Библиотека института биофизики СО РАН

Главная

Базы данных

Труды сотрудников ИБФ СО РАН - результаты поиска

Вид поиска

Каталог книг и продолжающихся изданий библиотеки Института биофизики СО РАН

Иностранные журналы библиотеки Института биофизики СО РАН

Отечественные журналы библиотеки Института биофизики СО РАН

Каталог диссертаций ИБФ СО РАН

Труды сотрудников ИБФ СО РАН

Область поиска

в найденном

Формат представления найденных документов:
полный	информационный	краткий

Отсортировать найденные документы по:
автору	заглавию	году издания	типу документа

Поисковый запрос: (<.>K=network<.>)

Общее количество найденных документов : 33
Показаны документы с 1 по 20

1-20 21-33

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Rogozin D.Y., Zykov V.V., Degermendzhi A.G.
Заглавие : Ecology of purple sulfur bacteria in the highly stratified meromictic Lake Shunet (Siberia, Khakassia) in 2002-2009
Место публикации : Microbiology (Russian Federation). - 2012. - Vol. 81, Is. 6. - С. 727-735. - ISSN 00262617 (ISSN) , DOI 10.1134/S0026261712060148
Ключевые слова (''Своб.индексиров.''): bacteriochlorophyll a--chemocline--meromictic lake--purple sulfur bacteria--seasonal dynamics--bacteria (microorganisms)--chromatiaceae
Аннотация: Phototrophic sulfur bacteria form dense accumulations in the chemocline zones of stratified lakes where light reaches the sulfide-containing layers of water. Many works are dedicated to the ecophysiology of these microorganisms in meromictic lakes. However, the role of these microorganisms in the trophic network of these ecosystems, the ways of biomass utilization, and the contribution to the turnover of biogenic elements have so far been insufficiently understood. This work deals with the analysis of many years' seasonal dynamics of the biomass of purple sulfur bacteria and the physicochemical conditions of their environment in Lake Shunet (Siberia, Khakassia, Russia), unraveling the causes of their anomalous development in the chemocline of this lake, as well as the comparative analysis of such type of ecosystems. Lake Shunet is characterized by markedly pronounced stratification and the high density of purple sulfur bacteria (PSB) in the chemocline, which is comparable to that of Lake Mahoney (Canada) where the number of PSB is the greatest among those known in the world. It was shown that, in the period 2002-2009, the total amount of bacterio-chlorophyll a in the water column of Lake Shunet increased and did not correlate with the seasonal variations in temperature and illumination in the chemocline. It was established that PSB cells in the purple layer experienced the effect of self-shading. The sedimentation rate of purple sulfur bacteria in Lake Shunet was low due to the pronounced density gradient in the chemocline zone. Thus, the high number of PSB in the chemocline was due to the combination of strong illumination, a high sulfide concentration, and a high water density gradient, which was responsible for stable stratification and contributed to the accumulation of the cells in a narrow layer. The data obtained could be useful for the paleoreconstruction of climatically deter-mined changes in the level of the lake and its periods of meromixis by the presence of carotenoids and bacte-riochlorophylls in the bottom sediments. В© 2012 Pleiades Publishing, Ltd.
Scopus
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Medvedeva S.E., Boyandin A., Lankin Y., Kotov D., Rodicheva E., Popova L.
Заглавие : BIOLUMBASE - The database of natural and transgenic bioluminescent organisms
Место публикации : Luminescence. - 2005. - Vol. 20, Is. 2. - С. 90-96. - ISSN 15227235 (ISSN) , DOI 10.1002/bio.809
Ключевые слова (''Своб.индексиров.''): bioluminescence--database--luminous bacteria--lux gene--marine--article--bacterial strain--bacterium culture--bacterium isolation--bioluminescence--data base--gene construct--medical information--transgenics--wide area network--bacteria--bacterial proteins--databases, factual--ecology--luminescence--luminescent proteins--marine biology--organisms, genetically modified--photobacterium--transgenes
Аннотация: The Institute of Biophysics SB RAS hosts and maintains a specialized collection of luminous bacteria (CCIBSO 836) containing over 700 strains isolated in various regions of the world's oceans. The culture collection is a source of lux genes and biologically active substances. The wide application of bioluminescence in medicine and ecology has given importance to analys-ing information on the structure and functioning of bioluminescence systems in natural and transgenic microorganisms, as well as on their features that are closely interrelated with bioluminescence. The aims of our BIOLUMBASE database are: gathering information on microorganisms with lux genes, their analysis and free access, and distribution of this data throughout the global network. The database includes two sections, natural and transgenic luminous microorganisms, and is updated by our own experimental results, the published literature and internet resources. For the future, a publicly available internet site for BIOLUMBASE is planned. This will list the strains and provide comprehensive information on the properties and functions of luminous bacteria, the mechanisms of regulation of bioluminescence systems, constructs with lux genes, and applications of bioluminescence in microbiology, ecology, medicine and biotechnology. It is noteworthy that this database will also be useful for evaluation of biological hazards of transgenic strains. Users will be able to carry out bibliographic and strain searches starting from any feature of interest. Copyright В© 2005 John Wiley & Sons, Ltd.
Scopus
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Rodicheva E.K., Medvedeva S.E., Vydryakova G.A., Chugaeva Yu.V., Kuznetsov A.M.
Заглавие : Gene pool maintenance and the prospects for using a special-purpose luminous bacteria collection
Место публикации : Applied Biochemistry and Microbiology. - 1998. - Vol. 34, Is. 1. - С. 70-76. - ISSN 00036838 (ISSN)
Аннотация: The culture collection maintained at the Institute of Biophysics (IB), Siberian Division, Russian Academy of Sciences, is the only deposit in Russia and CIS which contains about 700 strains of five species of marine luminous bacteria sampled in various sites of the World Ocean. The strains collected are used for identification of luminous bacteria; studying their physiology, biochemistry, and cytology; and developing concepts of organization and metabolism of luminous bacteria under natural and laboratory conditions. Methods of their storage and practical use are developed. The results of these studies are summarized in a data bank, which will be incorporated into the general network of data banks on microbial cultures kept in Russia and into the international network of data banks on microorganisms (MSDN). Systematization of information on luminous bacteria possessing a unique visual marker allows their extensive use in basic research and genetic engineering, for environmental and medical applications, and for biotechnological purposes.
Scopus
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Eremeeva E.V., Markova S.V., Frank L.A., Visser AJWG, van Berkel WJH, Vysotski E.S.
Заглавие : Bioluminescent and spectroscopic properties of His-Trp-Tyr triad mutants of obelin and aequorin
Колич.характеристики :9 с
Место публикации : Photochem. Photobiol. Sci.: ROYAL SOC CHEMISTRY, 2013. - Vol. 12, Is. 6. - С. 1016-1024. - ISSN 1474-905X, DOI 10.1039/c3pp00002h
Примечания : Cited References: 46. - The work was supported by RFBR grant 12-04-00131, by the Programs of the Government of Russian Federation "Measures to Attract Leading Scientists to Russian Educational Institutions" (grant 11.G34.31.0058), "Molecular and Cellular Biology" of RAS, President of Russian Federation "Leading science school" (grant 1044.2012.2). E.V.E. was supported by Wageningen University Sandwich PhD-Fellowship Program.
Предметные рубрики: CA2+-REGULATED PHOTOPROTEINS
CA2+-BINDING PHOTOPROTEIN
