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)

ZHUKOV I., SIKORSKA E., ORLIKOWSKA M., GÓRNIEWICZ-LORENS M., KĘPCZYŃSKI M., JURCZAK P., DPPA as a potential cell membrane component responsible for binding amyloidogenic protein human cystatin C. Molecules (2024) 29(15): 3446 (18 p.) DOI: 10.3390/molecules29153446 IF 4.2 (2023)
ŻYGOWSKA J., ORLIKOWSKA M., ZHUKOV I., BAL W., SZYMAŃSKA A., Copper interaction with cystatin C: effects on protein structure and oligomerization. FEBS Journal (2024) 291(9): 1974-1991 DOI: 10.1111/febs.17092 IF 5.5 (2023)
JURCZAK P., ZHUKOV I., ORLIKOWSKA M., CZAPLEWSKA P., SIKORSKA E., Monitoring the interactions between POPG phospholipid bilayer and amyloid-forming protein human cystatin C. Does the bilayer influence the oligomeric state and structure of the protein? Biochimica et Biophysica Acta-Biomembranes (2024) 1866(3): 184285 (11 p.) DOI: 10.1016/j.bbamem.2024.184285 IF 2.8 (2023)
SERAFIN P., SZELESZCZUK Ł., ZHUKOV I., SZŰCS E., GOMBOS D., STEFANUCCI A., MOLLICA A., PISKLAK D.M., KLECZKOWSKA P., Opioid/Dopamine Receptor Binding Studies, NMR and Molecular Dynamics Simulation of LENART01 Chimera, an Opioid-Bombesin-like Peptide. Molecules (2024) 29(1): 272 (16 p.) DOI: 10.3390/molecules29010272 IF 4.2 (2023)
KARSKA N., ZHUKOV I., LIPIŃSKA A.D., RODZIEWICZ-MOTOWIDŁO S., KRUPA P., Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation? Biochimica et Biophysica Acta-Biomembranes (2023) 1865(8): 184200 (12 p.) DOI: 10.1016/j.bbamem.2023.184200 IF 2.8 (2023)
LISOWSKA M., LICKISS F., GIL-MIR M., HUART A-S., TRYBALA Z., WAY L., HERNYCHOVA L., KREJCI A., MULLER P., KREJCIR R., ZHUKOV I., JURCZAK P., RODZIEWICZ-MOTOWIDŁO S., BALL K., VOJTESEK B., HUPP T., KALATHIYA U., Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade. Frontiers in Microbiology (2022) 13: 875556 (18 p.) DOI: 10.3389/fmicb.2022.875556 IF 5.2 (2022)
SZCZEPANEK-PARULSKA E., BUDNY B., BOROWCZYK M., ZHUKOV I., SZUTKOWSKI K., ZAWADZKA K., TAHIR R., MINCZYKOWSKI A., NIEDZIELA M., RUCHAŁA M., NKX2-5 Variant in Two Siblings with Thyroid Hemiagenesis. International Journal of Molecular Sciences (2022) 23(6): 3414 (10 p.) DOI: 10.3390/ijms23063414 IF 5.6 (2022)
GIELNIK M., ZHUKOVA L., ZHUKOV I., GRÄSLUND A., KOZAK M., WÄRMLÄNDER S.K.T.S., The engineered peptide construct NCAM1-Aβ inhibits fibrillization of the human prion protein (PrP). Acta Biochimica Polonica (2022) 69(1): 257-261 DOI: 10.18388/abp.2020_5679 IF 1.7 (2022)
UFNALSKA I., DREW S.C., ZHUKOV I., SZUTKOWSKI K., WAWRZYNIAK U.E., WRÓBLEWSKI W., FRACZYK T., BAL W., Intermediate Cu(II)-thiolate species in the reduction of Cu(II)GHK by glutathione: a handy chelate for biological Cu(II) reduction. Inorganic Chemistry(2021) 60(23): 18048−18057 DOI: 10.1021/acs.inorgchem.1c02669 IF 5.436 (2021)
GIELNIK M., TAUBE M., ZHUKOVA L., ZHUKOV I., WÄRMLÄNDER S.K.T.S., SVEDRUŽIĆ Ž., KWIATEK W.M., GRÄSLUND A., KOZAK M., Zn(II) binding causes interdomain changes in the structure and flexibility of the human prion protein. Scientific Reports (2021) 11(1): 21703 (15 p.) DOI: 10.1038/s41598-021-00495-0 IF 4.996 (2021)
TKACHUK Z., MELNICHUK N., NIKOLAIEV R.O, SZUTKOWSKI K., ZHUKOV I., The natural oligoribonucleotides functionalized by D-mannitol affected interactions of hemagglutinin with glycan receptor indicating anti-influenza activity. Membranes (2021) 11(10): 757 (13 p.) DOI: 10.3390/membranes11100757 IF 4.562 (2021)
