Pracownie usługowo-badawcze

Dr Igor Zhukov

Środowiskowa Pracownia Biologicznego NMR

Zakres usług i badań

Our facility provides services for the nuclear magnetic resonance (NMR) spectroscopy of biomolecules (peptides, proteins, RNA, DNA). One-dimensional and multidimensional NMR experiments on 1H, 19F, 15N, 13C, and 31P nuclei can be performed. Variable temperatures that meet most requirements of biological studies are available.

Contact person

Igor Żukow (PhD), email: igor@ibb.waw.pl, tel.: +48 22 592 20 48

Usługi

Opis usług

Our facility has expertise in the structural analysis of biomolecules in solution based on two- and three-dimensional homo- and heteronuclear spectra. Our experience includes experimental data for resonance assignments and information about molecular dynamic processes retrieved from 15N relaxation experiments. We use several techniques to extract information about binding small substrates to large proteins, which can be applicable to select inhibitors of the proteins of interest. Such techniques are indispensable in structural studies of proteins, oligonucleotides, oligosaccharides, and their complexes.

Aparatura

The facility is equipped with two three-channel Varian NMR spectrometers working at a magnetic field strength of 9.4 and 11.7 T, corresponding to 400 and 500 MHz 1H resonance frequencies, respectively. Standard one-dimensional spectra of 1H and nuclei from a broad-frequency range (lower limit: 40.5 MHz for 15N; upper limit: 161.9 MHz for 31P) can be recorded. Triple probe heads allow the measurement of two- and three-dimensional homo- and heteronuclear spectra. Measurements can be performed at temperatures of 0-70°C.

Współpraca

    • Kosma Szutkowski, NanoBioMedical Centre, Adam Mickiewicz University, Poznań, Poland, www.cnbm.amu.edu.pl.
    • Maciej Kozak, Physical Department, Adam Mickiewicz University, Poznań, Poland, www.amu.edu.pl
    • Sylwia Rodziewicz-Motowidlo, Faculty of Chemistry, University of Gdańsk, Poland, www.ug.edu.pl
    • Marjana Nović, National Institute of Chemistry, Ljubljana, Slovenia, www.ki.si
    • Dusan Turk, Josef Stefan Institute, Ljubljana, Slovenia, www.ijs.si
    • Zbigniew Domiński, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA, www.med.unc.edu

Klienci

    • Consorcium Silicon Group Ltd. Great Britain

Badania

Opis badań

The main scientific interests of our facility focus on structural analysis and molecular dynamic processes on a protein backbone based on 15N relaxation measurements. The NMR spectrometers in the facility acquire experimental data for uniformly labeled (15N- or 13C15N-) proteins with a molecular mass up to 20 kDa. The facility has expertise with the evaluation of high-resolution three-dimensional structures of small proteins, posttranslational modifications, analysis of interaction peptides, or ligands with proteins. We are interested in exploring molecular dynamic processes based on 15N relaxation experiments. Our research projects also include studies of the trans-membrane fragments in different types of micelles or phospholipids with application diffusion measurements on 31P and 2H isotopes. We utilize NMR techniques to create effective inhibitors against selected proteins. We recently began structural analyses of proteins and peptides with paramagnetic ions, such as Cu(II), with NMR techniques based on the effects of paramagnetic relaxation enhance (PRE).

Wybrane publikacje

    • Structural Analysis and Dynamic Processes of the Transmembrane Segment Inside Different Micellar Environments—Implications for the TM4 Fragment of the Bilitranslocase Protein Szutkowski, K., Sikorska, E., Bakanovych, I., Choudhury, A. R., Perdih, A., Jurga, S., Novic, M., and Zhukov, I. (2019). Structural International journal of molecular sciences, 20(17), 4172.
    • Structural analysis of the Sant/Myb domain of flash and yarp proteins and their complex with the c-terminal fragment of npat by nmr spectroscopy and computer simulations Bucholc, K., Skrajna, A., Adamska, K., Yang, X. C., Krajewski, K., Poznański, J., Dadlez, M., Dominski, Z., and Zhukov, I. (2020). International journal of molecular sciences, 21(15), 5268.
    • Rational drug-design approach supported with thermodynamic studies—a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Winiewska-Szajewska, M., Płonka, D., Zhukov, I., & Poznański, J. (2019) Scientific Reports, 9, 1-11.
    • The RxLR motif of the host targeting effector AVR3a of phytophthora infestans is cleaved before secretion Wawra, S., Trusch, F., Matena, A., Apostolakis, K., Linne, U., Zhukov, I., Stanek, J., Kozminski, W., Davidson, I., Secombes, C.J., Bayer, P., and van West, P. (2017). The Plant Cell, 29, 1184-1195.
    • NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution Maszota‐Zieleniak, M., Jurczak, P., Orlikowska, M., Zhukov, I., Borek, D., Otwinowski, Z., Skowron, P., Pietralik, Z., Kozak, M., Szymanska, A., and Rodziewicz‐Motowidło, S. (2020) The FEBS Journal, 287, 361-376.