SEQUENCE-ANALYSIS
CRYSTAL-STRUCTURE
VIOLET BIOLUMINESCENCE
ANGSTROM RESOLUTION
MNEMIOPSIS-LEIDYI
LIGHT-EMISSION
W92F OBELIN
CLONING
Аннотация: Ca2+-regulated photoproteins are responsible for the bioluminescence of a variety of marine organisms, mostly coelenterates. The photoproteins consist of a single polypeptide chain to which an imidazopyrazinone derivative (2-hydroperoxycoelenterazine) is tightly bound. According to photoprotein spatial structures the side chains of His175, Trp179, and Tyr190 in obelin and His169, Trp173, Tyr184 in aequorin are at distances that allow hydrogen bonding with the peroxide and carbonyl groups of the 2-hydroperoxycoelenterazine ligand. We replaced these amino acids in both photoproteins by residues with different hydrogen bond donor-acceptor capacity. All mutants exhibited luciferase-like bioluminescence activity, hardly present in the wild-type photoproteins, and showed low or no photoprotein activity, except for aeqH169Q (24% of wild-type activity), obeW179Y (23%), obeW179F (67%), obeY190F (14%), and aeqY184F (22%). The results clearly support the supposition made from photoprotein spatial structures that the hydrogen bond network formed by His-Trp-Tyr triad participates in stabilizing the 2-hydroperoxy adduct of coelenterazine. These residues are also essential for the positioning of the 2-hydroperoxycoelenterazine intermediate, light emitting reaction, and for the formation of active photoprotein. In addition, we demonstrate that although the positions of His-Trp-Tyr residues in aequorin and obelin spatial structures are almost identical the substitution effects might be noticeably different.
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Vysotski E.S., Liu Z.J., Markova S.V., Blinks J.R., Deng L..., Frank L.A., Herko M..., Malikova N.P., Rose J.P., Wang B.C., Lee J...
Заглавие : Violet bioluminescence and fast kinetics from W92F obelin: Structure-based proposals for the bioluminescence triggering and the identification of the emitting species
Колич.характеристики :12 с
Место публикации : Biochemistry: AMER CHEMICAL SOC, 2003. - Vol. 42, Is. 20. - С. 6013-6024. - ISSN 0006-2960, DOI 10.1021/bi027258h
Примечания : Cited References: 45
Предметные рубрики: RAY CRYSTALLOGRAPHIC ANALYSIS
PHOTOPROTEIN AEQUORIN
ANGSTROM RESOLUTION
RECOMBINANT OBELIN
CALCIUM
LUMINESCENCE
LONGISSIMA
EVOLUTION
PROTEINS
COELENTERAZINE
Аннотация: Obelin from the hydroid Obelia longissima and aequorin are members of a subfamily of Ca2+-regulated photoproteins that is a part of the larger EF-hand calcium binding protein family. On the addition of Ca2+, obelin generates a blue bioluminescence emission (lambda(max) = 485 nm) as the result of the oxidative decarboxylation of the bound substrate, coelenterazine. The W92F obelin mutant is noteworthy because of the unusually high speed with which it responds to sudden changes of [Ca2+] and because it emits violet light rather than blue due to a prominent band with lambda(max) = 405 nm. Increase of pH in the range from 5.5 to 8.5 and using D2O both diminish the contribution of the 405 nm band, indicating that excited state proton transfer is involved. Fluorescence model studies have suggested the origin of the 485 nm emission as the excited state of an anion of coelenteramide, the bioluminescence reaction product, and 405 nm from the excited neutral state. Assuming that the dimensions of the substrate binding cavity do not change during the excited state formation, a His22 residue within hydrogen bonding distance to the 6-(p-hydroxy)-phenyl group of the excited coelenteramide is a likely candidate for accepting the phenol proton to produce an ion-pair excited state, in support of recent suggestions for the bioluminescence emitting state. The proton transfer could be impeded by removal of the Trp92 H-bond, resulting in strong enhancement of a 405 nm band giving the violet color of bioluminescence. Comparative analysis of 3D structures of the wild-type (WT) and W92F obelins reveals that there are structural displacements of certain key Ca2+-ligating residues in the loops of the two C-terminal EF hands as well as clear differences in hydrogen bond networks in W92F. For instance, the hydrogen bond between the side-chain oxygen atom of Asp 169 and the main-chain nitrogen of Arg112 binds together the incoming alpha-helix of loop III and the exiting cc-helix of loop IV in WT, providing probably concerted changes in these EF hands on calcium binding. But this linkage is not found in W92F obelin. These differences apparently do not change the overall affinity to calcium of W92F obelin but may account for the kinetic differences between the WT and mutant obelins. From analysis of the hydrogen bond network in the coelenterazine binding cavity, it is proposed that the trigger for bioluminescence reaction in these Ca2+-regulated photoproteins may be a shift of the hydrogen bond donor-acceptor separations around the coelenterazine-2-hydroperoxy substrate, initiated by small spatial adjustment of the exiting a-helix of loop IV.
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : van Oort B..., Eremeeva E.V., Koehorst RBM, Laptenok S.P., van Amerongen H..., van Berkel WJH, Malikova N.P., Markova S.V., Vysotski E.S., Visser AJWG, Lee J...
Заглавие : Picosecond Fluorescence Relaxation Spectroscopy of the Calcium-Discharged Photoproteins Aequorin and Obelin
Колич.характеристики :6 с
Коллективы : NATO Collaborative Linkage [979229]; RFBR [09-04-12-022]; 'Stichung voor Fundamenteel Onderzock der Materic (FOM)'; NWO; Wageningen University; European Community Marie Curie Research Training Network [MRTN-CT-2005-019481]; netherlands Organization [635 000 014]
Место публикации : Biochemistry: AMER CHEMICAL SOC, 2009. - Vol. 48, Is. 44. - С. 10486-10491. - ISSN 0006-2960, DOI 10.1021/bi901436m
Примечания : Cited References: 33. - This work was supported by NATO Collaborative Linkage Grant No 979229,Grants of SB RAS and RFBR 09-04-12-022, MCB program of RAS BvO was supported by 'Stichung voor Fundamenteel Onderzock der Materic (FOM)', which is financially supported by the NWO. and by I Rubicon grant of NWO E V E was supported by Wageningen University Sandwich Ph D-Fellowship program S P L was supported by Wageningen University Sandwich Ph D.-Fellowship program, European Community Marie Curie Research Training Network MRTN-CT-2005-019481 (From FLIM to FLIN), and Computational Science Gram 635 000 014 from the netherlands Organization for Scientific Research
Предметные рубрики: CA2+-REGULATED PHOTOPROTEINS
VIOLET BIOLUMINESCENCE
ANGSTROM RESOLUTION
RECOMBINANT OBELIN
CRYSTAL-STRUCTURE
W92F OBELIN
COELENTERAZINE
MECHANISM
EXPRESSION
PROTEINS
Аннотация: Addition of calcium tons to the Ca(2+)-regulated photoproteins, such its aequorin and obelin, produces it blue bioluminescence originating from fluorescence transition of the protein-bound product coelenteramide. The kinetics of several transient fluorescent species of the bound coelenteramide is resolved after picosecond-laser excitation and streak camera detection. The Initially formed spectral distributions at picosecond-times are broad, evidently comprised of two contributions, One at higher energy (similar to 25 000 cm(-1)) assigned as from the Ca(2+)-discharged photoprotein-bound coelenteramide in its neutral state. This component decays much more rapidly (t(1/2) similar to 2 ps) in the case of the Ca(2+)-discharged obelin than aequorin (t(1/2) similar to 30 ps). The Second component at lower energy shows several intermediates in the 150-500 ps miles. with it Final species having spectral maxima 19 400 cm(-1), bound to Ca(2+)-discharged obelin. and 2 1300 cm(-1), bound to Ca(2+)-discharged aequorin, and both have it fluorescence decay lifetime of 4 ns It is proposed that the rapid kinetics of these fluorescence transients oil the picosecond time scale, correspond to times For relaxation of the protein Structural environment of the binding cavity
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Eremeeva E.V., Markova S.V., van Berkel WJH, Vysotski E.S.