KARSKA N., GRAUL M., SIKORSKA E., ŚLUSARZ M.J., ZHUKOV I., KASPRZYKOWSKI F., KUBIŚ A., LIPIŃSKA A.D., RODZIEWICZ-MOTOWIDŁO S., Investigation of the effects of primary structure modifications within the RRE motif on the conformation of synthetic bovine herpesvirus 1-encoded UL49.5 protein fragments. Chemistry and Biodiversity (2021) 18(2): e2000883 DOI: 10.1002/cbdv.202000883 IF 2.745 (2021)
MIECZKOWSKI A., SPEINA E., TRZYBIŃSKI D., WINIEWSKA-SZAJEWSKA M., WIŃSKA P., BORSUK E.M., PODSIADŁA-BIAŁOSKÓRSKA M., PRZYGODZKI T., DRABIKOWSKI K., STAŃCZYK L., ZHUKOV I., WATALA C., WOŹNIAK K., Diketopiperazine-based, flexible tadalafil analogues: synthesis, crystal structures and biological activity profile. Molecules (2021) 26(4): 794 DOI: 10.3390/molecules26040794 IF 4.927 (2021)
JURCZAK P., SZUTKOWSKI K., LACH S., JURGA S., CZAPLEWSKA P., SZYMAŃSKA A., ZHUKOV I., DMPC phospholipid bilayer as a potential interface for human cystatin C oligomerization: analysis of protein-liposome interactions using NMR spectroscopy. Membranes (2021) 11(1): 13 (14 p.) DOI: 10.3390/membranes11010013 IF 4.562 (2021)
JURCZAK P., SIKORSKA E., CZAPLEWSKA P., RODZIEWICZ-MOTOWIDŁO S., ZHUKOV I., SZYMAŃSKA A., The influence of the mixed DPC:SDS micelle on the structure and oligomerization process of the human cystatin C. Membranes (2021) 11(1): 17 (22 p.) DOI: 10.3390/membranes11010017 IF 4.562 (2021)
MITAL M., SZUTKOWSKI K., BOSSAK-AHMAD K., SKROBECKI P., DREW S.C., POZNANSKI J., ZHUKOV I., FRACZYK T., BAL W., The Palladium(II) complex of Aβ4−16 as suitable model for structural studies of biorelevant copper(II) complexes of N-truncated beta-amyloids. International Journal of Molecular Sciences (2020) 21(23): 9200 DOI: 10.3390/ijms21239200 IF 5.923 (2020)
BUCHOLC K., SKRAJNA A., ADAMSKA K., YANG X-C., KRAJEWSKI K., POZNANSKI J., DADLEZ M., DOMIŃSKI Z., ZHUKOV I., 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. International Journal of Molecular Sciences (2020) 21(15): 5268 DOI:10.3390/ijms21155268 IF 5.923 (2020)
MASZOTA-ZIELENIAK M., JURCZAK P., ORLIKOWSKA M., ZHUKOV I., BOREK D., OTWINOWSKI Z., SKOWRON P., PIETRALIK Z.,KOZAK M., SZYMAŃSKA A., RODZIEWICZ-MOTOWIDŁO S., NMR and crystallographic structural studies of the extremely stable monomeric variant of human cystatin C with single amino acid substitution. FEBS Journal (2020) 287(2): 361-376 DOI: 10.1111/febs.15010 IF 5.542 (2020)
SPODZIEJA M., KUNCEWICZ K., SIERADZAN A., KARCZYŃSKA A., IWASZKIEWICZ J., CESSON V., WĘGRZYN K., ZHUKOV I., MASZOTA-ZIELENIAK M., MICHIELIN O., SPEISER D.E., ZOETE V., DERRE L., RODZIEWICZ-MOTOWIDŁO S., Disulfide-linked peptides for blocking TLA/HVEM binding. International Journal of Molecular Sciences (2020) 21(2): 636 DOI: 10.3390/ijms21020636 IF 5.923 (2020)
SZUTKOWSKI K., SIKORSKA E., BAKANOVYCH I., CHOUDHURY A.R., PERDIH A., JURGA S., NOVIČ M., ZHUKOV I., Structural analysis and dynamic processes of the transmembrane segment inside different micellar environments-implications for the TM4 fragment of the bilitranslocase protein. International Journal of Molecular Sciences (2019) 20(17): 4172 (21 p.) DOI: 10.3390/ijms20174172 IF 4.556 (2019)

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.