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Laboratory of Structural Biology | Intercollegiate Faculty of Biotechnology UG&MUG

Laboratory of Structural Biology

Last modified: 
2020, February 5 - 12:26pm

PROFILE

We combine structural biology (x-ray crystallography and electron microscopy), protein biochemistry as well as thermodynamic and kinetic approaches to understand at the molecular level the function of large macromolecular machines involved in DNA replication and repair processes.

RESEARCH TEAM

Laboratory of Structural Biology

Intercollegiate Faculty of Biotechnology UG&MUG
Abrahama 58 Street, 80-307 Gdańsk, Poland

Office:  Ewa Kogut - tel.: +48 58 523 64 27 [e-mail]

 

zespół

 

STAFF LIST

Head: Assoc. Prof. Michał R. Szymański

Email:        michal.szymanski@ug.edu.pl
                  michal.szymanski@biotech.ug.edu.pl
tel.:      +48 58 523 6366
https://www.researchgate.net/profile/Michal_Szymanski2

Website: www.mrslab.ug.edu.pl

List of Employees and PhD students:

PhD Anna Karłowicz [e-mail]
telefon: +48 58 523 64 20

MSc eng. Andrzej Dubiel [e-mail]
telefon: +48 58 523 64 20

MSc Marta Grzelewska
MSc Adela Bledea

SCIENTIFIC AND RESEARCH PROJECTS

Tytuł projektu Kierownik projektu Źródło finansowania Kwota Lata realizacji
Dissecting the mechanism of DNA repair in human mitochondria (MitoRepairosome) Szymański Michał R.  ERC Starting Grant 1 500 000
EUR 
2020 - 2025
Structural basis for DNA repair in human mitochondria Szymański Michał R.  EMBO Installation Grant 150 000
EUR 
2019 - 2021
Targeting mitochondrial DNA repair for novel anti-cancer therapies  Szymański Michał R.  First TEAM 3 3 200 000
2018 - 2023
Unraveling the molecular basis of DNA damage recognition and processing in human mitochondria Szymański Michał R. POLONEZ 2 944 874
2017 - 2019

