24 research outputs found
A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction
No full textRhodopsins
are seven α-helical membrane proteins that are
of great importance in chemistry, biology, and modern biotechnology.
Any in silico study on rhodopsin properties and functioning requires
a high-quality three-dimensional structure. Due to particular difficulties
with obtaining membrane protein structures from the experiment, in
silico prediction of the three-dimensional rhodopsin structure based
only on its primary sequence is an especially important task. For
the last few years, significant progress was made in the field of
protein structure prediction, especially for methods based on comparative
modeling. However, the majority of this progress was made for soluble
proteins and further investigations are needed to achieve similar
progress for membrane proteins. In this paper, we evaluate the performance
of modern protein structure prediction methodologies (implemented
in the Medeller, I-TASSER, and Rosetta packages) for their ability
to predict rhodopsin structures. Three widely used methodologies were
considered: two general methodologies that are commonly applied to
soluble proteins and a methodology that uses constraints that are
specific for membrane proteins. The test pool consisted of 36 target-template
pairs with different sequence similarities that was constructed on
the basis of 24 experimental rhodopsin structures taken from the RCSB
database. As a result, we showed that all three considered methodologies
allow obtaining rhodopsin structures with the quality that is close
to the crystallographic one (root mean square deviation (RMSD) of
the predicted structure from the corresponding X-ray structure up
to 1.5 Å) if the target-template sequence identity is higher
than 40%. Moreover, all considered methodologies provided structures
of average quality (RMSD < 4.0 Å) if the target-template sequence
identity is higher than 20%. Such structures can be subsequently used
for further investigation of molecular mechanisms of protein functioning
and for the development of modern protein-based biotechnologies
Analysis of the Aging Processes of Writing Ink: Raman Spectroscopy versus Gas Chromatography Aspects
No full textThis work is devoted to the extremely popular but poorly developed scientific and forensic problem of the estimation of the actual dates of inscriptions placed on paper and made by ballpoint pens. It is shown that the degradation of writing inks with time may be controlled via Raman spectroscopy and gas chromatography. The time intervals for the implementation of each of these methods were determined using the ratios of the Raman peak intensities as degradation characteristics rather than their absolute values. In turn, this eliminates the effect of the concentration of a dye. The mutual influence of the volatile components and dyes of writing inks was also investigated and the time interval within which such influence is critical was found. According to the obtained results, a new methodological scheme for determining the age of documents, which were created at least 40 months ago, was proposed
In situ laser-induced synthesis of copper microstructures with high catalytic properties and sensory characteristics
No full textLow-Frequency Magnetic Scanning Device and Algorithm for Determining the Magnetic and Non-Magnetic Fractions of Moving Metallurgical Raw Materials
No full textThe development of an algorithm to automate the process of measuring the magnetic properties of macroscopic objects in motion is an important problem in various industries, especially in ferrous metallurgy and at factories where ferrous scrap is a strategic raw material. The parameter that requires work control is the hidden mass fraction of a non-magnetic substance that is present in the ferromagnetic raw material. The solution to this problem has no prototypes. In our work, a simple measuring device and a mathematical algorithm for calculating the mass fraction of the non-magnetic fraction in a strongly magnetic matrix were developed. The device is an inductance coil, in which the angle of the electromagnet losses is related to the mass of the magnetic material moving the coil. The magnitude of the instantaneous values of the lost angle integral was compared with the result of weighing the object on scales. This allowed us to calculate the proportion of the magnetic and non-magnetic fractions. The use of this prototype is herein illustrated. The experimental results of the determination of the magnetic-fractional composition depending on the mass of scrap metal and its bulk and the magnetic characteristics are presented
The development of methods of analysis of documents on the basis of the methods of Raman spectroscopy and fluorescence analysis
No full textInfluence of Raman spectra measurement conditions on the dating results of writing compositions
