16 results on '"Igor, Melnikov"'
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2. Crystal Structure of a Proteolytic Fragment of the Sensor Histidine Kinase NarQ
- Author
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Ivan Gushchin, Igor Melnikov, Vitaly Polovinkin, Andrii Ishchenko, and Valentin Gordeliy
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two-component systems ,histidine kinase ,transmembrane signaling ,in meso crystallization ,proteolysis ,Crystallography ,QD901-999 - Abstract
Two-component signaling systems (TCSs) are a large and important class of sensory systems in bacteria, archaea, and some eukaryotes, yet their mechanism of action is still not fully understood from the structural point of view. Many TCS receptors are elongated flexible proteins with transmembrane (TM) regions, and are difficult to work with. Consequently, truncated fragments of the receptors are often used in structural studies. However, it is not fully clear whether the structures of the fragments correspond well to their native structures in the context of full-length proteins. Recently, we crystallized a fragment of Escherichia coli nitrate/nitrite sensor histidine kinase, NarQ, encompassing the sensor, TM, and HAMP domains. Here we report that a smaller proteolytic fragment consisting of the sensor and TM domains can also be crystallized using the in meso approach. The structure of the fragment is similar to the previously determined one, with minor differences in the vicinity of the truncation site. The results show that the crystallization of such sensor−TM fragments can be accomplished and can provide information on the packing of transmembrane helices, albeit limited, and that the proteolysis may or may not be a problem during crystallization.
- Published
- 2020
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3. Methods for assessing the aesthetic quality indicators of systems, products and technologies in ergodesign
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Inna Dynina, Galina Garbuzova, and Igor Melnikov
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010309 optics ,020303 mechanical engineering & transports ,0203 mechanical engineering ,Risk analysis (engineering) ,Computer science ,media_common.quotation_subject ,0103 physical sciences ,Quality (business) ,02 engineering and technology ,01 natural sciences ,media_common - Abstract
It is shown that the real measure of the aesthetic value of systems, products and technologies, in contrast to the general measure, is in constant development, reflecting the corresponding changes in the aesthetic tastes and perceptions of consumers. It is substantiated that a full aesthetic measure is formed on the basis of a real aesthetic measure, taking into account the universally valid aesthetic and cultural values that characterize the aesthetic ideals of society in the field of culture, art, artistic design, ergonomics and design. The variants of the interaction of ergonomists and designers at various stages of ergodesign are considered. The nomenclature of aesthetic indicators of the quality of systems, products and technologies, such as the integrity of the composition, the rationality of the organization of form, artistic expressiveness, is given. Recommendations are developed on procedures for expert evaluation, aesthetic properties of systems, products and technologies using the theory of odd sets.
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- 2019
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4. Pedagogic design and efficiency of internet training courses
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Igor Melnikov and Galina Garbuzova
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Medical education ,business.industry ,ComputingMilieux_COMPUTERSANDEDUCATION ,The Internet ,business ,Psychology ,Training (civil) - Abstract
The basic peculiarity of flexible training courses consists in that they do not regulate so hard temporal and special limits in training and communication between lecturers and students. It is shown that the distance training efficiency is defined by design of Internet courses.
