Our study was aimed to anlayze the mechanism of the effect of acetylation of the Lys40 residue in α-tubulin TUBA4 from
A. thaliana
on its structure and interaction with ATG8a autophagy protein. ...Reconstruction of the spatial structures of the studied proteins was carried out by homology using experimentally proven crystal structures as a template. Studies of protein–protein interactions and their comparative analysis were performed using in silico methods. It has been demonstrated that acetylation of α-tubulin on the Lys40 residue leads to stabilization of its structure in comparison with its deacetylated form. Also, the analysis of the results of molecular dynamics calculation showed that the replacement of acetylated α-tubulin in complex with ATG8 protein to nonacetylated form leads to a decrease in the number of contact amino acid residues that, as a result, destabilizes the entire complex. Therefore, acetylation of α-tubulin on the Lys40 residue leads to stabilization of the protein itself and its complex with the ATG8 protein.
Protein kinases represent one of the largest eukaryotic enzyme superfamilies. However, only a few can directly phosphorylate tubulin and contribute to the modulation of the “tubulin code.” The ...authors previously confirmed the structural and functional homology of the plant protein kinase IREH1 and members of the mammalian MAST kinase family. Their participation in the regulation of the microtubule system in plant and animal cells was also experimentally confirmed. At the same time, the direct contribution of MAST/IRE to the “tubulin code” remains unclear. In the current study, based on bioinformatical and structural biology methods, the possibility of such an interaction was evaluated. The target sites of MAST/IRE-phosphorylation of tubulin were predicted based on similarity to the generalized specific profiles. Two potential MAST/IRE specific sites, conserved in human and
Arabidopsis
tubulins were selected: Thr73 (80) exists in most isotypes of α-tubulin and Ser115 was found in the majority of human and plant isotypes of β-tubulin. It was predicted that phosphorylation of the first site can affect the assembly of α/β-tubulin heterodimer, and phosphorylation of the second may affect the interaction between neighboring protofilaments of microtubules. The last site Ser433, was found in both γ-tubulin isotypes of
A. thaliana
, but it was absent in mammals. The external position of Ser433 in plant γ-tubulin allows for suggesting that phosphorylation of this amino acid can affect the structure of the γTuRC complex but it does not affect inner contacts of γTuSC and their interaction in the ring.
The variability of the allosteric binding site pocket located in the interdomain cleft (IDC) of FtsZ proteins was investigated. The point-cloud models of the IDC site pockets were constructed based ...on 11 structures for the
S. aureus
complexes of FtsZ protein with 2,6-diflurobenzamides—OLQ, 9PC, OM8, OMW ZI1, ZI6, ZI7, and ZI9—which is currently deposed in the RCSB Protein Data Bank. Significant variability in the volume and shape of the IDC site pocket, formed under adaptation to the ligand, was demonstrated. Four main conformational states of the site pocket, resulting from ligand-protein fitting were selected. It indicates that the docking of the ligands into the IDC site of individual 3D-models of FtsZ protein molecules is not effective. It was concluded that virtual screening efficiency can be significantly improved by the use of an ensemble of molecular targets considering the conformational variability of the IDC site pocket of bacterial FtsZ protein.
The analysis of the effect of ivermectin on phytopathogenic strains of
Fusarium graminearum
(F‑55644, F-55748) and
Fusarium oxysporum
f. sp.
lycopersici
(F-52897, F-55547) was carried out; as a ...result, its concentrations were established at which a fungistatic effect on the growth of colonies of the specified strains was observed (2 and 3 mg/mL). It was found that
F. oxysporum
strains were more susceptible in general to ivermectin than
F. graminearum
strains. Since it is known that ivermectin is able to interact with β-tubulin (causing a stabilization of microtubules), to explain the obtained results, a 3-dimensional model of the complex of this compound with
Fusarium
β-tubulin was developed and ivermectin-induced changes in the conformation of β-tubulin were determined, including, particularly, the stabilization and spiralization of the M‑loop of the β-tubulin molecule. This structural element of β-tubulin plays an important role in the lateral contacts between tubulin subunits of adjacent protofilaments within the microtubule. Since the M-loop stabilization reflects a very important feature of microtubule stabilizing agents' binding to the taxane site of β-tubulin, it can be supposed, that ivermectin possesses the same effect on
Fusarium
microtubules. The results obtained allow for considering ivermectin or its derivatives as potential compounds with fungicidal activity.
