Papers by Svetlana R Amirova
Journal of Proteomics & Bioinformatics, Aug 17, 2013
Scientific Reports, Jun 16, 2017
Angiopoietin-1 (Angpt1) is a glycoprotein ligand important for maintaining the vascular system. I... more Angiopoietin-1 (Angpt1) is a glycoprotein ligand important for maintaining the vascular system. It signals via a receptor tyrosine kinase expressed on the surface on endothelial cells, Tie2. This receptor can undergo regulated ectodomain cleavage that releases the ligand-binding domain (sTie2) into the circulation. The concentration of sTie2 is increased in a range of conditions, including peripheral arterial disease and myocardial infarction, where it has been suggested to bind and block Angpt1 resulting in vascular dysfunction. Here we use a joint mathematical modelling and experimental approach to assess the potential impact of sTie2 on the ability of Angpt1 to signal. We find that the concentrations of sTie2 relative to Angpt1 required to suppress signalling by the ligand are more than tenfold higher than those ever seen in normal or disease conditions. In contrast to the endogenous sTie2, an engineered form of sTie2, which presents dimeric ligand binding sites, inhibits Angpt1 signalling at seventy-fold lower concentrations. While loss of Tie2 ectodomain can suppress Angpt1 signalling locally in the cells in which the receptor is lost, our study shows that the resulting increase in circulating sTie2 is unlikely to affect Angpt1 activity elsewhere in the body.
Motivation: The most important achievements in protein secondary structure prediction are based o... more Motivation: The most important achievements in protein secondary structure prediction are based on two different approaches. The first one is the statistical approach and the second one is the physical-chemical approach. In the first approach we analyze appearance of different types of amino acids in given conformations. The second approach use conformational calculations and physical-chemical properties of a given molecule. Presently these approaches are developed independently. The creation of the method, which will contain advantages of the statistical and the physical-chemical approaches, is very important task. Results: We have developed the new approach for secondary structure prediction. Using our combined approach one can obtain the secondary structure of a given protein from its primary structure only. The base of our method is a joint using advantages provided by conformational calculations, data on primary structure and physical-chemical properties of proteins. For the combined approach to be demonstrated, we have predicted the protein secondary structure of four basic types: α-helix, helix 3/10, coil, and turn using only sequences of given proteins from Protein Data Bank.
Journal of Biomolecular Structure & Dynamics, Feb 1, 2007
In this paper we present a novel approach to membrane protein secondary structure prediction base... more In this paper we present a novel approach to membrane protein secondary structure prediction based on the statistical stepwise discriminant analysis method. A new aspect of our approach is the possibility to derive physical-chemical properties that may affect the formation of membrane protein secondary structure. The certain physical-chemical properties of protein chains can be used to clarify the formation of the secondary structure types under consideration. Another aspect of our approach is that the results of multiple sequence alignment, or the other kinds of sequence alignment, are not used in the frame of the method. Using our approach, we predicted the formation of three main secondary structure types (α-helix, βstructure and coil) with high accuracy, that is Q 3 = 76%. Predicting the formation of α-helix and non-α-helix states we reached the accuracy which was measured as Q 2 = 86%. Also we have identified certain protein chain properties that affect the formation of membrane protein secondary structure. These protein properties include hydrophobic properties of amino acid residues, presence of Gly, Ala and Val amino acids, and the location of protein chain end.
Nucleic Acids Research, Feb 7, 2011
The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and sper... more The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we present the first systems level study of the characteristics of this feedback controller, using an integrated experimental and modeling approach. Quantitative analysis of mutant yeast strains in which polyamine synthesis and interconversion were blocked revealed marked variations in frameshift responses to the different polyamines. Putrescine and spermine, but not spermidine, showed evidence of cooperative stimulation of frameshifting and the existence of multiple ribosome binding sites. Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites. Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects. Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethioninedecarboxylase and antizyme mutants, as well as in the wild-type genetic background.
Nucleic Acids Research, Feb 7, 2011
The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and sper... more The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we present the first systems level study of the characteristics of this feedback controller, using an integrated experimental and modeling approach. Quantitative analysis of mutant yeast strains in which polyamine synthesis and interconversion were blocked revealed marked variations in frameshift responses to the different polyamines. Putrescine and spermine, but not spermidine, showed evidence of cooperative stimulation of frameshifting and the existence of multiple ribosome binding sites. Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites. Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects. Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethioninedecarboxylase and antizyme mutants, as well as in the wild-type genetic background.