Заглавие : Role of key residues of obelin in coelenterazine binding and conversion into 2-hydroperoxy adduct
Колич.характеристики :7 с
Коллективы : RFBR [12-04-00131]; Programs of the Government of Russian Federation "Measures to Attract Leading Scientists to Russian Educational Institutions" [11.G34.31.0058]; "Molecular and Cellular Biology" of RAS, President of Russian Federation "Leading science school" [3951.2012.4]; Wageningen University Sandwich PhD-Fellowship Program
Место публикации : J. Photochem. Photobiol. B-Biol.: ELSEVIER SCIENCE SA, 2013. - Vol. 127. - С. 133-139. - ISSN 1011-1344, DOI 10.1016/j.jphotobiol.2013.08.012
Примечания : Cited References: 65. - The work was supported by RFBR grant 12-04-00131, by the Programs of the Government of Russian Federation "Measures to Attract Leading Scientists to Russian Educational Institutions" (grant 11.G34.31.0058), "Molecular and Cellular Biology" of RAS, President of Russian Federation "Leading science school" (grant 3951.2012.4). E.V.E. was supported by Wageningen University Sandwich PhD-Fellowship Program.
Предметные рубрики: CA2+-REGULATED PHOTOPROTEINS
SEQUENCE-ANALYSIS
CRYSTAL-STRUCTURE
APO-OBELIN
CA2+-BINDING PHOTOPROTEIN
VIOLET BIOLUMINESCENCE
AEQUORIN REGENERATION
ANGSTROM RESOLUTION
RECOMBINANT OBELIN
MNEMIOPSIS-LEIDYI
Ключевые слова (''Своб.индексиров.''): bioluminescence--coelenterazine--obelin--aequorin--photoprotein
Аннотация: Bioluminescence of a variety of marine organisms is caused by monomeric Ca2+-regulated photoproteins, to which a peroxy-substituted coelenterazine, 2-hydroperoxycoelenterazine, is firmly bound. From the spatial structure the side chains of Tyr138, His175, Trp179, and Tyr190 of obelin are situated within the substrate-binding pocket at hydrogen bond distances with different atoms of the 2-hydroperoxycoelenterazine. Here we characterized several obelin mutants with substitutions of these residues regarding their bioluminescence, coelenterazine binding, and kinetics of active obelin formation. We demonstrate that Tyr138, His175, Trp179, and Tyr190 are all important for coelenterazine activation; substitution of any of these residues leads to significant decrease of the apparent reaction rate. The hydrogen bond network formed by Tyr138, Trp179 and Tyr190 participates in the proper positioning of coelenterazine in the active site and subsequent stabilization of the 2-hydroperoxy adduct of coelenterazine. His175 might serve as a proton shuttle during 2-hydroperoxycoelenterazine formation. (C) 2013 Elsevier B.V. All rights reserved.
WOS
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Natashin P.V., Markova S.V., Lee J., Vysotski E.S., Liu Z.-J.
Заглавие : Crystal structures of the F88Y obelin mutant before and after bioluminescence provide molecular insight into spectral tuning among hydromedusan photoproteins
Место публикации : FEBS J. - 2014. - Vol. 281, Is. 5. - С. 1432-1445. - ISSN 17424658 (ISSN) , DOI 10.1111/febs.12715
Ключевые слова (''Своб.индексиров.''): aequorin--bioluminescence--coelenterazine, obelin--6 (4 hydroxyphenyl) derivative--aequorin--benzene derivative--calcium ion--hydromedusan--mutant protein--obelin--oxygen--photoprotein--unclassified drug--amino acid substitution--article--bioluminescence--calcium transport--crystal structure--fluorescence--hydrogen bond--priority journal--protein conformation--protein structure--wild type--coelenterata--aequorin--bioluminescence--ca2+-regulated photoprotein--coelenterazine, obelin--amino acid substitution--animals--conserved sequence--crystallography, x-ray--hydrogen bonding--hydrozoa--luminescent proteins--models, molecular--mutagenesis, site-directed--mutant proteins--protein conformation--spectrophotometry
Аннотация: Ca2+-regulated photoproteins are responsible for the bioluminescence of a variety of marine coelenterates. All hydromedusan photoproteins are a single-chain polypeptide to which 2- hydroperoxycoelenterazine is tightly but non-covalently bound. Bioluminescence results from oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. The bioluminescence spectral maxima of recombinant photoproteins vary in the range 462-495 nm, despite a high degree of identity of amino acid sequences and spatial structures of these photoproteins. Based on studies of obelin and aequorin mutants with substitution of Phe to Tyr and Tyr to Phe, respectively [Stepanyuk GA et al. (2005) FEBS Lett 579, 1008-1014], it was suggested that the spectral differences may be accounted for by an additional hydrogen bond between the hydroxyl group of a Tyr residue and an oxygen atom of the 6-(p-hydroxyphenyl) substituent of coelenterazine. Here, we report the crystal structures of two conformation states of the F88Y obelin mutant that has bioluminescence and product fluorescence spectra resembling those of aequorin. Comparison of spatial structures of the F88Y obelin conformation states with those of wild-type obelin clearly shows that substitution of Phe to Tyr does not affect the overall structures of either F88Y obelin or its product following Ca2+ discharge, compared to the conformation states of wild-type obelin. The hydrogen bond network in F88Y obelin being due to the Tyr substitution clearly supports the suggestion that different hydrogen bond patterns near the oxygen of the 6-(p-hydroxyphenyl) substituent are the basis for spectral modifications between hydromedusan photoproteins. Comparison of spatial structures and the hydrogen bond network formed into the substrate-binding cavity of WT obelin, F88Y obelin, and aequorin clearly shows that the main cause determining different light emission colors of hydromedusan photoproteins is a different arrangement of the hydrogen-bond network near OH group of 6-(p-hydroxyphenyl) substituent of coelenterazine due to the presence of either Phe or Tyr residue. © 2014 FEBS.
Scopus
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Eremeeva E.V., Burakova L.P., Krasitskaya V.V., Kudryavtsev A.N., Shimomura O..., Frank L.A.
Заглавие : Hydrogen-bond networks between the C-terminus and Arg from the first alpha-helix stabilize photoprotein molecules
Колич.характеристики :7 с
Коллективы : RFBR [12-04-00753-a]; Government of Russian Federation [11.G34.31.0058]
Место публикации : Photochem. Photobiol. Sci.: ROYAL SOC CHEMISTRY, 2014. - Vol. 13, Is. 3. - С. 541-547. - ISSN 1474-905X, DOI 10.1039/c3pp50369k. - ISSN 1474-9092
Примечания : Cited References: 22. - The work was supported by RFBR grant 12-04-00753-a, by the Program of the Government of Russian Federation "Measures to Attract Leading Scientists to Russian Educational Institutions" (grant 11.G34.31.0058).
Предметные рубрики: GREEN FLUORESCENT PROTEIN
CA2+-REGULATED PHOTOPROTEIN
BIOLUMINESCENT IMMUNOASSAY
COELENTERAZINE BINDING
ANGSTROM RESOLUTION
ENERGY-TRANSFER
FUSION PROTEIN
APO-OBELIN
AEQUORIN
EXPRESSION
Аннотация: Previous studies have stated that aequorin loses most of its bioluminescence activity upon modification of the C-terminus, thus limiting the production of photoprotein fusion proteins at its N-terminus. In the present work, we investigate the importance of the C-terminal proline and the hydrogen bonds it forms for photoprotein active complex formation, stability and functional activity. According to the crystal structures of obelin and aequorin, two Ca2+-regulated photoproteins, the carboxyl group of the C-terminal Pro forms two hydrogen bonds with the side chain of Arg21 (Arg15 in aequorin case) situated in the first a-helix. Whereas, deletion or substitution of the C-terminal proline could noticeably change the bioluminescence activity, stability or the yield of an active photoprotein complex. Therefore, modifications of the first alpha-helix Arg has a clear destructive effect on the main photoprotein properties. A C-terminal hydrogen-bond network is proposed to be important for the stability of photoprotein molecules towards external disturbances, when taking part in the formation of locked protein conformations and isolation of coelenterazine-binding cavities.
WOS
Найти похожие