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- 2018
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5. On cogrowth function of algebras and its logarithmical gap
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Ivan Mitrofanov, Alexei Kanel-Belov, and Igor Melnikov
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General Mathematics ,Image (category theory) ,010102 general mathematics ,Function (mathematics) ,Mathematics - Rings and Algebras ,01 natural sciences ,16S15, 37B10 ,Combinatorics ,Mathematics::Group Theory ,Rings and Algebras (math.RA) ,Bounded function ,0103 physical sciences ,Associative algebra ,FOS: Mathematics ,Mathematics - Combinatorics ,Combinatorics (math.CO) ,010307 mathematical physics ,0101 mathematics ,Alphabet ,Algebra over a field ,Word (group theory) ,Computer Science::Formal Languages and Automata Theory ,Mathematics - Abstract
Let $A \cong k\langle X \rangle / I$ be an associative algebra. A finite word over alphabet $X$ is $I${\it-reducible} if its image in $A$ is a $k$-linear combination of length-lexicographically lesser words. An {\it obstruction} in a subword-minimal $I$-reducible word. A {\em cogrowth} function is number of obstructions of length $\le n$. We show that the cogrowth function of a finitely presented algebra is either bounded or at least logarithmical. We also show that an uniformly recurrent word has at least logarithmical cogrowth., 5 pages
- Published
- 2019
6. Experience with the Vacuum Insulated Tubing VIT Utilization at Gas Fields in the Northern Part of Western Siberia
- Author
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Alexander Belomestnov, Kirill Marchenko, and Igor Melnikov
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Natural gas field ,Getter ,Geochemistry ,Steam injection ,Permafrost ,Western siberia ,Geology - Abstract
Objectives/Scope Evaluating of VIT performance Methods, Procedures, Process Statistics, Finite Element Analysis (FEA), Computational Fluid Dynamics (CFD) Results, Observations, Conclusions The utilization of Vacuum Insulated Tubing (VIT) is necessitated by the growing oil and gas development in northern regions of the Earth and application of thermal oil recovery methods. Conceptually, VIT consists of two (external and internal) pipes coaxially fixed at the ends, with the annular space filled with thermal insulation including getters (gas absorbers). After the pipes are assembled, air is evacuated from the annular space to create vacuum. Getters are fully activating within vacuumizing. Prior to commercial utilization at Gazprom, the VIT was tested at the Gazprom VNIIGAZ Institute (Russia) on a dedicated thermophysical testing bench. Tests were designed to measure the Coefficient of thermal conductivity (k-factor) of the VIT Vacuum Shield Thermal Insulation. Results obtained during the tests are as follows: with hot air (84…93°C) passing through the tube, the temperature of its external surface remained within the range of 28…35°C, while k-factor was 0.004…0.008 W/(m*K). Gazprom requirements k-factor with max. 0.012 W/(m*K). When VIT successfully passed bench tests, they were approved for utilization in the commercial development of the Bovanenkovskoye field operated by Gazprom. In order to gauge heat flux and effective k-factor of VIT walls at different gas flow rates and fluid temperatures, the design provides for satellite pipes to be installed within the gas well's cement column. At the moment, wellhead soil temperature observations are carried out regularly at VIT-equipped wells. Some gas wells have been monitored for 3 years now. The results of monitoring of 18 well pads (163 wells) the temperature stabilization of the permafrost soil at which is carried out only through the operation of seasonally active cooling systems (without the use of VIT) show temperature increases in the soil along the wellbore. Wells operated with VIT and cooling systems keep freezing temperatures within the cement column throughout the entire annual cycle. For steam injection technologies, may be used theoretically estimation about how temperature of steam decreases from top to bottom of well depending on VIT k-factor and length of VIT string. Such information needs for VIT well design. Novel/Additive Information Empirical information about VIT utilization
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- 2018
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7. Chapter 3. The Mesh&Collect Pipeline for the Collection of Multi-crystal Data Sets in Macromolecular Crystallography
- Author
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Ulrich Zander, Igor Melnikov, Max H. Nanao, Alexander Popov, Nicolas Foos, Gordon A. Leonard, Christoph Mueller-Dieckmann, Gianluca Santoni, and Gleb Bourenkov
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Data set ,Complete data ,Data collection ,Computer science ,Crystal data ,Macromolecular crystallography ,The Renaissance ,Data mining ,computer.software_genre ,Merge (version control) ,computer - Abstract
The advent at 3rd generation synchrotron sources of extremely brilliant beamlines for macromolecular crystallography (MX) has meant that for systems which produce only small crystals, the practice of multi-crystal data collection, in which partial data sets collected from a series of crystals of the same target are merged to produce a final, complete data set, is enjoying a renaissance. In principle such experiments are straightforward. All that is needed is to mount all the crystals required on the sample support, to collect the partial data sets in series and then to merge them to produce the final data set. However, multi-crystal data collection is actually fraught with difficultly. The positions of the crystals on the sample support must be determined; individual partial data sets should be collected without inducing too much radiation damage; and the correct choice of partial data sets to merge in order to produce the best final data set must be made. Here, we describe an automatic pipeline, Mesh&Collect, which facilitates multi-crystal experiments, present newer developments designed to improve the quality of the final data sets obtained, give examples of the successes that can be obtained and describe the pitfalls to be avoided in such experiments.
