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.
Key words:
diphenylalanine, peptide nanotube, molecular modeling, semi-empirical methods, DFT, ab initio methods, molecular mechanics, chirality, topology, self-assembly.
Part of this work was developed as part of the CICECO-Aveiro Materials Institute project, POCI-01-0145-FEDER-007679 funded from Fundação para a Ciência e a Tecnologia (FCT) Ref. UID/CTM/50011/2013, and funded from national funds through FCT/MEC, and co-funded by FEDER in accordance with the PT2020 Partnership Agreement. P.Z. thanks the project FCT PTDC/QEQ-QAN/6373/2014. S.K. thanks the project FCT PTDC/CTM-CTM/31679/2017.
Received 10.02.2019, 04.03.2019, Published 12.03.2019
Document Type:
Article
UDC:
530.1:537.226.33:541.1:577:681.2
Language: English
Citation:
V. S. Bystrov, P. S. Zelenovskiy, A. S. Nuraeva, S. Kopyl, O. A. Zhulyabina, V. A. Tverdislov, “Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: modeling of structure and properties”, Mat. Biolog. Bioinform., 14:1 (2019), 94–125
\Bibitem{BysZelNur19}
\by V.~S.~Bystrov, P.~S.~Zelenovskiy, A.~S.~Nuraeva, S.~Kopyl, O.~A.~Zhulyabina, V.~A.~Tverdislov
\paper Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: modeling of structure and properties
\jour Mat. Biolog. Bioinform.
\yr 2019
\vol 14
\issue 1
\pages 94--125
\mathnet{http://mi.mathnet.ru/mbb374}
\crossref{https://doi.org/10.17537/2019.14.94}
Linking options:
https://www.mathnet.ru/eng/mbb374
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