10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Wawrzak Z..., Sandalova T..., Steffens J.J., Basarab G.S., Lundqvist T..., Lindqvist Y..., Jordan D.B.
Заглавие : High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH
Колич.характеристики :15 с
Место публикации : Proteins: WILEY-LISS, 1999. - Vol. 35, Is. 4. - P425-439. - ISSN 0887-3585, DOI 10.1002/(SICI)1097-0134(19990601)35:4425::AID-PROT63.0.CO;2-1
Примечания : Cited References: 33
Предметные рубрики: MAGNAPORTHE-GRISEA
HEMAGGLUTININ
GLYCOPROTEIN
REFINEMENT
MELANIN
DISEASE
SITE
Ключевые слова (''Своб.индексиров.''): structure-based design--enzyme inhibitors--x-ray crystallography--fungicides--melanin biosynthesis
Аннотация: Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at preventing the fungal disease caused by Magnaporthe grisea. A method for cocrystallization of enzyme with inhibitors at neutral pH has produced several crystal structures of enzyme-inhibitor complexes at resolutions ranging from 1.5 to 2.2 Angstrom Four high resolution structures of different enzyme-inhibitor complexes are described. In contrast to the original X-ray structure of the enzyme, the four new structures have well-defined electron density for the loop region comprising residues 115-119 and a different conformation between residues 154 and 160. The structure of the enzyme complex with an aminoquinazoline inhibitor showed that the inhibitor is in a position to form a hydrogen bond with the amide of the Asn131 side chain and with two water molecules in a fashion similar to the salicylamide inhibitor in the original structure, thus confirming design principles. The aminoquinazoline structure also allows for a more confident assignment of donors and accepters in the hydrogen bonding network, The structures of the enzyme complexes with two dichlorocyclopropane carboxamide inhibitors showed the two chlorine atoms nearly in plane with the amide side chain of Asn131. The positions of Phe53 and Phe158 are significantly altered in the new structures in comparison to the two structures obtained from crystals grown at acidic pH, The multiple structures help define the mobility of active site amino acids critical for catalysis and inhibitor binding. Proteins 1999;35:425-439. (C) 1999 Wiley-Liss, Inc.
WOS
Найти похожие