Science Discovery, 2015
Acoustic method was analyzed to obtain fast droplets coalescence inside nature clouds up to rainy... more Acoustic method was analyzed to obtain fast droplets coalescence inside nature clouds up to rainy big sizes with gravity sedimentation. Droplets are triggered by sound waves which provide the same high speed for coalescence process near 300 m/s. Optimal acoustic generator is proposed, optimal regimes for cloud droplets have been found at low frequencies of f ∼ 100 Hz with low acoustical power. Aadditional acoustic possibilities for rain stimulations provide fast improvement for hot arid weather in local areas on tens-kilometer scales.
American Journal of Environmental Protection, 2016
The detailed microphysical model is presented for the cases of injection the glaciogenic particle... more The detailed microphysical model is presented for the cases of injection the glaciogenic particles inside natural clouds; nowadays glaciogen aerosols are solid CO 2 or liquid N 2. The model includes calculation for quantity of ice crystals that are forming in the overcooled areas, and effect for water droplets grow in a far zone near glaciogen. The comparison with common AgI is presented and discussed.
Journal of Proteomics & Bioinformatics, Aug 17, 2013
We consider axon as a cylinder that has acoustic waveguide regimes to concentrate the propagated ... more We consider axon as a cylinder that has acoustic waveguide regimes to concentrate the propagated signals with appropriate deformation of membrane areas. The highest temperature results near the cylinder axis that can cause low-frequency (0.1 - 10 kHz) longitudinal vibrations of axon due to thermal expansion of material. These frequency shifts are very sensitive to the changes in surrounding viscosity, calculations are presented. The same resonance frequencies of both parts of neuron (axon and Soma) were calculated based on structures sizes, but anaesthesia effect could be explained by different frequency changes for both neuron parts to anesthetics admixture in surrounding.
Global Journal of Science Frontier Research, 2015
Our approach incorporates the effective stepwise CO2 purification in the free atmosphere by spray... more Our approach incorporates the effective stepwise CO2 purification in the free atmosphere by spraying of alkaline compounds together with acoustic acting inside the cloud via an aircraft. The alkalis cause significantly increases of the CO2 solubility in further rainy droplets during their gravitational fall to provide the effective carbon transport from under-cloud atmosphere to the ground. The second step proposes an acoustic influence where droplets are triggered inside clouds by sound waves for coalescence. Special acoustic generators are considered, also optimal regimes for cloud droplets have been found at low frequencies with necessary acoustical power. The proposed alkaline method can compensate for annual carbon emission by its application at 0.4% – 0.1% at our planet surface.
Science Intensive Technologies, 2021
The ideas and calculations presented in the article relate to the field of meteorology and climat... more The ideas and calculations presented in the article relate to the field of meteorology and climatology and for extinguishing forest fires. It is proposed to use an unmanned aerial vehicle (UAV) combined with a portable device for the dosed addition of hygroscopic reagents for precipitation enhancement in natural clouds. The complex, like the UAV with special device for dozed reagents, is characterized by mobility and the possibility of its usage in hard-to-reach woodlands. The advantage is that UAV is easy to use and does not require large airfields with a long runway and other special aviation equipment necessary for the operation of large aircraft. It should also be noted that the mass of the necessary chemical reagents is many times greater than the mass of received water in the form of precipitation from clouds according to the developed and currently available technologies. The algorithm and examples of calculating the key points of the application of the complex and the method...
Applications of Digital Image Processing XXIX, 2006
The proposed method offers one possibility to restore climate in order to avoid overheating. The ... more The proposed method offers one possibility to restore climate in order to avoid overheating. The method to create a supplemental icy cover is considered in the paper. We investigate theoretically the creation of artificial rafts in the border of water-ice area in the north seas. Firstly, such artificial rafts or films can be used as additional mirror for san energy. Secondly, these rafts can decrease local water vibration for the ice to form easily in north regions. And finally, these rafts can be treated as crystallization centers in the supercooled water.
EThOS - Electronic Theses Online ServiceGBUnited Kingdo
We consider axon as a cylinder that has acoustic waveguide regimes to concentrate the propagated ... more We consider axon as a cylinder that has acoustic waveguide regimes to concentrate the propagated signals with appropriate deformation of membrane areas. The highest temperature results near the cylinder axis that can cause low-frequency (0.1-10 kHz) longitudinal vibrations of axon due to thermal expansion of material. These frequency shifts are very sensitive to the changes in surrounding viscosity, calculations are presented. The same resonance frequencies of both parts of neuron (axon and Soma) were calculated based on structures sizes, but anaesthesia effect could be explained by different frequency changes for both neuron parts to anesthetics admixture in surrounding.
