Pracownie badawcze

Prof. dr hab. Piotr Zielenkiewicz

Zakład Bioinformatyki

Zakres badań

Our laboratory applies in silico approaches to address molecular biology problems.

Badania

Najważniejsze osiągnięcia badawcze

  • We established the general methodology for the construction of protein-protein interaction peptide inhibitors and successfully applied it to a number of biologically meaningful examples.
  • We discovered novel potent deltaF508-CFTR correctors as potential drugs against Cystic Fibrosis (CF)
  • We proposed a comprehensive, genome-wide model of translation.
  • We described the role of plant miRNAs in the antiinflammatory properties of selected edible plants.

Opis badań

Scientific interests of our laboratory include, but are not limited to:

  • Protein-protein recognition and the design of protein-protein interaction inhibitors.
  • Macromolecular crowding.
  • Modeling and modifying the regulation of basic cellular processes and metabolic pathways.
  • Protein modeling.
  • Analyses of genome sequence data (particularly in the context of phylogenetic analysis).
  • Development of drug design methodologies.
  • Analyses of protein interaction networks.
  • Literature mining.

Metodologia

In our laboratory, we use software tools for:

  • Sequence and structure analysis (e.g., EMBOSS).
  • Visualization and structure modeling (e.g., Chimera, YASARA, Swiss-PDBViewer).
  • Pathway and metabolic pathway modeling and analysis (e.g., Cytoscape, IPA, Gepasi)
  • Docking (e.g., DOCK).
  • Molecular dynamics (e.g., AMBER, GROMACS).
  • Home-developed tools (e.g., kalasanty, pafnucye, plec, oddt, transimulation, ht-sas, elise, tools4mirs).

Our HPC infrastructure is built around HP blade servers with Intel Xeon X5650 6-core processors and AMD Opteron 6174 12-core processors. Each core has 2 MB of RAM. The servers are diskless and connected with a high speed (32 Mb/s) InfiniBand QDR40 connection. This interconnect provides direct memory access and enables ultra-low latency between computing nodes. The infrastructure consists of 32 Intel-based servers and 16 AMD servers, for a total of 1152 cores. This environment is further enriched by 8 GPU Nvidia TESLA C2080 cards with 448 cores each. Storage is built around LustreFS, a special-purpose modular system that is designed for high I/O memory (6 rack servers, 72 Intel cores) and a HITACHI AMS2500 storage system with 0.5 PB of storage size. Additionally, five application servers provide virtualization capacities, with a total of 240 cores and 1 TB of RAM installed). Software that is used in this installation is almost exclusively free and open source stack (Linux, Torque, Maui, Xen, MySQL, Apache, and others). Altogether, our HPC environment is able to achieve over 40 Tflops.

Wybrane publikacje

  • Discovery of novel potent ΔF508-CFTR correctors that target the nucleotide binding domain. Odolczyk N, Fritsch J, Norez C, Servel N, da Cunha MF, Bitam S, Kupniewska A, Wiszniewski L, Colas J, Tarnowski K, Tondelier D, Roldan A, Saussereau EL, Melin-Heschel P, Wieczorek G, Lukacs GL, Dadlez M, Faure G, Herrmann H, Ollero M, Becq F, Zielenkiewicz P, Edelman A. EMBO Mol Med. 2013 Oct;5(10):1484-501. doi: 10.1002/emmm.201302699.
  • A comprehensive, quantitative, and genome-wide model of translation. Siwiak M, Zielenkiewicz P. PLoS Comput Biol. 2010 Jul 29;6(7):e1000865. doi: 10.1371/journal.pcbi.1000865.
  • Mapping Protein-Protein Interactions of the Resistance-Related Bacterial Zeta Toxin-Epsilon Antitoxin Complex (ε₂ζ₂) with High Affinity Peptide Ligands Using Fluorescence Polarization. Fernández-Bachiller MI, Brzozowska I, Odolczyk N, Zielenkiewicz U, Zielenkiewicz P, Rademann J. Toxins (Basel). 2016 Jul 16;8(7):222. doi: 10.3390/toxins8070222.

