Saint Petersburg, Russia
Saint Petersburg, Russia

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Varizhuk A.,Engenlhardt Institute of Molecular Biology | Ischenko D.,Moscow Institute of Physics and Technology | Tsvetkov V.,FSBI Research Institute of Influenza | Novikov R.,RAS N. D. Zelinsky Institute of Organic Chemistry | And 6 more authors.
Biochimie | Year: 2017

The definition of DNA and RNA G-quadruplexes (G4s) has recently been broadened to include structures with certain defects: bulges, G-vacancies or mismatches. Despite the striking progress in computational methods for assessing G4 folding propensity, predicting G4s with defects remains problematic, reflecting the enhanced sequential diversity of these motifs. “Imperfect” G4 motifs, i.e., those containing interrupted or truncated G-runs, are typically omitted from genomic analyses. We report here studies of G4s with defects and compare these structures with classical (“perfect”) quadruplexes. Thermal stabilities and ligand interactions are also discussed. We exploited a simple in-house computational tool for mining putative G4s with defects in the human genome. The obtained profiles of the genomic distribution of imperfect G4 motifs were analyzed. Collectively, our findings suggest that, similar to classical G4s, imperfect G4s could be considered as potential regulatory elements, pathology biomarkers and therapeutic targets. © 2017 The Authors

Egorov V.V.,RAS Petersburg Nuclear Physics Institute | Lebedev D.V.,RAS Petersburg Nuclear Physics Institute | Shaldzhyan A.A.,FSBI Research Institute of Influenza | Sirotkin A.K.,FSBI Research Institute of Influenza | And 5 more authors.
Prion | Year: 2014

The fibrillogenesis of a peptide corresponding to residues 35-51 of human α-lactalbumin (1GYDTQAIVENNESTEYG17) can be dramatically enhanced by the addition of a tetrapeptide TDYG homologous to its C-terminus (TEYG). Generation of spontaneous hydrolytic products similar to this peptide was demonstrated by mass-spectrometry analysis of GYDTQAIVE NNESTEYG peptide solution components during fibrillogenesis. Possible mechanisms and roles of short peptides in protein metabolism are discussed. © 2014 Taylor & Francis Group, LLC.

Egorov V.V.,RAS Petersburg Nuclear Physics Institute | Matusevich O.V.,Saint Petersburg State University | Shaldzhyan A.A.,FSBI Research Institute of Influenza | Skvortsov A.N.,FSBI Research Institute of Influenza | And 8 more authors.
International Journal of Peptides | Year: 2013

A mirror-symmetry motif was discovered in the N-terminus of the influenza virus PB1 protein. Structure of peptide comprised of the corresponding part of PB1 (amino acid residues 6-25) was investigated by circular dichroism and in silico modeling. We found that peptide PB1 (6-25) in solution assumes beta-hairpin conformation. A truncated peptide PB1 (6-13), containing only half of the mirror-symmetry motif, appeared to stabilize the beta-structure of the original peptide and, at high concentrations, was capable of reacting with peptide to form insoluble aggregates in vitro. Ability of PB1 (6-13) peptide to interact with the N-terminal domain of PB1 protein makes it a potential antiviral agent that inhibits PA-PB1 complex formation by affecting PB1 N-terminus structure. © 2013 Vladimir V. Egorov et al.

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