Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes
authors Bystrov, VS; Zelenovskiy, PS; Nuraeva, AS; Kopyl, S; Zhulyabina, OA; Tverdislov, VA
nationality International
journal JOURNAL OF MOLECULAR MODELING
author keywords Diphenylalanine; Peptide nanotube; Molecular modeling; Semi-empirical methods; DFT; Ab initio; Molecular mechanics; Topology; Self-assembly; Chirality
keywords X-RAY CRYSTALLOGRAPHY; SEMIEMPIRICAL METHODS; FORCE-FIELD; NUCLEIC-ACIDS; SIMULATION; ENERGY; PHENYLALANINE; OPTIMIZATION; PARAMETERS; APPROXIMATIONS
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 E-0 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.
publisher SPRINGER
issn 1610-2940
year published 2019
volume 25
issue 7
digital object identifier (doi) 10.1007/s00894-019-4080-x
web of science category Biochemistry & Molecular Biology; Biophysics; Chemistry, Multidisciplinary; Computer Science, Interdisciplinary Applications
subject category Biochemistry & Molecular Biology; Biophysics; Chemistry; Computer Science
unique article identifier WOS:000472929600001
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journal analysis (jcr 2017):
journal impact factor 1.507
5 year journal impact factor 1.539
category normalized journal impact factor percentile 28.262
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