11.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Bartsev S.I.
Заглавие : Naturally deducing estimate for the coefficient of CELSS closure
Колич.характеристики :8 с
Место публикации : SPACE LIFE SCIENCES: CLOSED ARTIFICIAL ECOSYSTEMS AND LIFE SUPPORT SYSTEMS. Ser. ADVANCES IN SPACE RESEARCH: PERGAMON-ELSEVIER SCIENCE LTD, 2003. - Vol. 31: Meeting of F4 1 Session of the 34th Scientific Assembly of COSPAR (OCT, 2002, HOUSTON, TEXAS), Is. 7. - P1675-1682. - ISBN 0273-1177, DOI 10.1016/S0273-1177(03)00107-8
Примечания : Cited References: 4
Аннотация: The term Closed Ecological System (CES) is in wide use. However there is no generally accepted measure of the closure of ecological systems. In order to obtain reproducibility of experiments with natural and man-made CES (with respect to degree of closure) some universal estimate needs to be developed. Understanding ecological systems as a network and closure as the degree of matter recycling allows the use of matrix graphs. Graphs are very natural forms for the presentation of the network of matter flows in ecosystems. An estimate equal to the sum of products of weights of oriented edges that constitute contour is suggested as a measure of the degree of closure in ecosystems. It is shown that this estimate can be uniformly applied to ecosystems of arbitrary size and configuration of flows. (C) 2003 COSPAR. Published by Elsevier Science Ltd. All rights reserved.
WOS
Найти похожие

