Browsing by Author "Fedin, Matvey, V"

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    Exploring the interactions of short RNAs with the human 40S ribosomal subunit near the mRNA entry site by EPR spectroscopy
    (Oxford University Press, 2019) Malygin, Alexey A.; Krumkacheva, Olesya A.; Graifer, Dmitry M.; Timofeev, Ivan O.; Ochkasova, Anastasia S.; Meschaninova, Mariya, I; Venyaminova, Alya G.; Fedin, Matvey, V; Bowman, Michael; Karpova, Galina G.; Bagryanskaya, Elena G.; Institute of Chemical Biology & Fundamental Medicine, Siberian Branch of the RAS; Russian Academy of Sciences; Vorozhtsov Novosibirsk Institute of Organic Chemistry; Novosibirsk State University; International Tomography Center, Siberian Branch of Russian Academy of Sciences; University of Alabama Tuscaloosa
    The features of previously unexplored labile complexes of human 40S ribosomal subunits with RNAs, whose formation is manifested in the cross-linking of aldehyde derivatives of RNAs to the ribosomal protein uS3 through its peptide 55-64 located outside the mRNA channel, were studied by EPR spectroscopy methods. Analysis of subatomic 40S subunit models showed that a likely site for labile RNA binding is a cluster of positively charged amino acid residues between the mRNA entry site and uS3 peptide 55-64. This is consistent with our finding that the 3'-terminal mRNA fragment hanging outside the 40S subunit prevents the cross-linking of an RNA derivative to this peptide. To detect labile complexes of 40S subunits with RNA by DEER/PELDOR spectroscopy, an undecaribonucleotide derivative with nitroxide spin labels at terminal nucleotides was utilized. We demonstrated that the 40S subunit channel occupancy with mRNA does not affect the RNA derivative binding and that uS3 peptide 55-64 is not involved in binding interactions. Replacing the RNA derivative with a DNA one revealed the importance of ribose 2'-OH groups for the complex formation. Using the single-label RNA derivatives, the distance between the mRNA entry site and the loosely bound RNA site on the 40S subunit was estimated.
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    Unexpected one-pot formation of the 1H-6a,8a-epiminotri-cyclopenta[a,c,e][8]annulene system from cyclopentanone, ammonia and dimethyl fumarate. Synthesis of highly strained polycyclic nitroxide and EPR study
    (Beilstein-Institut, 2019) Dobrynin, Sergey A.; Kirilyuk, Igor A.; Gatilov, Yuri, V; Kuzhelev, Andrey A.; Krumkacheva, Olesya A.; Fedin, Matvey, V; Bowman, Michael K.; Bagryanskaya, Elena G.; Russian Academy of Sciences; Vorozhtsov Novosibirsk Institute of Organic Chemistry; Novosibirsk State University; International Tomography Center, Siberian Branch of Russian Academy of Sciences; University of Alabama Tuscaloosa
    The unexpected formation of a highly strained polycyclic amine was observed in a one-pot synthesis from cyclopentanone, dimethyl fumarate and ammonium acetate. This multistep reaction includes 1,3-dipolar cycloaddition of dimethyl fumarate to the cyclic azomethine glide formed in situ from cyclopentanone and ammonia. The polycyclic amine product was easily converted into a sterically shielded polycyclic nitroxide. The EPR spectra and spin relaxation behavior of the nitroxide were studied in solution. The spin relaxation seems well suited for the use as a biological spin label and are comparable with those of cyclic nitroxides with two spirocyclic moieties adjacent to the N-O-center dot group.