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

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

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

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

DFT (VASP) and semi-empirical (HyperChem) calculations for the l- and d-chiral diphenylalanine (l-FF and d-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. 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 and total l-FF and d-FF PNT with embedded water/ice cluster are discussed. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.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 computational parts of the study was completed within the framework of the non-commercial Agreement on scientific-technical cooperation between Institute of Mathematical Problems of Biology (IMPB) of the Keldysh Institute of Applied Mathematics RAS (KIAM RAS) and Department of Physics and I3N Institution of the University of Aveiro, Portugal

Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L–D–L–D in proteins and D–L–D–L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines

A Method for Calculating the Sign and Degree of Chirality of Supercoiled Protein Structures

Chirality plays an important role in studies of natural protein structures. Therefore, much attention is paid to solving the problems associated with the development of criteria and methods for assessing the chirality of biomolecules. In this paper, a new method for calculating the sign and degree of chirality of superhelices is proposed. The method makes it possible to characterize the chirality sign and to quantify coiled-coils and collagen superhelices. The degree of chirality is understood as a value indicating the intensity of twisting of individual helices around the axis of the superhelix. The calculation requires information about the relative spatial arrangement of the alpha carbon of the amino acid residues of the helices that make up the superhelix. The use of a small amount of raw data makes the method easy to apply, and the validity of the results of this study is confirmed through the analysis of real protein structures