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111.
Alexey?A. Malygin Dmitri?M. Graifer Maria?I. Meschaninova Aliya?G. Venyaminova Olesya?A. Krumkacheva Matvey?V. Fedin Galina?G. Karpova Elena?G. Bagryanskaya 《Biophysical journal》2015,109(12):2637-2643
mRNAs are involved in complicated supramolecular complexes with human 40S and 80S ribosomes responsible for the protein synthesis. In this work, a derivative of nonaribonucleotide pUUCGUAAAA with nitroxide spin labels attached to the 5′-phosphate and to the C8 atom of the adenosine in sixth position (mRNA analog) was used for studying such complexes using double electron-electron resonance/pulsed electron-electron double resonance spectroscopy. The complexes were assembled with participation of tRNAPhe, which targeted triplet UUC of the derivative to the ribosomal peptidyl site and predetermined location of the adjacent GUA triplet coding for Val at the aminoacyl (A) site. The interspin distances were measured between the two labels of mRNA analog attached to the first nucleotide of the peptidyl site bound codon and to the third nucleotide of the A site bound codon, in the absence/presence of second tRNA bound at the A site. The values of the obtained interspin distances agree with those calculated for available near-atomic structures of similar complexes of 40S and 80S ribosomes, showing that neither 60S subunit nor tRNA at the A site have a noticeable effect on arrangement of mRNA at the codon-anticodon interaction area. In addition, the shapes of distance distributions in four studied ribosomal complexes allowed conclusions on conformational flexibility of mRNA in these complexes. Overall, the results of this study are the first, to our knowledge, demonstration of double electron-electron resonance/pulsed electron-electron double resonance application for measurements of intramolecular distances in multicomponent supramolecular complexes involving intricate cellular machineries and for evaluating dynamic properties of ligands bound to these machineries. 相似文献
112.
Ariel Jaitovich Martín Angulo Emilia Lecuona Laura A. Dada Lynn C. Welch Yuan Cheng Galina Gusarova Ermelinda Ceco Chang Liu Masahiko Shigemura Esther Barreiro Cam Patterson Gustavo A. Nader Jacob I. Sznajder 《The Journal of biological chemistry》2015,290(14):9183-9194
Patients with chronic obstructive pulmonary disease, acute lung injury, and critical care illness may develop hypercapnia. Many of these patients often have muscle dysfunction which increases morbidity and impairs their quality of life. Here, we investigated whether hypercapnia leads to skeletal muscle atrophy. Mice exposed to high CO2 had decreased skeletal muscle wet weight, fiber diameter, and strength. Cultured myotubes exposed to high CO2 had reduced fiber diameter, protein/DNA ratios, and anabolic capacity. High CO2 induced the expression of MuRF1 in vivo and in vitro, whereas MuRF1−/− mice exposed to high CO2 did not develop muscle atrophy. AMP-activated kinase (AMPK), a metabolic sensor, was activated in myotubes exposed to high CO2, and loss-of-function studies showed that the AMPKα2 isoform is necessary for muscle-specific ring finger protein 1 (MuRF1) up-regulation and myofiber size reduction. High CO2 induced AMPKα2 activation, triggering the phosphorylation and nuclear translocation of FoxO3a, and leading to an increase in MuRF1 expression and myotube atrophy. Accordingly, we provide evidence that high CO2 activates skeletal muscle atrophy via AMPKα2-FoxO3a-MuRF1, which is of biological and potentially clinical significance in patients with lung diseases and hypercapnia. 相似文献
113.
114.
Galina M. Zats Marina Kovaliov Amnon Albeck Shimon Shatzmiller 《Journal of peptide science》2015,21(6):512-519
Antimicrobial peptides (AMPs) appear to be good candidates for the development of new antibiotic drugs. We describe here the synthesis of peptidomimetic compounds that are based on a benzodiazepine scaffold flanked with positively charged and hydrophobic amino acids. These compounds mimic the essential properties of cationic AMPs. The new design possesses the benzodiazepine scaffold that is comprised of two glycine amino acids and which confers flexibility and aromatic hydrophobic ‘back’, and two arms used for further synthesis on solid phase for incorporation of charged and hydrophobic amino acids. This approach allowed us a better understanding of the influence of these features on the antimicrobial activity and selectivity. A novel compound was discovered which has MICs of 12.5 µg/ml against Staphylococcus aureus and 25 µg/ml against Escherichia coli, similar to the well‐known antimicrobial peptide MSI‐78. In contrast to MSI‐78, the above mentioned compound has lower lytic effect against mammalian red blood cells. These peptidomimetic compounds will pave the way for future design of potent synthetic mimics of AMPs for therapeutic and biomedical applications. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
115.
