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Akparov V.K.,Research Institute for Genetics and Selection of Industrial Microorganisms | Timofeev V.I.,RAS Shubnikov Institute of Crystallography | Kuranova I.P.,RAS Shubnikov Institute of Crystallography
Crystallography Reports | Year: 2011

Crystals of recombinant carboxypeptidase T (CPT) from Thermoactinomyces vulgaris were grown in a capillary by the counterdiffusion method in the absence of calcium ions. The three-dimensional structure of CPT was solved at 1.69-Å resolution using the X-ray diffraction data collected from the crystals of the enzyme on the SPring-8 synchrotron radiation facility and was then refined to Rfact = 16.903% and Rfree = 18.165%. The coordinates of the refined model were deposited in the Protein Data Bank (PDB ID: 3QNV). A comparison of this structure with the structure of wild-type CPT containing bound calcium ions, which was determined earlier, revealed a number of conformational changes both in the calcium-binding sites and the enzyme active site. Based on the results of this comparison, the possible factors responsible for the difference in the catalytic activity of the two forms of the enzyme are considered. © 2011 Pleiades Publishing, Ltd. Source


Fertig E.J.,Johns Hopkins University | Ding J.,Dana-Farber Cancer Institute | Favorov A.V.,Johns Hopkins University | Favorov A.V.,Research Institute for Genetics and Selection of Industrial Microorganisms | And 2 more authors.
Bioinformatics | Year: 2010

Summary: Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS improves on other enrichment measurement methods by combining a Markov chain Monte Carlo (MCMC) matrix factorization algorithm (GAPS) with a threshold-independent statistic inferring activity on gene sets. The software is provided as open source C++ code built on top of JAGS software with an R interface. © The Author 2010. Published by Oxford University Press. All rights reserved. Source


Kulakovskiy I.V.,RAS Engelhardt Institute of Molecular Biology | Belostotsky A.A.,Research Institute for Genetics and Selection of Industrial Microorganisms | Kasianov A.S.,RAS Engelhardt Institute of Molecular Biology | Esipova N.G.,RAS Engelhardt Institute of Molecular Biology | And 3 more authors.
Bioinformatics | Year: 2011

Motivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved. Source


Kulakovskiy I.V.,RAS Engelhardt Institute of Molecular Biology | Boeva V.A.,Research Institute for Genetics and Selection of Industrial Microorganisms | Boeva V.A.,French Institute of Health and Medical Research | Boeva V.A.,MINES ParisTech | And 2 more authors.
Bioinformatics | Year: 2010

Summary: ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster. © The Author 2010. Published by Oxford University Press. All rights reserved. Source


Lavrov K.V.,Research Institute for Genetics and Selection of Industrial Microorganisms | Yanenko A.S.,Research Institute for Genetics and Selection of Industrial Microorganisms
Russian Journal of Genetics | Year: 2013

The gene for new Rhodococcus erythropolis TA37 acylamidase, which possesses unique substrate specificity, has been cloned and expressed in E. coli. Substrates for this enzyme are not only simple amides, such as acetamide and propionamide, but also N-substituted amides, such as 4′-nitroacetanilide. The 1431-bp gene was expressed in E. coli BL21 (DE3) cells on pET16b plasmid under the control of a promoter of the φ{symbol} 10 gene from the T7 phage. The molecular mass of recombinant acylamidase in E. coli was 55 kDa, which corresponded to that of native acylamidase from Rhodococcus erythropolis TA37. Recombinant acylamidase was able to hydrolize N-substituted amides. A search of a nucleotide database and multiple alignment revealed that acylamidase belonged to the Amidase protein family PF01425, but its nucleotide and amino acid sequences differed significantly from those of the described amidases. © 2013 Pleiades Publishing, Inc. Source

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