In this review, we describe dielectric properties of biological tissues and liquids in the context of terahertz (THz) biophotonics. We discuss a model of the THz dielectric permittivity of water and ...water-containing media, which yields analysis of the relaxation and damped resonant molecules modes. We briefly describe modern techniques of THz spectroscopy and imaging employed in biophotonics with a strong emphasize on a THz time-domain spectroscopy. Furthermore, we consider the methods of sub-wavelength resolution THz imaging and the problem of THz wave delivery to hard to access tissues and internal organs. We consider the THz dielectric properties of biological solutions and liquids. Although strong absorption by water molecules prevents THz-waves from penetration of hydrated tissues and probing biological molecules in aqueous solutions, we discuss approaches for overcoming these drawbacks – novel techniques of freezing and temporal dehydration by application of hyperosmotic agents which have a potential for cancer detection. We review recent applications of THz technology in diagnosis of malignancies and aiding histology paying particular attention to the origin of contrast observed between healthy and pathological tissues. We consider recent applications of THz reflectometry in sensing the thinning dynamics of human pre-corneal tear film. Modern modalities of THz imaging, which relies on the concepts of multi-spectral and multi-temporal domains and employing the principles of color vision, phase analysis and tomography are discussed. Novel methods of THz spectra analysis based on machine learning, pattern recognition, chemical imaging and the revealing of the spatial distribution of various substances in a tissue, are analyzed. Advanced thermal model describing biological object irradiated by THz waves and phantoms mimicking the optical properties of tissues at THz frequencies are presented. Finally, application of the high-resolution THz spectroscopy in analytic chemistry, biology and medicine are described.
The phenomenon of phase change transition has been a fascinating research subject over decades due to a possibility of dynamically controlled materials properties, allowing the creation of optical ...devices with unique features. The present paper unravels the optical characteristics and terahertz (THz) dielectric permittivity of a novel phase change material (PCM), GeTe
, prepared by pulsed laser deposition (PLD) and their remarkable contrast in crystalline and amorphous states, in particular, a difference of 7 orders of magnitude in conductivity. The THz spectra were analyzed using the harmonic oscillator and Drude term. Using GeTe
PLD films, we designed and prepared a THz metasurface in the form of periodic structure and revealed a possibility of tuning the THz resonance either by a thermal control or light-induced crystallization response, thus achieving the dynamic and tunable functionality of the metastructure. We propose controlling the state of metasurface by observing the intensity characteristics of the Raman peak of 155 cm
. Density functional theory (DFT) modeling demonstrates that in the process of crystallization the mode intensity of 155 cm
assigned to Te-Te stretching in amorphous chain fragments decreases and disappears at full crystallization.
We report the results of experimental studies of the photoelectric properties of a
p–i–n
GaAs photodiode with InAs/GaAs(001) double asymmetric quantum dots (DAQDs) grown by self-assembling in the ...metal–organic vapor-phase epitaxy process. Three peaks were observed in the dependence of the photocurrent on the reverse bias measured at monochromatic photoexcitation of the DAQDs at the wavelength corresponding to the energy of interband optical transitions between the ground hole and electron states in the larger quantum dots (QDs). These peaks were related to the tunneling of the photoexcited electrons between the QDs, including a dissipative one (with emission and absorption of optical phonons). The experimental results agree qualitatively with the theoretical field dependence of the probability of 1D dissipative tunneling between QDs.
Screening of antimitotic activity and phytotoxicity of new 2,4- and 2,6-dinitroaniline derivates has been performed using the Allium-test. All substances that are derivatives of 2,4-dinitroanilines, ...2,6-dinitro-(4-fluoromethyl)-aniline, and of (methylsulfonyl) nitrobenzol, proved to change the value of the mitotic index, cause cytogenetic disorders, and have a phytotoxic effect on the roots of Allium cepa seedlings. The results obtained suggest that N-(2,4-dinitrophenyl)-orto-aminobenzoic acid, N, N, -diethyl-2,6-dinitro-4-(trifluoromethyl)-aniline, and 1-methylsulfonyl-3-nitrobenzol are potential herbicides; further studying of their effects is proposed.
In this work, we have experimentally investigated the features of tunneling current-voltage (I-V) curves in the case of ID-dissipative tunneling in the limit of weak dissipation for various both ...synthesized (and in the process of synthesis) metallic nanoparticles (NPs) (Ni, Co, Fe) in a combined atomic force microscope/scanning tunneling microscope (AFM/StM) system in an external electric field. It is shown that for individual tunneling I-V curves, a single peak is observed at one of the polarities. In the process of synthesizing metallic nanoparticles with a change in polarity, instead of nanoclusters, it is possible to synthesize toroidal structures (shown by the example of "growing" Ni-NPs). The investigated effects of 1D-dissipative tunneling made it possible to develop the author's method of controlled growth of quantum dots in a combined AFM/STM system. A qualitative agreement was obtained between the experimental and theoretical results, which allows us to assume the possibility of experimental observation of the macroscopic dissipative tunneling effects and thereby confirm the hypothesis expressed in the pioneering works of A. J. Leggett, A. I. Larkin, Yu. N. Ovchinnikov and other authors.
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