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- 2018
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8. The complex analysis of X-ray mesh scans for macromolecular crystallography
- Author
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Igor, Melnikov, Olof, Svensson, Gleb, Bourenkov, Gordon, Leonard, and Alexander, Popov
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X-ray mesh scans ,macromolecular crystallography ,Macromolecular Substances ,Data Collection ,sample localization ,Crystallography, X-Ray ,Research Papers ,MeshBest ,Software ,data-collection strategies - Abstract
A method and software program, MeshBest, for the detection of individual crystals based on two-dimensional X-ray mesh scans are presented., In macromolecular crystallography, mesh (raster) scans are carried out either as part of X-ray-based crystal-centring routines or to identify positions on the sample holder from which diffraction images can be collected. Here, the methods used in MeshBest, software which automatically analyses diffraction images collected during a mesh scan and produces a two-dimensional crystal map showing estimates of the dimensions, centre positions and diffraction qualities of each crystal contained in the mesh area, are presented. Sample regions producing diffraction images resulting from the superposition of more than one crystal are also distinguished from regions with single-crystal diffraction. The applicability of the method is demonstrated using several cases.
- Published
- 2017
9. Fast iodide-SAD phasing for high-throughput membrane protein structure determination
- Author
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Alexander Popov, Vadim Cherezov, Alexey Mishin, Valentin Borshchevskiy, Alexey Alekseev, Ivan Gushchin, Valentin Gordeliy, Mikhail B. Shevtsov, Vitaly Shevchenko, Vitaly Polovinkin, Igor Melnikov, Francisco Rodriguez-Valera, Gordon A. Leonard, and Kirill Kovalev
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0301 basic medicine ,Vesicle-associated membrane protein 8 ,experimental phasing ,Protein domain ,Iodide ,Biology ,Crystallography, X-Ray ,Biochemistry ,Receptors, G-Protein-Coupled ,03 medical and health sciences ,Protein Domains ,Scattering, Small Angle ,Humans ,serial crystallography ,Integral membrane protein ,Research Articles ,x-ray crystallography ,chemistry.chemical_classification ,Multidisciplinary ,Peripheral membrane protein ,SciAdv r-articles ,SAD ,Iodides ,Transport protein ,030104 developmental biology ,Membrane ,chemistry ,Membrane protein ,Biophysics ,iodide ,ddc:500 ,Research Article - Abstract
A potentially universal method for the de novo solution of the crystal structures of membrane proteins is described., We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide–single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins—the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein–coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.
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- 2017
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10. Inward H
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Vitaly, Shevchenko, Thomas, Mager, Kirill, Kovalev, Vitaly, Polovinkin, Alexey, Alekseev, Josephine, Juettner, Igor, Chizhov, Christian, Bamann, Charlotte, Vavourakis, Rohit, Ghai, Ivan, Gushchin, Valentin, Borshchevskiy, Andrey, Rogachev, Igor, Melnikov, Alexander, Popov, Taras, Balandin, Francisco, Rodriguez-Valera, Dietmar J, Manstein, Georg, Bueldt, Ernst, Bamberg, and Valentin, Gordeliy
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Models, Molecular ,Rhodopsin ,genetic structures ,Light ,Protein Conformation ,Retina ,Cell Line ,Escherichia coli ,Humans ,Chromatography, High Pressure Liquid ,Research Articles ,Cell Models ,Binding Sites ,Spectrum Analysis ,fungi ,food and beverages ,SciAdv r-articles ,Life Sciences ,Hydrogen-Ion Concentration ,Proton Pumps ,Archaea ,Optogenetics ,Liposomes ,sense organs ,Protons ,Protein Binding ,Research Article - Abstract
Neurons expressing a novel rhodopsin can be activated by light; a complete story of protein structure and function follows., Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina (NsXeR) and suggest a mechanism of inward proton pumping. We demonstrate that the NsXeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.