Publikacje

KAZIMIERCZUK K., ZAWADZKA A., KOŹMIŃSKI W., ZHUKOV I., Determination of spin-spin couplings from ultrahigh resolution 3D NMR spectra obtained by optimized random sampling and multidimensional fourier transformation. Journal of the American Chemical Society (2008) 130: 5404-5405 IF 7,885
GOZDEK A., ZHUKOV I., POLKOWSKA-NOWAKOWSKA A., POZNAŃSKI J., STANKIEWICZ-DROGOŃ A., PAWŁOWICZ J.M., ZAGÓRSKI-OSTOJA W., BOROWSKI P., BOGUSZEWSKA-CHACHULSKA A.M., NS3 peptide, a novel potent Hepatitis C virus NS3 helicase inhibitor: its mechanism of action and antiviral activity in the replicon system. Antimicrobial Agents and Chemotherapy (2008) 52(2): 393-401 IF 4,390
ZHUKOV I., EJCHART A., BIERZYŃSKI A., Structural and Motional Changes Induces in apo-S100A1 protein by the disulfide formation between Its Cys 85 residue and ß-mercaptoethanol. Biochemistry (2008) 47: 640-650 IF 3,368
ZHUKOV I., BAYER P., SCHOLERMANN B., EJCHART A., 15N magnetic relaxation study of backbone dynamics of the ribosome- associated cold shock response protein Yfia of Esterichia coli. Acta Biochimica Polonica (2007) 54(4): 769-775 IF 1,363
KAZIMIERCZUK K., ZAWADZKA A., KOŹMIŃSKI W., ZHUKOV I., Lineshapes and artifacts in Multidimensional Fourier Transform of arbitrary sampled NMR data sets. Journal of Magnetic Resonance (2007) 188: 344-356 IF 2,076
JAREMKO Ł., JAREMKO M., FILIPEK R., WOJCIECHOWSKI M., SZCZEPANOWSKI R.H., BOCHTLER M., ZHUKOV I., NMR assignment of a structurally uncharacterised fragment of recombinant mouse ubiquitin-activating enzyme. Journal of Biomolecular NMR (2006) 36: 43 IF 1,791
KAZIMIERCZUK K., ZAWADZKA A., KOŹMIŃSKI W., ZHUKOV I., Random sampling of evolution time space and fourier transform processing. Journal of Biomolecular NMR (2006) 36: 157-168 IF 1,791
KAZIMIERCZUK K., KOŹMIŃSKI W., ZHUKOV I., Two-dimensional fourier transform of arbitrarily sampled NMR data sets. Journal of Magnetic Resonance (2006) 179: 323-328 IF 2,076
EJCHART A., ZHUKOV I., NMR-based structure determination of proteins in solution. Chapter in: The Proteomics Protocols Handbook. Ed. J.M. Walker. Humana Press (2005): 967-982
ZARĘBSKA Z., ZIELIŃSKA J., ZHUKOV I., MAŚLIŃSKI W., Apoptosis induced by membrane damage in human lymphocytes; effects of arachidonic acid and its photoproducts. Acta Biochimica Polonica (2005) 52: 179-194 IF 1,363
KOŹMIŃSKI W., ZHUKOV I., PECUL M., SADLEJ J., A protein backbone ψ and φ angle dependence of 2JN(i),Cα(i - 1): The new NMR experiment and quantum chemical calculations. Journal of Biomolecular NMR (2005) 31: 87-95 IF 1,791
ZHUKOVA L., ZHUKOV I., BAL W., WYSŁOUCH-CIESZYŃSKA A., Redox modifications of the C-terminal cysteine residue cause structural changes S100A1 and S100B proteins. Biochimica et Biophysica Acta. Molecular Cell Research (2004) 1742: 191-201 IF 3,482
KOŹMIŃSKI W., ZHUKOV I., The set of triple-resonance sequences with a multiple quantum coherence evolution period. Journal of Magnetic Resonance (2004) 171: 338-344 IF 2,461
KOŹMIŃSKI W., ZHUKOV I., The DQ-HN{CACB} and DQ-HN(CO){CACB} sequences with evolution of double quantum Cα-Cβ coherences. Journal of Magnetic Resonance (2004) 171: 186-191 IF 2,461