No full textWhen establishing the age of a document using spectral methods, the result is influenced not only by the storage conditions, but also by the methods of measuring the spectra and mathematical processing of the results. This work analyzes the influence the modes of measuring Raman spectra have on the result of measuring the writing composition spec-tra. The analysis area includes the correlation coefficients of the full spectral matrices as a criterion for the reliability of the determination date. The influence of focusing accuracy, correctness of subtraction of the baseline, sample irradiation time, and varying the number of repetitions is investigated. In the study, chemometric tools for the analysis of Raman spectra were also applied. The influence of mathematical spectra processing shows that the components PC4, P5, and PC6 are most closely related to the shelf life, although they do not make the maximum contribution to the variance in the system. Taking into account all the requirements for measuring spectra, the PCA method applied to the Raman spectra of writing compositions allows clustering samples by manufacturer’s brands and by the sample shelf life.When establishing the age of a document using spectral methods, the result is influenced not only by the storage conditions, but also by the methods of measuring the spectra and mathematical processing of the results. This work analyzes the influence the modes of measuring Raman spectra have on the result of measuring the writing composition spec-tra. The analysis area includes the correlation coefficients of the full spectral matrices as a criterion for the reliability of the determination date. The influence of focusing accuracy, correctness of subtraction of the baseline, sample irradiation time, and varying the number of repetitions is investigated. In the study, chemometric tools for the analysis of Raman spectra were also applied. The influence of mathematical spectra processing shows that the components PC4, P5, and PC6 are most closely related to the shelf life, although they do not make the maximum contribution to the variance in the system. Taking into account all the requirements for measuring spectra, the PCA method applied to the Raman spectra of writing compositions allows clustering samples by manufacturer’s brands and by the sample shelf life
Glass/Au Composite Membranes with Gold Nanoparticles Synthesized inside Pores for Selective Ion Transport
No full textNanocomposite membranes have been actively developed in the last decade. The involvement of nanostructures can improve the permeability, selectivity, and anti-fouling properties of a membrane for improved filtration processes. In this work, we propose a novel type of ion-selective Glass/Au composite membrane based on porous glass (PG), which combines the advantages of porous media and promising selective properties. The latter are achieved by depositing gold nanoparticles into the membrane pores by the laser-induced liquid phase chemical deposition technique. Inside the pores, gold nanoparticles with an average diameter 25 nm were formed, which was confirmed by optical and microscopic studies. To study the transport and selective properties of the PG/Au composite membrane, the potentiometric method was applied. The uniform potential model was used to determine the surface charge from the experimental data. It was found that the formation of gold nanoparticles inside membrane pores leads to an increase in the surface charge from −2.75 mC/m2 to −5.42 mC/m2. The methods proposed in this work allow the creation of a whole family of composite materials based on porous glasses. In this case, conceptually, the synthesis of these materials will differ only in the selection of initial precursors
Azobenzene/Tetraethyl Ammonium Photochromic Potassium Channel Blockers: Scope and Limitations for Design of Para-Substituted Derivatives with Specific Absorption Band Maxima and Thermal Isomerization Rate
No full textAzobenzene/tetraethyl ammonium photochromic ligands (ATPLs) are photoactive compounds with a large variety of photopharmacological applications such as nociception control or vision restoration. Absorption band maximum and lifetime of the less stable isomer are important characteristics that determine the applicability of ATPLs. Substituents allow to adjust these characteristics in a range limited by the azobenzene/tetraethyl ammonium scaffold. The aim of the current study is to find the scope and limitations for the design of ATPLs with specific spectral and kinetic properties by introducing para substituents with different electronic effects. To perform this task we synthesized ATPLs with various electron acceptor and electron donor functional groups and studied their spectral and kinetic properties using flash photolysis and conventional spectroscopy techniques as well as quantum chemical modeling. As a result, we obtained diagrams that describe correlations between spectral and kinetic properties of ATPLs (absorption maxima of E and Z isomers of ATPLs, the thermal lifetime of their Z form) and both the electronic effect of substituents described by Hammett constants and structural parameters obtained from quantum chemical calculations. The provided results can be used for the design of ATPLs with properties that are optimal for photopharmacological applications
Copper-based nanocatalysts produced via laser-induced ex situ generation for homo- and cross-coupling reactions
No full textThe investigation of dye aging dynamics in writing inks using Raman spectroscopy
No full textThe durability against light and aging dynamics of heteroatomic aromatic dyes and pigments containing nitrogen atoms used in writing inks was studied using Raman spectroscopy. The mechanisms of their thermal and photo-decomposition were proposed and the rates of these processes were determined. According to Raman spectroscopy, it was found that depending on the presence of one or another colorant, there are three main types (Type A, Type B and Type C) of blue dye inks used in ballpoint, gel and capillary pens which were studied in this work. Each type is characterized by a certain set of signals in Raman spectra. Time dependencies of Raman signal intensities for each type revealed the dynamics of the processes occurred with colorants included in the studied inks from the moment when they were printed on paper. Thus, the results obtained in this study can be used for the age estimation of the paper documents up to 15 years.Saint-Petersburg State Universit