- Published
- 2016
11. Mechanism of transmembrane signaling by sensor histidine kinases
- Author
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Ivan, Gushchin, Igor, Melnikov, Vitaly, Polovinkin, Andrii, Ishchenko, Anastasia, Yuzhakova, Pavel, Buslaev, Gleb, Bourenkov, Sergei, Grudinin, Ekaterina, Round, Taras, Balandin, Valentin, Borshchevskiy, Dieter, Willbold, Gordon, Leonard, Georg, Büldt, Alexander, Popov, and Valentin, Gordeliy
- Subjects
Models, Molecular ,Protein Domains ,Escherichia coli Proteins ,Escherichia coli ,Membrane Proteins ,Crystallization ,Phosphoproteins ,Signal Transduction - Abstract
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the
- Published
- 2016
12. 3D analysis of X-ray mesh scans and data collection strategies for macromolecular crystallography
- Author
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Gleb Bourenkov, Igor Melnikov, and Alexander Popov
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Inorganic Chemistry ,Crystallography ,Data collection ,Materials science ,Structural Biology ,3d analysis ,Macromolecular crystallography ,X-ray ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry - Published
- 2018
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13. The Gaming Addiction Problem and its Economic and Social Consequences: A Comprehensive, Dynamic Approach
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Ramesh, Kini, primary and Igor, Melnikov, additional
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- 2016
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14. Fast iodide-SAD phasing for membrane protein structure determination
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Valentin Gordeliy, Vadim Cherezov, Vitaly Polovinkin, Alexander Popov, Gordon A. Leonard, Valentin Borshchevskiy, Vitaly Shevchenko, Mikhail B. Shevtsov, Igor Melnikov, and Kirill Kovalev
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Inorganic Chemistry ,chemistry.chemical_classification ,Membrane protein ,Structural Biology ,Chemistry ,Iodide ,Biophysics ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry ,Phaser - Published
- 2016
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15. The analysis of the mesh scan data for macromolecular data collection
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Igor Melnikov, Alexander Popov, Gleb Bourenkov, and Olof Svensson
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Inorganic Chemistry ,Data collection ,Structural Biology ,Computer science ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry ,Computational science - Published
- 2015
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16. An in situ experimental study of young sea ice formation on an Antarctic lead
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Igor Melnikov
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Atmospheric Science ,Population ,Soil Science ,Aquatic Science ,Oceanography ,Ice core ,Geochemistry and Petrology ,Earth and Planetary Sciences (miscellaneous) ,Sea ice ,Melt pond ,education ,Earth-Surface Processes ,Water Science and Technology ,education.field_of_study ,geography ,geography.geographical_feature_category ,Ecology ,Lead (sea ice) ,Paleontology ,Forestry ,Arctic ice pack ,Brinicle ,Geophysics ,Space and Planetary Science ,Environmental science ,Seawater - Abstract
Three series of experimental results were obtained in situ during the U.S.Russian Ice Station Weddell 1 Expedition 1992 in the western Weddell Sea. Changes in salinity, silicate, and chlorophyll a concentrations were examined over sampling scales of hours, days, and months as microalgal populations grew in young sea ice. Sea ice growth rates were 0.38 cm h -1 for ice up to 9 cm (May 19-20), 0.13 cm h -1 for ice growth to 28 cm over the next 8 days, and 0.03 cm h -1 during 81 days of observations on ice 42-97 cm thick (March 18-June 7). It was shown that at the initial stage of ice formation, salt and nutrient accumulation occurred, then ice desalination intensified with increasing ice thickness. Brine within the ice showed a 12-hour period of oscillatory motion during the first day of ice growth and a 1.5- to 2-hour oscillation in the skeletal layer of 28-cm ice. Small numbers of diatoms were entrapped from seawater during the initial ice formation. Their reproduction (in terms of chlorophyll a concentration) markedly increased after the third day of ice formation. The highest concentrations of chlorophyll a (100 to 1000 times higher than the underlying seawater) were recorded within the bottom, brown-colored layer of all young ice cores studied during the 81-day experiment. The species composition of ice algal populations (99 species) was more diverse and rich than observed for phytoplankton (18 species) in surface seawater. The temporal and spatial distribution of all parameters studied were controlled by meteorological factors and brine drainage mechanisms
- Published
- 1995
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