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