Facilities

Igor Zhukov, PhD

Biological NMR Facility

Service and research scope

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.

Service

Service Description

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.

Equipment

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.

Collaborations

    • 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

Customers

    • Consorcium Silicon Group Ltd. Great Britain

Research

Research Description

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).

Selected Publications

    • 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.

Publications (IBB PAS affiliated)

GIELNIK M., PIETRALIK Z.,ZHUKOV I., SZYMAŃSKA A., KWIATEK W.M., KOZAK M., PrP (58–93) peptide from unstructured N-terminal domain of human prion protein forms amyloid-like fibrillar structures in the presence of Zn2+ ions. RSC Advances (2019) 9(39): 22211-22219 DOI: 10.1039/c9ra01510h IF 3.119 (2019)
WINIEWSKA-SZAJEWSKA M., PŁONKA D., ZHUKOV I., POZNANSKI J., Rational drug-design approach supported with thermodynamic studies — a peptide leader for the efficient bi-substrate inhibitor of protein kinase CK2. Scientific Reports (2019) 9: 11018 (13 p.) DOI: 10.1038/s41598-019-47404-0 IF 3.998 (2019)
NOWAKOWSKI M., CZAPLA-MASZTAFIAK J., ZHUKOV I., ZHUKOVA L., KOZAK M., KWIATEK W.M., Electronic properties of a PrPC–Cu(II) complex as a marker of 5-fold Cu(II) coordination. Metallomics (2019) 11(3): 632-642 DOI: 10.1039/c8mt00339d IF 3.796 (2019)
KARSKA N., GRAUL M., SIKORSKA E., ZHUKOV I., ŚLUSARZ M.J., KASPRZYKOWSKI F., LIPIŃSKA A.D., RODZIEWICZ-MOTOWIDŁO S., Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics. Biochimica et Biophysica Acta - Biomembranes (2019) 1861(5): 926-938 DOI: 10.1016/j.bbamem.2019.02.005 IF 3.411 (2019)
SZUTKOWSKI K., KOŁODZIEJSKA Ż., PIETRALIK Z.,ZHUKOV I., SKRZYPCZAK A., MATERNA K., KOZAK M., Clear distinction between CAC and CMC revealed by high-resolution NMR diffusometry for a series of bis-imidazolium gemini surfactants in aqueous solutions. RSC Advances (2018) 8(67): 38470-38482 DOI: 10.1039/c8ra07081d IF 3.049 (2018)
NOWAKOWSKI M., CZAPLA-MASZTAFIAK J., KOZAK M., ZHUKOV I., ZHUKOVA L., SZLACHETKO J., KWIATEK W.M., Preliminary results of human PrPC protein studied by spectroscopic techniques. Nuclear Instruments and Methods in Physics Research B (2017) 411: 121-128 DOI: 10.1016/j.nimb.2017.06.022 IF 1.323 (2017)
WAWRA S., TRUSCH F., MATENA A., APOSTOLAKIS K., LINNE U., ZHUKOV I., STANEK J., KOZMINSKI W., DAVIDSON I., SECOMBES C.J., BAYER P., VAN WEST P., The RxLR motif of the host targeting effector AVR3a of Phytophthora infestans is cleaved before secretion. Plant Cell (2017) 29(6): 1184-1195 DOI: 10.1105/tpc.16.00552 IF 8.228 (2017)
MARSZAŁEK I., KREZEL A., GOCH W., ZHUKOV I., PACZKOWSKA I., BAL W., Revised stability constant, spectroscopic properties and binding mode of Zn(II) to FluoZin-3, the most common zinc probe in life sciences. Journal of Inorganic Biochemistry (2016) 161: 107-114 DOI: 10.1016/j.jinorgbio.2016.05.009 IF 3.205
SIKORSKA E., WYRZYKOWSKI D., SZUTKOWSKI K., GREBER K., LUBECKA E., ZHUKOV I., Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles. Journal of Thermal Analysis and Calorimetry 2015: 4918 (13 p.) DOI: 10.1007/s10973-015-4918-0 IF 2.042
CHOUDHURY A.R., SIKORSKA E., VAN DEN BOOM J., BAYER P., POPENDA Ł., SZUTKOWSKI K., JURGA S., BONOMI M., SALI A., ZHUKOV I., PASSAMONTI S., NOVIČ M., Structural model of the bilitranslocase transmembrane domain supported by NMR and FRET data. PLOS ONE (2015) 10(8): e0135455 (16 p.) DOI: 10.1371/journal.pone.0135455 IF 3.234
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., REMPOLA B., BOLEWSKA K., LOZINSKI T., EJCHART A., POZNAŃSKA A., WIERZCHOWSKI K.L., POZNANSKI 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
KOPERA E., BAL W., LENARČIČ-ŽIVKOVIĆ M., DVORNYK A., KLUDKIEWICZ B., GRZELAK A., ZHUKOV I., ZAGORSKI-OSTOJA W., JASKOLSKI M., KRZYWDA SZ., Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor. PLOS ONE (2014) 9(9):e106936 (11p.) doi: 10.1371/journal.pone.0106936 IF 3.534
JAREMKO M., JAREMKO L., 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., KOZMINSKI 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., POZNANSKI J., ZHUKOV I., WYSLOUCH-CIESZYNSKA 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 L., JAREMKO M., ZHUKOV I., BELCZYK-CIESIELSKA A., BIERZYNSKI 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 L., 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

Leader

IGOR ZHUKOV (ŻUKOW), PhD

  • AUTHOR IDENTIFIERS

ORCID: 0000-0002-9912-1018

  • SOCIAL MEDIA

LinkedIn: igorzhv

  • DEGREES

2001 – Ph.D. Institute of Biochemistry and Biophysics, Polish Academy of Sciences, biochemistry
1984 – M.Sc. Radio-Physical Department, Saint Petersburg Technical University, physics of dielectrics and polymers

  • PROFESSIONAL EMPLOYMENT/ EXPERIENCE

2001 – present – Laboratory of Biological NMR, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, PL
2013 – 2017 – NanoBioMedical Centre, Adam Mickiewicz University: Poznań PL
2007 – 2012  – Slovenian NMR Centre, National Institute of Chemistry: Ljubljana, SI
1984 – 1998 – Laboratory of Dielectric Properties of Polymers, Institute of Macromolecular Compounds: Saint Petersburg, RU

Team

Grants

  • Molecular basis of neurodegenerative diseases - the influence of selected metallic nanoparticles. Igor Zhukov (co-PI) (consortium Leader: Maciej Leszek Kozak, Adam Mickiewicz University, Poznań). OPUS-21, National Science Center, 2022-2026.