Please use this identifier to cite or link to this item: http://hdl.handle.net/10995/75557
Title: Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties
Authors: Bystrov, V. S.
Zelenovskiy, P. S.
Nuraeva, A. S.
Kopyl, S.
Zhulyabina, O. A.
Tverdislov, V. A.
Issue Date: 2019
Publisher: Russian Academy of Sciences,Department of the Earth Sciences
Citation: Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties / V. S. Bystrov, P. S. Zelenovskiy, A. S. Nuraeva et al. // Mathematical Biology and Bioinformatics. — 2019. — Vol. 14. — Iss. 1. — P. 94-125.
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 E 0 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. © 2019 Mathematical Biology and Bioinformatics.
Keywords: AB INITIO METHODS
CHIRALITY
DFT
DIPHENYLALANINE
MOLECULAR MECHANICS
MOLECULAR MODELING
PEPTIDE NANOTUBE
SELF-ASSEMBLY
SEMI-EMPIRICAL METHODS
TOPOLOGY
URI: http://hdl.handle.net/10995/75557
Access: info:eu-repo/semantics/openAccess
RSCI ID: 38500472
SCOPUS ID: 85065036744
PURE ID: 9805297
ISSN: 1994-6538
DOI: 10.17537/2019.14.94
metadata.dc.description.sponsorship: 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.
Appears in Collections:Научные публикации, проиндексированные в SCOPUS и WoS CC

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