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21.
Amar Singh Taras Dauzhenka Petras J. Kundrotas Michael J. E. Sternberg Ilya A. Vakser 《Proteins》2020,88(9):1180-1188
Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important to investigate the applicability of docking techniques to modeled proteins. We present new comprehensive benchmark sets of protein models for the development and validation of protein docking, as well as a systematic assessment of free and template-based docking techniques on these sets. As opposed to previous studies, the benchmark sets reflect the real case modeling/docking scenario where the accuracy of the models is assessed by the modeling procedure, without reference to the native structure (which would be unknown in practical applications). We also expanded the analysis to include docking of protein pairs where proteins have different structural accuracy. The results show that, in general, the template-based docking is less sensitive to the structural inaccuracies of the models than the free docking. The near-native docking poses generated by the template-based approach, typically, also have higher ranks than those produces by the free docking (although the free docking is indispensable in modeling the multiplicity of protein interactions in a crowded cellular environment). The results show that docking techniques are applicable to protein models in a broad range of modeling accuracy. The study provides clear guidelines for practical applications of docking to protein models. 相似文献
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Dynamic microtubules produce an asymmetric E-cadherin–Bazooka complex to maintain segment boundaries
Natalia A. Bulgakova Ilya Grigoriev Alpha S. Yap Anna Akhmanova Nicholas H. Brown 《The Journal of cell biology》2013,201(6):887-901
Distributing junctional components around the cell periphery is key for epithelial tissue morphogenesis and homeostasis. We discovered that positioning of dynamic microtubules controls the asymmetric accumulation of E-cadherin. Microtubules are oriented preferentially along the dorso-ventral axis in Drosophila melanogaster embryonic epidermal cells, and thus more frequently contact E-cadherin at dorso-ventral cell–cell borders. This inhibits RhoGEF2, reducing membrane recruitment of Rho-kinase, and increasing a specific E-cadherin pool that is mobile when assayed by fluorescence recovery after photobleaching. This mobile E-cadherin is complexed with Bazooka/Par-3, which in turn is required for normal levels of mobile E-cadherin. Mobile E-cadherin–Bazooka prevents formation of multicellular rosette structures and cell motility across the segment border in Drosophila embryos. Altogether, the combined action of dynamic microtubules and Rho signaling determines the level and asymmetric distribution of a mobile E-cadherin–Bazooka complex, which regulates cell behavior during the generation of a patterned epithelium. 相似文献
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Marina V. Shirmanova Ekaterina O. Serebrovskaya Konstantin A. Lukyanov Ludmila B. Snopova Marina A. Sirotkina Natalia N. Prodanetz Marina L. Bugrova Ekaterina A. Minakova Ilya V. Turchin Vladislav A. Kamensky Sergey A. Lukyanov Elena V. Zagaynova 《Journal of biophotonics》2013,6(3):283-290
KillerRed is known to be a unique red fluorescent protein displaying strong phototoxic properties. Its effectiveness has been shown previously for killing bacterial and cancer cells in vitro. Here, we investigated the photototoxicity of the protein on tumor xenografts in mice. HeLa Kyoto cell line stably expressing KillerRed in mitochondria and in fusion with histone H2B was used. Irradiation of the tumors with 593 nm laser led to photobleaching of KillerRed indicating photosensitization reaction and caused significant destruction of the cells and activation of apoptosis. The portion of the dystrophically changed cells increased from 9.9% to 63.7%, and the cells with apoptosis hallmarks from 6.3% to 14%. The results of this study suggest KillerRed as a potential genetically encoded photosensitizer for photodynamic therapy of cancer. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) 相似文献
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Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States 下载免费PDF全文
Lawrence G. Oates David S. Duncan Ilya Gelfand Neville Millar G. Philip Robertson Randall D. Jackson 《Global Change Biology Bioenergy》2016,8(3):539-549
Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land‐use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N2O emissions and potential environmental drivers of these fluxes from a three‐year establishment‐phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures (switchgrass, miscanthus, and poplar), and perennial polycultures (native grass mixture, early successional community, and restored prairie) all grown using best management practices specific to the system. Cumulative three‐year N2O emissions from annuals were 142% higher than from perennials, with fertilized perennials 190% higher than unfertilized perennials. Emissions ranged from 3.1 to 19.1 kg N2O‐N ha?1 yr?1 for the annuals with continuous corn > corn–soybean–canola rotation and 1.1 to 6.3 kg N2O‐N ha?1 yr?1 for perennials. Nitrous oxide peak fluxes typically were associated with precipitation events that closely followed fertilization. Bayesian modeling of N2O fluxes based on measured environmental factors explained 33% of variability across all systems. Models trained on single systems performed well in most monocultures (e.g., R2 = 0.52 for poplar) but notably worse in polycultures (e.g., R2 = 0.17 for early successional, R2 = 0.06 for restored prairie), indicating that simulation models that include N2O emissions should be parameterized specific to particular plant communities. Our results indicate that perennial bioenergy crops in their establishment phase emit less N2O than annual crops, especially when not fertilized. These findings should be considered further alongside yield and other metrics contributing to important ecosystem services. 相似文献
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Amorphous Cobalt Boride (Co2B) as a Highly Efficient Nonprecious Catalyst for Electrochemical Water Splitting: Oxygen and Hydrogen Evolution 下载免费PDF全文
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Ilya G. Kichigin Massimo Giovannotti Alex I. Makunin Bee L. Ng Marsel R. Kabilov Alexey E. Tupikin Vincenzo Caputo Barucchi Andrea Splendiani Paolo Ruggeri Willem Rens Patricia C. M. O’Brien Malcolm A. Ferguson-Smith Alexander S. Graphodatsky Vladimir A. Trifonov 《Molecular genetics and genomics : MGG》2016,291(5):1955-1966