Alexey Teplyakov Galina Obmolova Gabriela Canziani Yonghong Zhao Lester Gutshall Sonia S. Jung Gary L. Gilliland 《Journal of molecular recognition : JMR》2011,24(4):570-575
Alzheimer's disease is a progressive neurodegenerative disease characterized by extracellular deposits of β‐amyloid (Aβ) plaques. Aggregation of the Aβ42 peptide leading to plaque formation is believed to play a central role in Alzheimer's disease pathogenesis. Anti‐Aβ monoclonal antibodies can reduce amyloid plaques and could possibly be used for immunotherapy. We have developed a monoclonal antibody C706, which recognizes the human Aβ peptide. Here we report the crystal structure of the antibody Fab fragment at 1.7 Å resolution. The structure was determined in two crystal forms, P21 and C2. Although the Fab was crystallized in the presence of Aβ16, no peptide was observed in the crystals. The antigen‐binding site is blocked by the hexahistidine tag of another Fab molecule in both crystal forms. The poly‐His peptide in an extended conformation occupies a crevice between the light and heavy chains of the variable domain. Two consecutive histidines (His4–His5) stack against tryptophan residues in the central pocket of the antigen‐binding surface. In addition, they form hydrogen bonds to the acidic residues at the bottom of the pocket. The mode of his‐tag binding by C706 resembles the Aβ recognition by antibodies PFA1 and WO2. All three antibodies recognize the same immunodominant B‐cell epitope of Aβ. By similarity, residues Phe–Arg–His of Aβ would be a major portion of the C706 epitope. Copyright © 2010 John Wiley & Sons, Ltd. 相似文献
116.
miRTour: Plant miRNA and target prediction tool 总被引:1,自引:0,他引:1
MicroRNAs (miRNAs) are important negative regulators of gene expression in plant and animals, which are endogenously produced from their own genes. Computational comparative approach based on evolutionary conservation of mature miRNAs has revealed a number of orthologs of known miRNAs in different plant species. The homology-based plant miRNA discovery, followed by target prediction, comprises several steps, which have been done so far manually. Here, we present the bioinformatics pipeline miRTour which automates all the steps of miRNA similarity search, miRNA precursor selection, target prediction and annotation, each of them performed with the same set of input sequences. AVAILABILITY: The database is available for free at http://bio2server.bioinfo.uni-plovdiv.bg/miRTour/ 相似文献
117.
Khomyakova EA Zubin EM Smirnov IP Pozmogova GE Stetsenko DA Oretskaya TS 《Nucleosides, nucleotides & nucleic acids》2011,30(7-8):577-584
An efficient method for the synthesis of DNA or RNA oligonucleotide 2'-hydrazides is described. Fully deprotected oligonucleotides containing a hydrazide group at the 2'-position of a uridine residue were obtained by a novel two-step procedure: periodate cleavage of an oligonucleotide with 1,2-diol group followed by conversion of the aldehyde to hydrazide with an extended linker arm using a homobifunctional reagent succinic dihydrazide and NaBH(3)CN. The resulting oligonucleotide 2'-hydrazides were efficiently conjugated by a click-type reaction at acidic pH to aliphatic or aromatic aldehydes with or without NaBH(3)CN reduction to afford novel 2'-conjugates. 相似文献
118.
Nazaret Hidalgo Giulia Mangiameli Teresa Manzano Galina G. Zhadan John F. Kennedy Valery L. Shnyrov Manuel G. Roig 《Biotechnology and Bioprocess Engineering》2011,16(4):821-829
The degradation and removal of a series of dyes used in the textile industry for polyester/wool (PES/WO) blends and present
in effluents, such as Green, Ash-Grey, Black, Navy Blue, Red and Yellow Domalan, and Orange and Red Bemacid, by catalytic
action, in the presence of H2O2, of extracts of a novel peroxidase from postharvest lentil stubble was investigated. The extracts of this peroxidase (LSP)
were effective in degrading these lastgeneration textile dyes, especially Green Domalan, Orange Bemacid, Grey and Black Domalan.
A sensitivity study was carried out for Green Domalan biodegradation to determine the effects of process parameters such as
pH, H2O2, enzyme and dye concentrations, contact and centrifugation times, and temperature. Standard ecotoxicity studies performed
with Vibrio fischeri revealed that the dye solutions treated with peroxidase and H2O2 were less ecotoxic than the untreated ones. 相似文献
119.
Chertkov O Brown PJ Kysela DT de Pedro MA Lucas S Copeland A Lapidus A Del Rio TG Tice H Bruce D Goodwin L Pitluck S Detter JC Han C Larimer F Chang YJ Jeffries CD Land M Hauser L Kyrpides NC Ivanova N Ovchinnikova G Tindall BJ Göker M Klenk HP Brun YV 《Standards in genomic sciences》2011,5(3):287-297
The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008. 相似文献
120.
Chertkov O Sikorski J Nolan M Lapidus A Lucas S Del Rio TG Tice H Cheng JF Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Ovchinnikova G Pati A Chen A Palaniappan K Djao OD Land M Hauser L Chang YJ Jeffries CD Brettin T Han C Detter JC Rohde M Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2011,4(1):13-22
Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献