12.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Bartsev S.I.
Заглавие : Essence of life and multiformity of its realization: expected signatures of life
Колич.характеристики :5 с
Место публикации : SPACE LIFE SCIENCES: SEARCH FOR SIGNATURES OF LIFE, AND SPACE FLIGHT ENVIRONMENTAL EFFECTS ON THE NERVOUS SYSTEM. Ser. ADVANCES IN SPACE RESEARCH-SERIES: PERGAMON-ELSEVIER SCIENCE LTD, 2004. - Vol. 33: 2nd World Space Congress/34th COSPAR Scientific Assembly (OCT 10-19, 2002, HOUSTON, TX), Is. 8. - P1313-1317. - ISBN 0273-1177, DOI 10.1016/j.asr.2003.08.032
Примечания : Cited References: 23
Предметные рубрики: COMPLEX NETWORKS
EMERGENCE
EVOLUTION
Ключевые слова (''Своб.индексиров.''): astrobiology--signatures of life--essence of life--multiformity of life
Аннотация: The question on the essence of life as phenomenon is the key one for astrobiology, since the answer to this question determines "breadth of our outlook". Taking Earth's version of life as the pattern extremely under-estimates our estimation of the probability of life origin and respectively expected probability of extraterrestrial life discovery. In the paper the hypothetical key attribute of life in general is selected on the base of comparative analyses and deductive inference. Simulation conducted on the base of neural network model shows that the same function could be realized by means of great variety of structures, which originated in the course of an evolutionary process. So multiplicity of evolutionary outcomes essentially increases the probability of final result - realization of an integrated function providing fitness to environment. Life as the integrated function can be realized via great variety of development ways and structures. A logical consequence of definitions for life as phenomenon is suggested. Final one is "Life is specific organization of informational and energetic processes coupling, enabling choice-making, and displayed as anomalies of different kinds". Anomalies of visible form, mechanical movement, chemical composition and noticeable response are considered. Presented in the paper sweeping generalization is not rigorously proven, however it can play heuristic role in increasing the level of specificity of searching for extraterrestrial life. (C) 2004 COSPAR. Published by Elsevier Ltd. All rights reserved.
WOS
Найти похожие

13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kashkin V.B., Lankin Y.P., Sakash I.Y.
Заглавие : Predicting the state of the Earth's ozone layer for different time intervals with the use of neural networks
Колич.характеристики :7 с
Место публикации : Izv. Atmos. Ocean. Phys.: INTERPERIODICA, 2005. - Vol. 41, Is. 4. - P469-475. - ISSN 0001-4338
Примечания : Cited References: 10
Предметные рубрики: ERRORS
Аннотация: The problems of studying and simulating the Earth's ozone layer are discussed. It is shown that the construction of models for the total ozone content (TOC) in the stratosphere with the use of neural networks is promising. The neural-network algorithm used is described. TOC forecasts for different time periods are made using neuronetwork models.
WOS
Найти похожие