PUBLICATIONS

  1. Szymanski, M.R., Yu, A., Gmyrek, A.M., White, M.A., Molineux, I.J., Lee, J.C., Yin W.Y. A novel domain in human EXOG converts apoptotic endonuclease to DNA- repair exonuclease. Nature Communications. 2017 May 3;8:14959.
    Recommended by F1000.
  2. Li, M., Mislak, A.C., Foli, Y., Agbosu, E., Bose, V., Bhandari, S., Szymanski, M.R., Shumate, C.K., Yin, W., Anderson, K.S., Paintsil, E. DNA Polymerase-γ R953C Mutant Linked to ART-Associated Mitochondrial Toxicity. Antimicrobial Agents and Chemotherapy. 2016 Aug 22;60(9):5608-11.
  3. Sohl, C.D*., Szymanski, M.R*., Mislak, A.C., Shumate, K.C., Amiralaei, S., Schinazi, F.R., Anderson K.S., Yin W.Y. Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase γ. Proceedings of National Academy of Sciences of the United States of America. 2015 Jul 14;112(28):8596-601.
    *equal contribution
  4. Szymanski, M.R., Kuznetsov, V.B., Shumate, C., Meng, Q., Lee, Y-S., Patel, G., Patel, S.S., Yin W.Y. Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase. EMBO J. 2015 Jul 14; 34(14):1959-70.
  5. Szymanski, M.R., Jezewska, M.J., Bujalowski, W. The Escherichia Coli Primosomal DnaT Protein Exists in Solution as a Monomer – Trimer Equilibrium System. Biochemistry. 2013 Mar 19;52(11):1845-57.
  6. Szymanski, M.R., Jezewska, M.J., Bujalowski, W. Energetics of the Escherichia Coli DnaT Protein Trimerization Reaction. Biochemistry. 2013 Mar 19;52(11):1858-73.
  7. Szymanski, M.R., Bujalowski, P.J., Jezewska, M.J., Gmyrek, A.M., and Bujalowski, W. The N-terminal domain of the Escherichia coli PriA helicase contains both the DNA- and nucleotide-binding sites. Energetics of domain-DNA interactions and allosteric effect of the nucleotide cofactors. Biochemistry. 2011 Nov 1;50(43):9167-83.
  8. Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Binding of Two PriAPriB Complexes to the Primosome Assembly Site Initiates Primosome Formation. Journal of Molecular Biology. 2011 Aug 5;411(1):123-42.
  9. Szymanski, M.R., Jezewska, M.J., Bujalowski, P.J., Bussetta, C., Ye, M., Choi K.H., Bujalowski, W. Full-Length Dengue Virus RNA Dependent RNA Polymerase – RNA/ DNA Complexes. Stoichiometries and Energetics of Intrinsic Affinities, Cooperativities, Base and Conformational Specificities. Journal of Biological Chemistry. 2011 Sep 23;286(38):33095-108.
  10. Jezewska, M.J., Szymanski, M.R., and Bujalowski, W. Kinetic mechanism of the ssDNA recognition by the polymerase X from African Swine Fever Virus. Dynamics and energetics of intermediate formations. Biophysical Chemistry. 2011 Sep;158(1):9-20.
  11. Jezewska, M.J., Szymanski, M.R., and Bujalowski, W. Interactions of the DNA polymerase X from African Swine Fever Virus with the ssDNA. Properties of the total DNA-binding site and the strong DNA-binding subsite. Biophysical Chemistry. 2011 Sep;158(1):26-37.
  12. Jezewska, M.J., Szymanski, M.R., and Bujalowski, W. The primary DNAbinding subsite of the rat pol beta. Energetics of interactions of the 8-kDa domain of the enzyme with the ssDNA. Biophysical Chemistry. 2011 Jul;156(2-3):115-27.
  13. Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. The Escherichia coli PriA helicase-double-stranded DNA complex: location of the strong DNA-binding subsite on the helicase domain of the protein and the affinity control by the two nucleotide-binding sites of the enzyme. Journal of Molecular Biology. 2010 Sep 17;402(2):344-62.
  14. Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Interactions of the Escherichia coli primosomal PriB protein with the single-stranded DNA. Stoichiometries, intrinsic affinities, cooperativities, and base specificities. Journal of Molecular Biology. 2010 Apr 23;398(1):8-25.
  15. Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. The Escherichia coli PriA helicase specifically recognizes gapped DNA substrates: effect of the two nucleotide-binding sites of the enzyme on the recognition process. Journal of Biological Chemistry. 2010 Mar 26;285(13):9683-96.
  16. Andreeva, I.E., Roychowdhury, A., Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Mechanisms of interactions of the nucleotide cofactor with the RepA protein of plasmid RSF1010. Binding dynamics studied using the fluorescence stopped-flow method. Biochemistry. 2009 Nov 10;48(44):10620-36.
  17. Szymanski, M.R., Fiebach, A.R., Tratschin, J.D., Gut, M., Ramanujam, V.M., Gottipati, K., Patel, P., Ye, M., Ruggli, N., and Choi, K.H. Zinc binding in pestivirus N(pro) is required for interferon regulatory factor 3 interaction and degradation. Journal of Molecular Biology. 2009 Aug 14;391(2):438-49.
  18. Roychowdhury, A., Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Interactions of the Escherichia coli DnaB-DnaC protein complex with nucleotide cofactors. 1. Allosteric conformational transitions of the complex. Biochemistry. 2009 Jul 28;48(29):6712-29.
  19. Roychowdhury, A., Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Mechanism of NTP hydrolysis by the Escherichia coli primary replicative helicase DnaB protein. 2. Nucleotide and nucleic acid specificities. Biochemistry. 2009 Jul 28;48(29):6730-46.
  20. Roychowdhury, A., Szymanski, M.R., Jezewska, M.J., and Bujalowski, W. Escherichia coli DnaB helicase-DnaC protein complex: allosteric effects of the nucleotides on the nucleic acid binding and the kinetic mechanism of NTP hydrolysis. 3. Biochemistry. 2009 Jul 28;48(29):6747-63.
  21. Andreeva, I.E., Szymanski, M.R., Jezewska, M.J., Galletto, R., and Bujalowski, W. Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF1010: analyses using fluorescence stopped-flow intensity and anisotropy methods. Journal of Molecular Biology. 2009 May 15;388(4):751-75.
  22. Duret, G., Szymanski, M., Choi, K.J., Yeo, H.J., and Delcour, A.H. The TpsB translocator HMW1B of haemophilus influenzae forms a large conductance channel. Journal of Biological Chemistry. 2008 Jun 6;283(23):15771-8.

INTERNATIONAL SCIENTIFIC COOPERATION

Dr. Bartosz Szczesny, University of Texas Medical Branch at Galveston, Galveston, TX, USA
Dr. Whitney Yin, University of Texas Medical Branch at Galveston, Galveston, TX, USA
Dr. Wlodek M. Bujalowski (UTMB), University of Texas Medical Branch at Galveston, Galveston, TX, USA