Laboratories

Piotr Zielenkiewicz, PhD, DSc, Prof.

Department of Bioinformatics

Position: Professor

ORCID: 0000-0001-8151-6874

E-mail:

Research Scope

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

Research

Main Scientific Achievements

  • 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.

Research Description

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.

Methodology

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.

Selected Publications

  • 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.

Collaborations

  • 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

Publications (IBB PAS affiliated)

STĘPNIEWSKA-DZIUBIŃSKA M., ZIELENKIEWICZ P., SIEDLECKI P., Improving detection of protein-ligand binding sites with 3D segmentation Scientific Reports (2020) 10(1): 5035 DOI:10.1038/s41598-020-61860-z IF 4.380 (2020)
MILEWSKA M., BURDZIŃSKA A., ZIELNIOK K., SIENNICKA K., STRUZIK S., ZIELENKIEWICZ P., PĄCZEK L., Copper does not induce tenogenic differentiation but promotes migration and increases lysyl oxidase activity in adipose-derived mesenchymal stromal cells. Stem Cells International (2020) 2020: 9123281 DOI: 10.1155/2020/9123281 IF 5.443 (2020)
BRENNECKE P., RASINA D., AUBI O., HERZOG K., LANDSKRON J., CAUTAIN B., VICENTE F., QUINTANA J., MESTRES J., STECHMANN B., ELLINGER B., BREA J., KOLANOWSKI J.L., PILARSKI R., ORZAEZ M., PINEDA-LUCENA A., LARAIA L., NAMI F., ZIELENKIEWICZ P., PARUCH K., HANSEN E., VON KRIES J.P., NEUENSCHWANDER M., SPECKER E., BARTUNEK P., SIMOVA S., LEŚNIKOWSKI Z., KRAUSS S., LEHTIÖ L., BILITEWSKI U., BRÖNSTRUP M., TASKĖN K., JIRGENSONS A., LICKERT H., CLAUSEN M.H., ANDERSEN J.H., VICENT M.J., GENILLOUD O., MARTINEZ A., NAZARĖ M., FECKE W., GRIBBON P., EU-OPENSCREEN: a novel collaborative approach to facilitate chemical biology. SLAS Discovery (2019) 24(3): 398-413 (Special Issue) DOI: 10.1177/2472555218816276 IF 2.195 (2019)
RYDZANICZ M., WACHOWSKA M., COOK E.C., LISOWSKI P., KUŹNIEWSKA B., SZYMAŃSKA K., DIECKE S., PRIGIONE A., SZCZAŁUBA K., SZYBIŃSKA A., KOPPOLU A., PIEŃKOWSKI V.M., KOSIŃSKA J., WIWEGER M., KOSTRZEWA G., BRZOZOWSKA M., DOMAŃSKA-PAKIEŁA D., JURKIEWICZ E., STAWIŃSKI P., GROMADKA A., ZIELENKIEWICZ P., DEMKOW U., DZIEMBOWSKA M., KUŹNICKI J., CREAMER T.P., PŁOSKI R., Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression. European Journal of Human Genetics (2019) 27(1): 61-69 DOI: 10.1038/s41431-018-0254-8 IF 3.657 (2019)
LUKASIK A., ZIELENKIEWICZ P., An overview of miRNA and miRNA target analysis tools. Chapter 5 in: Plant MicroRNAs: Methods and Protocols, Methods in Molecular Biology, Humana Press. Ed. S. de Folter, vol. 1932; ISBN 978-1-4939-9041-2 [363 p.] 2019, p.65-87 DOI: 10.1007/978-1-4939-9042-9_5
REICHERT M., LUKASIK A., ZIELENKIEWICZ P., MATRAS M., MAJ-PALUCH J., STACHNIK M., BORZYM E., Host microRNA analysis in cyprinid Herpesvirus-3 (CyHV-3) infected common carp. BMC Genomics (2019) 20: 46 (16 p.) DOI: 10.1186/s12864-018-5266-9 IF 3.594 (2019)
PERYCZ M., ZIELENKIEWICZ P., KACZANOWSKI S., Human and rodent malaria parasites differ in their histone methylation machinery — a bioinformatic study. Serdica Journal of Computing (2018) 12(3): 131-162 IF - (2018)