14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artamonova V. S., Kolmakova O. V., Kirillova E. A., Makhrov A. A.
Заглавие : Phylogeny of Salmonoid Fishes (Salmonoidei) Based on mtDNA COI Gene Sequences (Barcoding)
Колич.характеристики :15 с
Коллективы : Russian Science Foundation [16-14-10001]
Место публикации : Contemp. Probl. Ecol.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2018. - Vol. 11, Is. 3. - С. 271-285. - ISSN 1995-4255, DOI 10.1134/S1995425518030022. - ISSN 1995-4263(eISSN)
Примечания : Cited References:102. - We are very grateful to colleagues who helped collect samples: E.G. Berestovskii, I.N. Bolotov, E.A. Borovikova, I.V. Vikhrev, L.A. Glushchenko, V.V. Ignatenko, D.P. Karabanov, A.P. Novoselov, V.M. Spitsyn, V.A. Shirokov, and I.L. Shchurov; employees of Trout Hatchery "Adler", the Federal Breeding and Genetic Center for Fish Culture, and Vygsky and Kemsky fish hatcheries; and residents of Barabash-Levada, Len-lu, and Chupa settlements. We also thank S.S. Alekseev for identifying sharp-snouted and blunt-snouted lenoks. This work was supported by the Russian Science Foundation, project no. 16-14-10001.
Предметные рубрики: MOLECULAR DATING ANALYSIS
GROWTH-HORMONE INTRONS
SALMONIFORMES
Ключевые слова (''Своб.индексиров.''): evolution--network--molecular clock--amino acid sequence--reproductive--isolation--immobilization--fishes
Аннотация: We have analyzed the partial sequences of the mitochondrial COI gene along with the amino acid sequences of cytochrome oxidase subunit I, encoded by this gene region, in representatives of 11 genera of salmonoid fish. For amino acid sequences, two alternative networks are constructed with outgroups represented by either Esocoidei or Osmeroidei as the supposed ancestral groups. This way, Osmeroidei appear to be closer to the salmonoid fish than Esocoidei, and their presence in the network as an outgroup explains the available data on the morphology and karyology of salmonoids much better. A number of the results of this study are fundamentally new. In particular, the slowing down of the molecular evolution of the grayling (Thymallidae) is shown. We conclude that the charr (Salvelinus) is one of the modern genera of salmonoids closest to their ancestor. The hypothesis of the phylogenetic proximity of the genera Brachymystax, Hucho, and Salmo has been confirmed. We also discuss the possibility that it is namely the changes in the amino acid sequence of cytochrome oxidase subunit I that lead to postzygotic reproductive isolation between taxa.
WOS,
Смотреть статью,
Scopus
Найти похожие

15.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Vysotski E., Markova S., Natashin P., Stepanyuk G., Lee J., Malikova N., Liu Z.
Заглавие : Hydrogen bond network near OH group of 6-(p-hydroxyphenyl) substituent of coelenterazine determines the bioluminescence spectra differences among hydromedusan calcium-regulated photoproteins
Колич.характеристики :2 с
Коллективы : RFBR [17-04-00764]; China-Russia international collaboration grant from Chinese Academy of Sciences; Natural Science Foundation of China
Место публикации : FEBS Open Bio: WILEY, 2018. - Vol. 8. - С. 435-436. - ISSN 2211-5463
Примечания : Cited References:0. - This work was supported by RFBR grant 17-04-00764 and a China-Russia international collaboration grant from the Chinese Academy of Sciences and the Natural Science Foundation of China.
WOS
Найти похожие

16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Botvich I. Y., Zorkina T. M.
Заглавие : The Restoration Dynamics of Fallow Vegetation in the Steppe Zone of the Khakassia Republic Based on Terrain and Satellite Data
Место публикации : Biophysics: Pleiades Publishing, 2019. - Vol. 64, Is. 2. - С. 309-315. - ISSN 00063509 (ISSN) , DOI 10.1134/S0006350919020039
Аннотация: Abstract: The dynamics and specific features of the restoration of forbs–grass–wormwood and wormwood–grass phytocoenoses on fallow lands in the Altai region, the Republic of Khakassia, were determined on the basis of terrain and satellite data. The species composition, structure, and phytomass of the phytocoenoses were revealed. A gradual formation of structural elements of steppe communities in the studied areas was determined. This work showed the usefulness of time series of satellite data on the NDVI (Normalized Difference Vegetation Index) obtained with the use of MODIS (Moderate Resolution Imaging Spectroradiometer) for the study of specific features of restored fallows. In general the biological parameters, projective cover, and phytomass determine the value of the NDVI. Interannual NDVI variability reflects the rate and time period of fallow restoration. From a certain point, the parameters increased and became close to the steppe (control variant). It has been revealed that not only abiotic factors (climate and soils), but also biotic parameters (grazing and recreational load) affect the NDVI. In this connection, the duration of restoration stages does not always correspond to the published data. They vary under different conditions. Climatic data of the Abakan meteorological station (index 29862 in the network of the World Meteorological Organization) for the period from 2000 to 2017 were statistically treated. The long-term annual average norms of temperatures and precipitation amounts (year and month) for the World Meteorological Organization base period of 1961–1990 were calculated. The dynamics of the temperature and precipitation, using long-term series of data, has been analyzed. © 2019, Pleiades Publishing, Inc.
Scopus,
Смотреть статью
Найти похожие

17.

Вид документа : Статья из сборника (выпуск продолж. издания)
Шифр издания :
Автор(ы) : Bartsev S., Baturina P.
Заглавие : A heuristic neural network model in the research of properties of evolutionary trajectories
Место публикации : IOP Conference Series: Materials Science and Engineering: Institute of Physics Publishing, 2019. - Vol. 537: International Workshop on Advanced Technologies in Material Science, Mechanical and Automation Engineering - MIP: Engineering-2019 (4 April 2019 through 6 April 2019, ) Conference code: 149243, Is. 4. - , DOI 10.1088/1757-899X/537/4/042001
Аннотация: There is considerable data on molecular evolution, but there remains no approach to systematizing them within the framework of the key problems of biology. To search for the most common properties of evolving systems, the heuristic method has been proposed. Artificial networks of formal neurons were chosen as the heuristic model object. The paper examines the divergent component of evolutionary trajectory formation. As a result of the simulation, the dependence of the potential variability parameter on the position of the fitness function landscape was obtained. The simulation results are in agreement with the real data of molecular evolution experiments. © Published under licence by IOP Publishing Ltd.
Scopus,
Смотреть статью
Найти похожие

18.

