Laboratory of Ribosome Structure and Function

Galina G. Karpova,
prof., Dr.Chem.Sci. The Russia State Prize in Science and Technique (1999) Prize of International Publishing Company “Nauka/Interperiodika” (2003, 2009, 2010)
Phone: +7(383)363-51-40, Email

• Study of structural and functional organization of human ribosomal translational complexes.
• Investigation of structural basis of molecular processes responsible for non-canonical translation of viral and several specific cellular mRNAs.
• Study of molecular mechanisms that control expression of human ribosomal protein genes at the splicing level.
• Search of the proteins providing delivery of RNA to exosomes, and study of structural aspects of this process.

• A unique basis has been created for isolation of functionally active ribosomes from human placenta and for preparation of human recombinant ribosomal proteins. These, together with the application of a site-directed cross-linking approach, made the lab worldwide recognized leader in systematic studies of molecular basis of the work of human protein synthesizing machinery for more than 20 years.
• mRNA binding center of the human ribosome has been studied with use of mRNA analogues, photoactivatable derivatives of oligoribonucleotides (synthesized in Laboratory of RNA Chemistry of ICBFM SB RAS). We showed that small subunit rRNA nucleotides, neighboring with mRNA, form a conserved core of the ribosome structurally identical in all kingdoms, while protein environments of mRNAs in mammalian and bacterial ribosomes are drastically different. [Graifer D.G. et al., Nucleic Acids. Res. 2004. 32, 3282; Molotkov M. et al., RNA Biol. 2005. 2, 63; Molotkov M. et al., RNA Biol. 2006. 3, 122].
• An approach has been elaborated to obtain derivatives of complicated highly structured RNAs bearing a photoactivatable cross-linker at the designed location. It is based on complementary-addressed (sequence-specific) modification of RNA. We showed that these derivatives are suitable tools for studying positioning of the HCV IRES on small subunit of the human ribosome. With application of this approach, ribosomal proteins neighboring specific HCV IRES subdomains in the small ribosomal subunit were identified. [Laletina E. et al., Nucleic Acids Res. 2006. 34, 2027; Babaylova E.S. et al., Nucleic Acids Res. 2009. 37, 1141]. It was shown that rpSA (р40) contributes significantly to the affinity of HCV IRES to the 40S ribosome. [Malygin A.A. et al., Mol. Biol. 2009. 43, 997 (Translated from Molekul. Biol. 2009. 43, 1070)]. (These studies were carried out in collaboration with the group headed by Prof. I. Shatsky at Belozersky Institute of Physico-Chemical Biology at Moscow State University).
• Keystone aspects of termination of protein synthesis on human ribosomes related to the recognition of purines in mRNA stop codons by polypeptide chain release factor eRF1 were clarified. It was shown that adenines and guanines stop signals are recognized by different conformations of the N-domain of eRF1, which underlies ability of the factor to decode all three stop codons. Invariant dipeptide 31-GT-32 was shown to be the key player in this recognition. [Bulygin K.N. et al., RNA. 2010. 16, 1902; Bulygin K.N. et al., Nucleic Acids Res. 2011. 39, 7134]. (These studies were carried out in collaboration with laboratory headed by Dr. L. Frolova, Engelhardt Institute of Molecular Biology RAS).
• With use of recombinant human ribosomal proteins it was shown for the first time that regulation of splicing of pre-mRNAs of proteins S13, S16 and S26 occurs via a feedback mechanism, the excess of free protein leads to inhibition of first intron excision from pre-mRNA of the respective protein. In the case of protein S13 this mechanism was confirmed by experiments in vivo. [Malygin A.A. et al., Nucl. Acids Res. 2007. 35, 6414].

