from fixed FF dipoles, which create total strong polarization here and, accordingly, a strong electric field appears along the axis of the nanotube [ 24 , 25 , 26 , 27 , 28 , 29 ]).…”

“…An optimum possible number of water molecules per one unit cell of the D-FF and L-FF hexagonal crystal structures was determined. These structural data and water molecules are also considered in molecular models for D-FF and L-FF PNTs, which have at least two coils of the PNT helix structure [ 25 , 28 , 29 ] that correspond to the period of the hexagonal unit cell along the c axis. The influences of these water molecules on PNT properties are analyzed, including a change in the dipole moments and polarization of the PNTs, as well as a change in the structure and properties (dipole moment and polarization) of water clusters embedded in a PNT cavity for both chirality types.…”