Współpraca

  • Joerg Rademann, Freie Universitaet Berlin, D
  • Aleksander Edelman, INSERM, FR
  • Sarah Reece, Edinburgh University, UK
  • Chris Janse, Leiden University, NL
  • Wolfram Saenger, Freie Universitaet Berlin, D
  • Grażyna Faure-Kuźmińska, Institute Pasteur, Paris, France
  • Stephanie Trudel, Universitaire Amiens Picardie, Amiens, France

Publikacje (z afiliacją IBB PAN)

WÓJCIKOWSKI M., ZIELENKIEWICZ P., SIEDLECKI P., Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. Journal of Cheminformatics (2015) 7: 26(6 p.) DOI 10.1186/s13321-015-0078-2 IF 4.547
SIWIAK M., ZIELENKIEWICZ P., Co-regulation of translation in protein complexes. Biology Direct (2015) 10: 18(13p.) DOI 10.1186/s13062-015-0048-7 IF 4.658
ODOLCZYK N., ZIELENKIEWICZ P., Molecular modelling approaches for cystic fibrosis transmembrane conductance regulator studies. The International Journal of Biochemistry & Cell Biology (2014) 52: 39-46 IF 4.240
WÓJCIKOWSKI M., ZIELENKIEWICZ P., SIEDLECKI P., DiSCuS: an open platform for (not only) virtual screening results management. Journal of Chemical Information and Modeling (2014) 54(1): 347-354 IF 4.068
BAKUN M., SENATORSKI G., RUBEL T., ŁUKASIK A., ZIELENKIEWICZ P., DADLEZ M., PĄCZEK L., Urine proteomes of healthy aging humans reveal extracellular matrix (ECM) alterations and immune system dysfunction. AGE (2014) 36(1): 299–311 IF 3.445
ŁUKASIK A., PIETRYKOWSKA H., PĄCZEK L., SZWEYKOWSKA-KULIŃSKA Z., ZIELENKIEWICZ P., High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics (2013) 14: 801 (15 p.) IF 4.397
ODOLCZYK N., FRITSCH J., NOREZ C., SERVEL N., FARIA da CUNHA M., BITAM S., KUPNIEWSKA-KOZAK A., WISZNIEWSKI L., COLAS J., TARNOWSKI K.J., TONDELIER D., ROLDAN A., SAUSSEREAU E.L., MELIN-HESCHEL P., WIECZOREK G., LUKACS G., DADLEZ M., FAURE G., HERRMANN H., OLLERO M., BECQ F., ZIELENKIEWICZ P., EDELMAN A., Discovery of novel potent ΔF508-CFTR correctors that target the nucleotide binding domain. EMBO Molecular Medicine (2013) 5(10): 1484-1501 IF 7.795
SIWIAK M., ZIELENKIEWICZ P., Transimulation - protein biosynthesis web service. PLOS ONE (2013) 8(9): e73943 (8 p.) IF 3.730
PAWŁOWSKI P.H., ZIELENKIEWICZ P., The quantum casimir effect may be a universal force organizing the bilayer structure of the cell membrane. Journal of Membrane Biology (2013) 246(5): 383-389 IF 2.478
PAWŁOWSKI P.H., ZIELENKIEWICZ P., Theoretical model explaining the relationship between the molecular mass and the activation energy of the enzyme revealed by a large-scale analysis of bioinformatics data. Acta Biochimica Polonica (2013) 60(2): 239-247 IF 1.185

Zespół

Patenty

    • Compounds as modulators of a mutant CFTR protein and their use for treating diseases associated with CFTR protein malfunction. ODOLCZYK, Norbert ; ZIELENKIEWICZ, Piotr; WIECZOREK, Grzegorz; EDELMAN, Aleksander; TONDELIER, Danielle; FRITSCH, Janine. US ( 2018) 10,398,665, ; US 10,420,738,; US 10,463,639
    • Use of a mir172 molecule for decreasing inflammation. Łukasik, Anna; Zielenkiewicz, Piotr; Szweykowska-Kulińska, Zofia; Paczek, Leszek; Nowaczyk, Maria. (2018) EP3035941