Вид документа : Статья из сборника (выпуск продолж. издания)
Шифр издания :
Автор(ы) : Dolgova T., Bartsev S.
Заглавие : Neural networks playing 'matching pennies' with each other: Reproducibility of game dynamics
Место публикации : IOP Conference Series: Materials Science and Engineering: Institute of Physics Publishing, 2019. - Vol. 537: International Workshop on Advanced Technologies in Material Science, Mechanical and Automation Engineering - MIP: Engineering-2019 (4 April 2019 through 6 April 2019, ) Conference code: 149243, Is. 4. - , DOI 10.1088/1757-899X/537/4/042002
Аннотация: Reflection is an essential feature of consciousness and possibly the single most important one. This fact allows us to simplify the objective of the concept of 'neural correlates of consciousness' and to focus investigations on reflection itself. Reflexive games are the concentrated and pure embodiment of reflection manifestation without the addition of other higher cognitive functions. In this paper, we use the game 'matching pennies' ("Odd-Even") in order to trace the strategies and possible patterns of recurrent neural network operation. Experimental results show the splitting of all considered game patterns into two groups. A significant difference was observed in these groups of patterns, indicating a qualitative difference in game dynamics apparently due to the qualitatively different dynamic patterns of neuron excitations of the networks. A similar splitting of all players into two groups was found by other authors for human players, which differ in terms of the reflection availability. By this, we can assume that one of the causes of the splitting is that the presence of reflection in a particular group of recurrent neural networks dramatically changes the game meta-strategy. © Published under licence by IOP Publishing Ltd.
Scopus,
Смотреть статью
Найти похожие

19.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ronzhin N. O., Posokhina E. D., Mikhlina E. V., Simunin M. M., Nemtsev I. V., Ryzhkov I. I., Bondar V. S.
Заглавие : Production of a Composite Based on Alumina Nanofibers and Detonation Nanodiamonds for Creating Phenol Indication Systems
Место публикации : Dokl. Chem.: Pleiades Publishing, 2019. - Vol. 489, Is. 1. - С. 267-271. - ISSN 00125008 (ISSN), DOI 10.1134/S001250081911003X
Аннотация: Abstract: A composite of alumina nanofibers (ANF) and modified detonation nanodiamonds (MDND) was produced by mixing aqueous suspensions of the components in a weight ratio of 5 : 1 with subsequent incubation of the mixture for 15 min at 32°C. It was assumed that the formation of the composite is ensured by the difference of the zeta potentials of the components, which is negative for MDND and positive for ANF. Vacuum filtration of the mixture through a fluoroplastic filter (pore diameter 0.6 ?m) formed disks 40 mm in diameter, which were then heat-treated at 300°C to impart structural stability to the composite. Scanning electron microscopy detected that the obtained composite has a network structure, in which MDND particles are distributed over the surface of ANF. It was determined that the MDND particles incorporated in the composite catalyze the phenol–4-aminoantipyrine–H2O2 oxidative azo coupling reaction to form a colored product (quinoneimine). The applicability of the composite to repeated phenol detection in aqueous samples was demonstrated. © 2019, Pleiades Publishing, Ltd.
Scopus
Найти похожие

20.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ronzhin N. O., Posokhina E. D., Mikhlina E. V., Simunin M. M., Nemtsev I. V., Ryzhkov I. I., Bondar V. S.
Заглавие : Production of a Composite Based on Alumina Nanofibers and Detonation Nanodiamonds for Creating Phenol Indication Systems
Колич.характеристики :5 с
Коллективы : Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [18-29-19078 mk]
Место публикации : Dokl. Chem.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2019. - Vol. 489. - С. 267-271. - ISSN 0012-5008, DOI 10.1134/S001250081911003X. - ISSN 1608-3113(eISSN)
Примечания : Cited References:13. - This work was supported by the Russian Foundation for Basic Research (project no. 18-29-19078 mk).
Предметные рубрики: NANOPARTICLES
GRAPHENE
Аннотация: A composite of alumina nanofibers (ANF) and modified detonation nanodiamonds (MDND) was produced by mixing aqueous suspensions of the components in a weight ratio of 5 : 1 with subsequent incubation of the mixture for 15 min at 32 degrees C. It was assumed that the formation of the composite is ensured by the difference of the zeta potentials of the components, which is negative for MDND and positive for ANF. Vacuum filtration of the mixture through a fluoroplastic filter (pore diameter 0.6 mu m) formed disks 40 mm in diameter, which were then heat-treated at 300 degrees C to impart structural stability to the composite. Scanning electron microscopy detected that the obtained composite has a network structure, in which MDND particles are distributed over the surface of ANF. It was determined that the MDND particles incorporated in the composite catalyze the phenol-4-aminoantipyrine-H2O2 oxidative azo coupling reaction to form a colored product (quinoneimine). The applicability of the composite to repeated phenol detection in aqueous samples was demonstrated.
WOS
Найти похожие