1. Graifer D.M., Malygin A.A., Zharkov D.O., Karpova G.G. Eukaryotic ribosomal protein S3: A constituent of translational machinery and an extraribosomal player in various cellular processes. Biochimie. 2014. 99, 8-18.
2. Malygin A.A., Kossinova O.A., Shatsky I., Karpova G.G. HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation. Nucleic Acids Res. 2013. 41, 8706-8714.
3. Sharifulin D.E., Babaylova E.S., Kossinova O.A., Bartuli Y.S., Graifer D.M., Karpova G.G. Ribosomal protein S5e is implicated in translation initiation via its interaction with N-terminal domain of initiation factor eIF2. ChemBioChem. 2013. 14, 2136-2143.
4. Kossinova O., Malygin A.A., Krol A., Karpova G.G. A novel insight into the mechanism of mammalian selenoprotein synthesis. RNA. 2013. 19(8), 1147-1158.
5. Graifer D.M., Karpova G.G. Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries. RSC Adv. 2013. 3(9), 2858-2872.
6. Ivanov A.V., Malygin A.A., Karpova G.G. Mg2+ ions affect structure of central domain of 18S rRNA near ribosomal protein S13 binding site. Molecular Biology (Moscow). 2013. 47, 140–148.
7. Bulygin K.N., Malygin A.A., Hountondji C., Graifer D.M., Karpova G.G. Positioning of CCA-arms of the A- and the P-tRNAs towards the 28S rRNA in the human ribosome. Biochimie. 2013. 95(2), 195-203.
8. Malygin A.A., Shatsky I.N., Karpova G.G. Proteins of the human 40S ribosomal subunit involved in hepatitis C IRES binding as revealed from fluorescent labeling. Biochemistry (Moscow). 2013. 78, 53-59.
9. Graifer D.M., Karpova G.G. Structural aspects of ribosomal ligands interactions providing the work of the human translational machinery. In: Ribosomes. Zhou Lin and Wang Liu (Eds). Nova Science Publishers. Inc. NY. 2013, 1-30.
10. Graifer D.M., Karpova G.G. A strategy for determination of protein sites involved in the interactions with RNA ligands in the human translational machinery. In: Protein Purification and Analysis I - Methods and Applications. iConcept Press Ltd. Hong Kong. 2013, 57-76.
11. Graifer D.M., Karpova G.G. Structural and functional topography of the human ribosome. Acta Biochem. Biophys. Sin. 2012. 44, 281-299.
12. Sharifulin D.E., Khairulina Y.S., Ivanov A.V., Meshchaninova M.I., Venyaminova A.G., Graifer D.M., Karpova G.G. A central fragment of ribosomal protein S26 containing the eukaryote-specific motif YxxPKxYxK is a key component of the ribosomal binding site of mRNA region 5’ of the E site codon. Nucleic Acids Res. 2012. 40, 3056-3065.
13. Graifer D.M., Zhigailov A., Venyaminova A.G., Malygin A.A., Iskakov B., Karpova G.G. 2’-OH of mRNA are critical for the binding of its codons at the 40S ribosomal P site but not at the mRNA entry site. FEBS Lett. 2012. 586, 3731-3736.
14. Bulygin K.N., Khairulina Yu.S., Kolosov P.M., Ven’yaminova A.G., Graifer D.M., Vorobjev Yu.N., Frolova L.Yu., Karpova G.G. Adenine and guanine recognition of stop codon is mediated by different N domain conformations of translation termination factor eRF1. Nucleic Acids Res. 2011. 39, 7134–7146.
15. Malygin A.A., Babaylova E.S., Loktev V.B., Karpova G.G. A region in the C-terminal domain of ribosomal protein SA required for binding of SA to the human 40S ribosomal subunit. Biochimie. 2011. 93, 612-617.
16. Ilin A.A., Malygin A.A., Karpova G.G. Ribosomal protein S18e as a putative molecular staple for the 18S rRNA 3’-major domain core. Biochim. Biophys. Acta. 2011. 1814, 505-512.

RFBR (Grants of Russian Foundation for Basic Research)

• N.12-04-93111_a “Structural aspects of molecular mechanisms providing selenoprotein synthesis in mammals” (2012-2014)
• N.14-04-31202 “Molecular contacts of ribosomal protein S3e in the course of translation process in mammals” (2014-2015)
• N.14-04-00709 Structural basis of molecular interactions that provide translation initiation and termination in mammals” (2014-2016)
• N.14-04-00740 “Specific features of ribosomal proteins displayed in various processes in the cell” (2014-2016)
• N.14-04-00777 “Cellular proteins interacting with specific structural elements of exosomal RNAs (2014-2016)

Program of the Presidium of RAS
N6 “Molecular and cell biology”

• N.10 “Studying structural basis of molecular processes providing the work of human translational apparatus” (2013-2017)

• Preparative centrifuge Beckman J2-21 (USA);
• vacuum concentrator with a centrifuge UNIVAPO (Germany);
• high performance liquid chromatograph Milichrom A4 (EcoNova, Russia);
• power suppliers for gel electrophoresis of proteins and nucleic acids;
• UV-lamp SpotCure (UVP, UK) with light pipes for irradiation of reaction mixtures in standard plastic tubes 0.5-2 ml;
• PCR amplifier MJ MINI (Bio Rad, USA).