STĘPNIEWSKA-DZIUBIŃSKA M.M., ZIELENKIEWICZ P., SIEDLECKI P., Development and evaluation of a deep learning model for protein-ligand binding affinity prediction. Bioinformatics (2018) 34(21): 3666-3674 DOI: 10.1093/bioinformatics/bty374 IF 4.531 (2018)
LUKASIK A., BRZOZOWSKA I., ZIELENKIEWICZ U., ZIELENKIEWICZ P., Detection of plant miRNAs abundance in human breast milk. International Journal of Molecular Sciences (2018) 19(1): 37 (17 p.) DOI: 10.3390/ijms19010037 IF 4.183 (2018)
POZNANSKI J., SZCZESNY P., PAWLIŃSKI B., MAZUREK T., ZIELENKIEWICZ P., GAJEWSKI Z., PĄCZEK L., Arteriovenous oscillations of the redox potential: is the redox state influencing blood flow? Redox Report (2017) 22(5): 210-217 DOI: 10.1080/13510002.2016.1177933 IF 2.167 (2017)
STĘPNIEWSKA-DZIUBIŃSKA M.M., ZIELENKIEWICZ P., SIEDLECKI P., DeCAF—discrimination, comparison, alignment tool for 2D pharmacophores. Molecules (2017) 22(7): 1128 (12 p.) DOI: 10.3390/molecules22071128 IF 3.098 (2017)
LUKASIK A., ZIELENKIEWICZ P., Plant microRNAs—novel players in natural medicine? International Journal of Molecular Sciences (2017) 18(1): 9 (16 p.) DOI: 10.3390/ijms18010009 IF 3.687 (2017)
LUKASIK A., WOJCIKOWSKI M., ZIELENKIEWICZ P., Tools4miRs - one place to gather all the tools for miRNA analysis. Bioinformatics (2016) 32(17): 2722-2724 DOI: 10.1093/bioinformatics/btw189 IF 5.766
FAURE G., BAKOUH N., LOURDEL S., ODOLCZYK N., PREMCHANDAR A., SERVEL N., HATTON A., OSTROWSKI M.K., XU H., SAUL F., MOQUEREAU CH., BITAM S., PRANKE I., PLANELLES G., TEULON J., HERRMANN H., ROLDAN A., ZIELENKIEWICZ P., DADLEZ M., LUKACS G., SERMET-GAUDELUS I., OLLERO M., CORRINGER P.J., EDELMAN A., Rattlesnake phospholipase A2 increases CFTR-chloride channel current and corrects ?F508CFTR dysfunction: impact in cystic fibrosis. Journal of Molecular Biology (2016) 428(14): 2898-2915 DOI: 10.1016/j.jmb.2016.05.016 IF 4.517
FERNÁNDEZ-BACHILLER M.I., BRZOZOWSKA I., ODOLCZYK N., ZIELENKIEWICZ U., ZIELENKIEWICZ P., RADEMANN J., Mapping protein–protein interactions of the resistance-related bacterial zeta toxin–epsilon antitoxin complex (ε2ζ2) with high affinity peptide ligands using fluorescence polarization. Toxins (2016) 8(7): 222 (16 p.) DOI: 10.3390/toxins8070222 IF 3.571
GŁADKI A., ZIELENKIEWICZ P., KACZANOWSKI S., Dominance from the perspective of gene–gene and gene–chemical interactions. Genetica (2016) 144 (1): 23-36 DOI: 10.1007/s10709-015-9875-9 IF 1.343
RUTOWICZ K., PUZIO M., HALIBART-PUZIO J., LIRSKI M., KOTLIŃSKI M., KROTEŃ M.A., KNIŻEWSKI Ł., LANGE B., MUSZEWSKA A., ŚNIEGOWSKA-ŚWIERK K., KOŚCIELNIAK J., IWANICKA-NOWICKA R., BUZA K., JANOWIAK F., ŻMUDA K., JÕESAAR I., LASKOWSKA-KASZUB K., FOGTMAN A., KOLLIST H., ZIELENKIEWICZ P., TIURYN J., SIEDLECKI P., SWIEZEWSKI S.S., GINALSKI K., KOBLOWSKA M., ARCHACKI R., WILCZYNSKI B., RAPACZ M., JERZMANOWSKI A., A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis. Plant Physiology (2015) 169(3): 2080-2101 DOI: 10.1104/pp.15.00493 IF 6.841
WOJCIKOWSKI 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
TRUDEL S., ODOLCZYK N., DREMAUX J., TOFFIN J., REGNIER A., SEVESTRE H., ZIELENKIEWICZ P., ARNAULT J.P.,GUBLER B., The clinical response to vemurafenib in a patient with a rare BRAFV600DK601del mutation-positive melanoma. BMC Cancer (2014) 14: 727(8p.) doi:10.1186/1471-2407-14-727 IF 3.319

Team

Patents

    • 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