Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties

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.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

Molecular modeling of ZnO nanoclusters interacting with various dopant and PVDF

Authors wish to acknowledge the Russian Foundation for Basic Researches (RFBR) grant # 19-01-00519 А

Ferroelectric nanocomposites based on polymer ferroelectrics and graphene/oxide graphene: Computer modeling and SPFM experiments

The authors are thankful to the Russian Science Foundation (RSF grant # 16-19-10112) and to the Russian Foundation for Basic Researches (RFBR grants # 16-51-53917) for support. Prof. Xiang-Jian Meng expresses his gratitude to the National Natural Science Foundation of China (NNSFC) for support of the project: "The study on the new type of infrared detector based on ferroelectric tunnel junction"

Piezoelectric, ferroelectric, optoelectronic and photo-catalytic phenomena from defect levels in hydroxyapatite by first-principles

The authors thank the Russian Foundation for Basic Researches (RFBR grant 19-01-00519 A) and to the Fundação para a Ciência e a Tecnologia (FCT) through project UID/CTM/50025/2013

Two-dimensional 1H-NMR study of bacterioopsin-(34–65)-polypeptide conformation

AbstractConformation of the synthetic 32-residue polypeptide, an analog of membrane spanning segment B (residues 34–65) of the Halobacterium halobium bacteriorhodopsin in the membrane mimetic system, methanol/chloroform (1:1), was investigated by 1H-NMR spectroscopy. Previously it was shown by 19F-NMR spectroscopy that this medium retains the native conformation of membrane bound BR and its fragments. The spectrum resonance was assigned by means of the sequential signal assignment porcedure using phase-sensitive DQF-COSY, MLEV17 HOHAHA and NOESY techniques. Interproton nuclear Overhauser effects, spin-spin coupling constant of vicinal H-NCα-H protons and deuterium exchange rates of individual NH groups were derived from two-dimensional NMR spectra. The data unequivocally define the peptide conformation as the right-handed α-helix, extremely rigid in the central region from Phe 42 to Nle 60 and flexible in the N- and C-terminal parts

Investigation of physical properties of diphenylalanine peptide nanotubes having different chirality

The primary structure of all amino acids exists in 2 different chiralities: L (left) and D (right) [1]. However, in biological nature almost all amino acids are L. This choice is due to evolution process, but its reasons are not enough clear yet. To find some physical sources of such difference the investigation of 2 type of diphenylalanine (FF) peptide nanotubes (PNT), based on L-FF and D-FF, was performed. Both types of PNT were fabricated by standard method and their physical properties (X-ray structural data, optical dichroism, polarization, and piezoelectric response, etc.) were studied.Work was supported by RFBR grant # 15-01-04924 and by joint project Portugal-Turkey TUBITAK/0006/2014

Structures and properties of the self-assembling diphenylalanine peptide nanotubes containing water molecules: Modeling and data analysis

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.This work was partially supported by the Fundacão para a Ciência e a Tecnologia (FCT, Portugal) through project UID/CTM/50025/2013 and UIDB/50011/2020 & UIDP/50011/2020. P.Z. and S.K. are grateful to the FCT (Portugal) through the project “BioPiezo,” PTDC/CTM–CTM/31679/2017 (CENTRO-01-0145-FEDER-031679). The theoretical and computational parts of the study was completed within the framework of the non-commercial Agreement on scientific and technical cooperation between Institute of Mathematical Problems of Biology (IMPB) of KIAM RAS and Department of Physics and I3N institution of the University of Aveiro, Portugal. Part of this work was funded by national funds (OE), through FCT (Portugal), in the scope of the framework contract foreseen in the 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

Meta-Subject Approach to Study of Astronomy

The article discusses the issues of meta-subject approach in the study of astronomy as a design method for forming a worldview based on a scientific, philosophical and axiological understanding of phenomena and ideas. The components of the meta-subject approach, strategic decisions are revealed.В статье рассматриваются вопросы метапредметного подхода в изучении астрономии как проектного метода формирования мировоззрения на основе научного, философского и аксиологического осмысления явлений и идей. Раскрываются компоненты метапредметного подхода, стратегические решения