A method for removing atmospheric carbon dioxide (СО2) and water vapor is proposed. The method sp... more A method for removing atmospheric carbon dioxide (СО2) and water vapor is proposed. The method sprays clouds with alkaline compounds to significantly increase the solubility of СО2 in the cloud water, providing for much higher than normal levels of СО2 to be absorbed by rain droplets. The CO2 is transported to the ground for sequestration in surface and/or ground water, and available for carbon fixation by plants and organisms. Presented calculations estimate that 38 GT of atmospheric CO2 could be removed per year by applying the process over 0.08% to 2.4 % of the Earth's surface. Laboratory experiments that grew multiple edible plant species irrigated with the modified rainwater indicated yield benefits. A concept for removing atmospheric methane (CH4) is also presented. Powerful lasers would ionize the CH4 to form CO2 that could then be removed by the alkaline-enhanced rainfall method.
We consider two-dimensional long wave low frequency motion in a pre-stressed layer composed of Ne... more We consider two-dimensional long wave low frequency motion in a pre-stressed layer composed of Neo-Hookean material. Specifically, the pre-stress is a simple shear deformation. Derivation of the dispersion relation associated with traction-free boundary conditions is briefly reviewed. Appropriate approximations are established for the two associated long wave modes. From these approximations it is clear that there may be either two, one or no real long wave limiting phase speeds. These approximations are also used to establish the relative asymptotic orders of the displacement components and pressure increment. Using these relative orders to motivate the introduction of appropriate a scales, an asymptotically consistent model long wave low frequency motion is established. It is shown that in the presence of shear there is neither bending nor extension, or analogues of their previously established pre-stressed counterparts. In fact, both the in-plane and normal displacement component...
Scientific reports, Jan 16, 2017
Angiopoietin-1 (Angpt1) is a glycoprotein ligand important for maintaining the vascular system. I... more Angiopoietin-1 (Angpt1) is a glycoprotein ligand important for maintaining the vascular system. It signals via a receptor tyrosine kinase expressed on the surface on endothelial cells, Tie2. This receptor can undergo regulated ectodomain cleavage that releases the ligand-binding domain (sTie2) into the circulation. The concentration of sTie2 is increased in a range of conditions, including peripheral arterial disease and myocardial infarction, where it has been suggested to bind and block Angpt1 resulting in vascular dysfunction. Here we use a joint mathematical modelling and experimental approach to assess the potential impact of sTie2 on the ability of Angpt1 to signal. We find that the concentrations of sTie2 relative to Angpt1 required to suppress signalling by the ligand are more than ten-fold higher than those ever seen in normal or disease conditions. In contrast to the endogenous sTie2, an engineered form of sTie2, which presents dimeric ligand binding sites, inhibits Angpt1...
Analysis of a huge number of tasks from the sections of modern
physics leads to various mathemat... more Analysis of a huge number of tasks from the sections of modern
physics leads to various mathematical expressions,
containing almost always special functions. This book is designed
help a novice scientist or engineer master the language
special functions and facilitate the use of special
mathematical directories that give a large number of
possible options for each function from which to select
one most suitable. Some initial information is given
by the most common special functions,
grouped into several lectures that were read to students
senior students and postgraduate students - physicists; here it is simple and intelligible
the conclusion of a number of basic concepts is explained and traced,
occurring in the reference books. Examples of use are given
special functions and their operation in the analysis
physical processes and tasks. The book aims to teach
student and post-graduate student of independent scientific work, helps
carry out a theoretical study of the physical phenomenon under study.
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Papers by Svetlana R Amirova
physics leads to various mathematical expressions,
containing almost always special functions. This book is designed
help a novice scientist or engineer master the language
special functions and facilitate the use of special
mathematical directories that give a large number of
possible options for each function from which to select
one most suitable. Some initial information is given
by the most common special functions,
grouped into several lectures that were read to students
senior students and postgraduate students - physicists; here it is simple and intelligible
the conclusion of a number of basic concepts is explained and traced,
occurring in the reference books. Examples of use are given
special functions and their operation in the analysis
physical processes and tasks. The book aims to teach
student and post-graduate student of independent scientific work, helps
carry out a theoretical study of the physical phenomenon under study.
physics leads to various mathematical expressions,
containing almost always special functions. This book is designed
help a novice scientist or engineer master the language
special functions and facilitate the use of special
mathematical directories that give a large number of
possible options for each function from which to select
one most suitable. Some initial information is given
by the most common special functions,
grouped into several lectures that were read to students
senior students and postgraduate students - physicists; here it is simple and intelligible
the conclusion of a number of basic concepts is explained and traced,
occurring in the reference books. Examples of use are given
special functions and their operation in the analysis
physical processes and tasks. The book aims to teach
student and post-graduate student of independent scientific work, helps
carry out a theoretical study of the physical phenomenon under study.