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

SKOROBOGATOV O.Y., LOZHKO D., ZHUKOV I., KOZLOV O., TKACHUK Z., Study of dephosphorylated 2'-5'-linked oligoadenylates impact on apo-S100A1 protein conformation by heteronuclear NMR and circular dichroism. Biopolymers and Cell (2014) 30(4): 279-285 IF -
KACZKA P., WINIEWSKA M., ZHUKOV I., REMPOŁA B., BOLEWSKA K., ŁOZIŃSKI T., EJCHART A., POZNAŃSKA A., WIERZCHOWSKI K.L., POZNAŃSKI J., The TFE-induced transient native-like structure of the intrinsically disordered σ704 domain of Escherichia coli RNA polymerase. European Biophysics Journal (2014) 43(12): 581-594 IF 2.474
JAREMKO M., JAREMKO Ł., NOWAKOWSKI M., WOJCIECHOWSKI M., SZCZEPANOWSKI R.H., PANECKA R., ZHUKOV I., BOCHTLER M., EJCHART A., NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme. Journal of Structural Biology (2014) 185(1): 69-78 IF 3.369
CHOUDHURY A.R., PERDIH A., ŽUPERL Š., ,SIKORSKA E., SOLMAJER T., JURGA S., ZHUKOV I., NOVIČ M., Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy. Biochimica et Biophysica Acta- Biomembranes (2013) 1828(11): 2609–2619 IF 3.389
LOZHKO D., STANEK J., KAZIMIERCZUK K., ZAWADZKA-KAZIMIERCZUK A., KOŹMIŃSKI W., ZHUKOV I., KORNELYUK A.I., 1H, 13C, and 15N chemical shifts assignments for human endothelial monocyte-activating polypeptide EMAP II. Biomolecular NMR Assignments (2013) 7(1): 25-29 IF 0.636
LENARČIČ-ŽIVKOVIĆ M., ZARĘBA-KOZIOŁ M., ZHUKOVA L., POZNAŃSKI J., ZHUKOV I., WYSŁOUCH-CIESZYŃSKA A., Post-translational S-nitrosylation is an endogenous factor fine tuning the properties of human S100A1 protein. Journal of Biological Chemistry (2012) 287(48): 40457-40470 IF 4.773
PERDIH A., CHOUDHURY A.R., ŽUPERL Š., ,SIKORSKA E., ZHUKOV I., SOLMAJER T., NOVIČ M., Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase. PLOS ONE (2012) 7(6): e38967 IF 4.092
NOWAKOWSKI M., JAREMKO Ł., JAREMKO M., ZHUKOV I., BELCZYK-CIESIELSKA A., BIERZYŃSKI A., EJCHART A., Solution NMR structure and dynamics of human apo-S100A1 protein. Journal of Structural Biology (2011) 174: 391-399 IF 3.497
JAREMKO Ł., JAREMKO M., ELFAKI I., MUELLER J.W., EJCHART A., BAYER P., ZHUKOV I., Structure and dynamics of the first archaeal parvulin reveal a new functionally important loop in parvulin-type prolyl isomerases. Journal of Biological Chemistry (2011) 286(8): 6554-6565 IF 5.328
ILC G., GIACHIN G., JAREMKO M., JAREMKO Ł., BENETTI F., PLAVEC J., ZHUKOV I., LEGNAME G., NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features. PLoS One (2010) 5(7): e11715 IF 4,351
LEWANDOWSKA M., WAWRZYŃSKA A.K., MONIUSZKO G., ŁUKOMSKA J., ZIENTARA-RYTTER K., PIECHO M., HODUREK P., ZHUKOV I., LISZEWSKA F., NIKIFOROVA V., SIRKO A., A contribution to identification of novel regulators of plant response to sulfur deficiency: characteristics of a tobacco gene UP9C, its protein product and the effects of UP9C silencing. Molecular Plant (2010) 3(2): 347-360 IF 2,784
KACZKA P., POLKOWSKA-NOWAKOWSKA A., BOLEWSKA K., ZHUKOV I., POZNAŃSKI J., WIERZCHOWSKI K.L., Backbone dynamics of TFE-induced native-like fold of region 4 of Escherichia coli RNA polymerase σ70 subunit. Proteins: Structure, Function and Bioinformatics (2010) 78(3): 754-768 IF 3,085
BRASUŃ J., CEBRAT M., JAREMKO M., JAREMKO Ł., GŁADYSZ O., ZHUKOV I., Histidine analogues of oxytocin and vasopressin as efficient ligands for Zn2+ ions - Potentiometric and NMR studies. Journal of Inorganic Biochemistry (2009) 103: 1033-1038 IF 3,133
BRASUŃ J., CEBRAT M., JAREMKO Ł., JAREMKO M., ILC G., GŁADYSZ O., ZHUKOV I., The structural effects of the Cys-S-S-Cys bridge exchange by the His-Cu(II)-His motif studied on natural peptides - a promising tool for natural compounds-based design. Dalton Transactions (2009): 4853-4857 IF 3,580
JAREMKO Ł., JAREMKO M., PASIKOWSKI P., CEBRAT M., STEFANOWICZ P., LISOWSKI M., ARTYM J., ZIMECKI M., ZHUKOV I., SZEWCZUK Z., Rapid communication the immunosuppressive activity and solution structures of ubiquitin fragments. Biopolymers (2009) 91(6): 423-431 IF 2,823