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Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes

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Abstract

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: d and l. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the d-FF has large condensation energy E0 in the transverse direction, and form thicker and shorter PNT bundles than those based on l-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original l-FF and d-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV.

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Acknowledgments

The authors wish to acknowledge the Russian Foundation for Basic Research (RFBR grant 19-01-00519 А). P.Z and S.K. are grateful to FCT project PTDC/CTMCTM/31679/2017/ CENTRO-01-0145-FEDER-031679. Part of this work was funded by national funds (OE), through FCT in scope of the framework contract foreseen in numbers 4, 5 and 6 of the article 23, of the Decree-Law 57/2016, of August 29, changed by Law 57/2017, of July 19, and project CICECO-Aveiro Institue of Materials, FCT Ref. UID/CTM/50011/2019, financed by national funds through FCT/MCTES. Crystallographic data for D-FF nanotubes reported in the paper [72] have been deposited in the Cambridge Crystallographic Data Centre [73], no. CCDC 1853771.

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Authors and Affiliations

  1. Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290, Pushchino, Moscow Region, Russia

    Vladimir S. Bystrov

  2. School of Natural Sciences and Mathematics, Ural Federal University, 620000, Ekaterinburg, Russia

    Pavel S. Zelenovskiy & Alla S. Nuraeva

  3. Department of Chemistry and CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal

    Pavel S. Zelenovskiy

  4. Department of Physics and CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193, Aveiro, Portugal

    Svitlana Kopyl

  5. Faculty of Physics, Lomonosov Moscow State University, 119991, Moscow, Russia

    Olga A. Zhulyabina & Vsevolod A. Tverdislov

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  1. Vladimir S. Bystrov
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Bystrov, V.S., Zelenovskiy, P.S., Nuraeva, A.S. et al. Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes. J Mol Model 25, 199 (2019). https://doi.org/10.1007/s00894-019-4080-x

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