Laboratory of Biomolecular Systems Simulations

Research areas:

• Theoretical modeling of interactions of the TraR protein and autoinducer molecules involved in quorum sensing mechanism
• Molecular dynamics simulations of NF-κB - DNA complexes
• Torsional angle dynamics simulations
• Molecular dynamics simulations of complexes of fatty acyl-CoA reductase (FAR) with the fatty acids
• Theoretical modeling of protein-ligand complex formation and ligand escape path simulations from an active site
• Prediction of the DNA quadruplex folding pathway and an evaluation of DNA quadruplex stability in an aqueous solution
• Prediction of the ligand binding site and the protein-ligand complex configuration using the global docking strategy

Laboratory of Biomolecular Systems Simulations

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

tel.: +48 58 523 6340

STAFF LIST

Head: Assoc. Prof. Rajmund Kaźmierkiewicz
tel.: +48 58 523 6340 [e-mail] 

List of PhD and PhD students:

1. Grela Anna, Jamrożek Inga, Hubisz Marta, Iwanicki Adam, Hinc Krzysztof, Kaźmierkiewicz Rajmund, Obuchowski Michał. Positions 299 and 302 of the GerAA subunit are important for function of the GerA spore germination receptor in Bacillus subtilis. PLOS One 2018, 13(6); e0198561 (doi: 10.1371/journal.pone.0198561)

2. Agnieszka Borowik, Prylutskyy Yuriy, Kawelski Łukasz, Kyzyma Olena, Bulavin Leonid, Ivankov Oleksandr, Cherepanov Vsevolod, Wyrzykowski Dariusz, Kaźmierkiewicz Rajmund, Gołuński Grzegorz, Woziwodzka Anna, Evstigneev Maxim, Ritter Uwe,Jacek Piosik. Does C60fullerene act as a transporter of small aromatic molecules? Colloids and Surfaces B: Biointerfaces 2018, 164: 134-143 (doi: 10.1016/j.colsurfb.2018.01.026)

3. Banecka-Majkutewicz Zyta, Kadzinski  Leszek, Grabowski  Michał, Bloch Sylwia, Kazmierkiewicz Rajmund, Jakobkiewicz-Banecka Joanna, Gabig-Ciminska Magdalena, Wegrzyn Grzegorz, Wegrzyn Alicja, Banecki Bogdan. Evidence for interactions between homocysteine and genistein: insights into stroke risk and potential treatment.  Metabolic Brain Disease 2017,  32(6) : 1855-1860 (doi: 10.1007/s11011-017-0078-1)

4. Makarewicz Tomasz, Kaźmierkiewicz Rajmund. Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis. Journal of Molecular Modeling 2016, 22: 109 (doi: 10.1007/s00894-016-2982-4).

5. Kossakowska-Zwierucho Monika, Kaźmierkiewicz Rajmund, Bielawski Krzysztof P., Nakonieczna Joanna. Factors determining staphylococcus aureus susceptibility to photoantimicrobial chemotherapy: RsbU activity, ataphyloxanthin level, and membrane fluidity. Frontiers in Microbiology 2016, 7: 1141 (doi: 10.3389/fmicb.2016.01141).

6. Grabowski Michał, Banecki Bogdan, Kadziński Leszek, Jakóbkiewicz-Banecka Joanna, Kaźmierkiewicz Rajmund, Gabig-Cimińska Magdalena, Węgrzyn Grzegorz, Węgrzyn Alicja, Banecka-Majkutewicz Zyta. Genistein inhibits activities of methylenetetrahydrofolate reductase and lactate dehydrogenase, enzymes which use NADH as a substrate. Biochemical and Biophysical Research Communications 2015, 465(3): 363-367 (doi: 10.1016/j.bbrc.2015.08.004).

7. Pikora Mateusz, Giełdoń Artur. RASMOL AB - New functionalities in the program for structure analysis. Acta Biochimica Polonica 2015, 62(3): 629-631 (doi: 10.18388/abp.2015_972).

8. Prylutskyy Yu. I., Cherepanov V. V., Evstigneev M. P., Kuzyma O. A., Petrenko V. I., Styopkin V. I., Bulavin L. A., Davidenko N. A., Wyrzykowski D., Woziwodzka A., Piosik J., Kaźmierkiewicz R., Ritter U. Structural self-organization of C60 and cisplatin in physiological solution. Physical Chemistry Chemical Physics 2015, 17(39): 26084-26092 (doi: 10.1039/c5cp02688a).

9. Platt Randall J., Curtice Kigen J., Twede Vernon D.,Watkins Maren, Gruszczyński Paweł, Bulaj Grzegorz, Horvath Martin P., Olivera Baldomero M.. From molecular phylogeny towards differentiating pharmacology for NMDA receptor subtypes. Toxicon 2014, 81: 67-79 (doi: 10.1016/j.toxicon.2014.01.016).

10. Jędrzejewski Roch P., Kaźmierkiewicz Rajmund. Structure of Patt1 human proapoptotic histone acetyltransferase. Journal of Molecular Modeling 2013, 19(12): 5533-5538.

11. Makarewicz Tomasz, Kaźmierkiewicz Rajmund. Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL. Journal of Chemical Information and Modeling 2013, 53(5): 1229-1234.

12. Woziwodzka Anna, Gołuński Grzegorz, Wyrzykowski Dariusz, Kaźmierkiewicz Rajmund, Piosik Jacek. Caffeine and other methylxanthines as interceptors of food-borne aromatic mutagens: inhibition of Trp-P-1 and Trp-P-2 mutagenic activity. Chemical Research in Toxicology 2013, 26(11): 1660-1673.

13. Platt Randall J., Han Tiffany S., Green Brad R., Smith Misty D., Skalicky Jack, Gruszczyński Paweł, White H. Steve, Olivera Baldomero, Bulaj Grzegorz, Gajewiak Joanna. Stapling Mimics Noncovalent Interactions of gamma-Carboxyglutamates in Conantokins, Peptidic Antagonists of N-Methyl-D-Aspartic Acid Receptors. Journal of Biological Chemistry 2012, 287(24): 20727-20736.

14. Gruszczyński P., Smalara K., Obuchowski M., Kaźmierkiewicz R. ATP and its N6-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis. Journal of Molecular Modeling 2011, 17(5): 1081-1090.

15. Gruszczyński Paweł, Obuchowski Michał, Kaźmierkiewicz Rajmund. Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis. Journal of Computer-Aided Molecular Design 2010, 24(9): 733-747.

16. Zhang Min-Min, Gruszczyński Paweł, Walewska Aleksandra, Bulaj Grzegorz, Olivera Baldomero M., Yoshikami Doju. Cooccupancy of the outer vestibule of voltage-gated sodium channels by μ-conotoxin KIIIA and saxitoxin or tetrodotoxin. Journal of Neurophysiology 2010, 104(1): 88-97.

17. Florek A., Kaźmierkiewicz R. Modelowanie molekularne - przegląd zastosowań w naukach przyrodniczych [Molecula modelling - what does it exactly mean?]. W: Research, theory, and practice in chemistry didactics XIX, Part 2, Wydawnictwo Uniwersytet Hradec Kralove 2009 (ISBN 978-80-7041-839-0) 297-305.

18. Han T.S., Zhang M.-M., Walewska A., Gruszczyński P., Robertson C.R., Cheatham III T.E., Yoshikami D., Olivera B.M., Bulaj G. Structurally minimized μ-conotoxin analogues as sodium channel blockers: implications for designing conopeptide-based therapeutics. ChemMedChem 2009, 4(3): 406-414.

19. Twede V.D., Teichert R.W., Walker C.S., Gruszczyński P., Kaźmierkiewicz R., Bulaj G., Olivera B.M. Conantokin-Br from Conus brettinghami and selectivity determinants for the NR2D subunit of the NMDA receptor. Biochemistry 2009, 48(19): 4063-4073.