Interdisciplinary Laboratory of Biological Systems Modelling

Scientific interests:
  • development of multi dimensional models for the analysis of energy landscape of proteins with complex structures, as proteins with non trivial topology;
  • development of analytical methods as direct coupling analysis (DCA) and bioinformatics tools for analysis of amino acids evolution and their application to prediction of protein structures (including membrane proteins) and alternative protein folding mechanism;
  • development of the methods to analysis of mechanical properties of proteins, mechanical degradation and translation across membranes;
  • development and application of mathematical knot theory to determine the topology of open chain and its application to proteins and nucleic acids.

Co-organization of scientific events:

  • 17-21.09.214, Significance of Knotted Structures for Function of Proteins and Nucleic Acids, Warsaw, Poland
  • 17-20.06.2014, 4th Visegrad Symposium on Structural Systems Biology, Nove Hrady, Czech Republic
  • 17-22.11.2013, Entanglement in biology; how nature controls the topology of proteins and DNA (13w5133), Banff, Canada

Other grants:

  • DUNE, Ministry of Science and Higher Education, place of implementation: Polish Biophysical Society
  • Biophysical Society Grant, place of implementation: Faculty of Chemistry UW
  • Homing Plus, Fundation for Polish Science, place of implementation: Faculty of Chemistry UW
  • Preludium, National Science Centre, place of implementation: Faculty of Chemistry UW
Joanna Sułkowska, PhD
email: j.sulkowska@dev.dev.cent.uw.edu.pl/en
phone: +48 22 55 43675
room: 04.43
Strona internetowa: http://jsulkowska.dev.dev.cent.uw.edu.pl/en/


Transmembrane helix connectivity in Orai1 controls two gates for calcium-dependent transcription.
Frischauf, I., Litviňuková, M., Schober, R., Zayats, V., Svobodová, B., Bonhenry, D., ... & Stallinger, A. (2017).
2017
KnotGenome: a server to analyze entanglements of chromosomes
Sulkowska, J. I., Niewieczerzal, S., Jarmolinska, A. I., Siebert, J. T., Virnau, P., & Niemyska, W. (2018)
Nucleic acids research
„GapRepairer–a server to model a structural gap and validate it using topological analysis.”
Jarmolinska, A. I., Kadlof, M., Dabrowski-Tumanski, P., & Sulkowska, J. I. (2018).
Bioinformatics, 1, 8
LinkProt: database collecting information about biological links.
Dabrowski-Tumanski, P., Jarmolinska, A. I., Niemyska, W., Rawdon, E. J., Millett, K. C., & Sulkowska, J. I. (2017)
Nucleic acids research, 45(D1), D243-D249.
Topological knots and links in proteins.
Dabrowski-Tumanski, P., & Sulkowska, J. I. (2017).
Proceedings of the National Academy of Sciences, 201615862.
TrmD: A Methyl Transferase for tRNA Methylation With m1G37.
Hou, Y. M., Matsubara, R., Takase, R., Masuda, I., & Sulkowska, J. I. (2017).
In The Enzymes (Vol. 41, pp. 89-115). Academic Press.
Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume.
Niewieczerzal, S., & Sulkowska, J. I. (2017).
PloS one, 12(5), e0176744.
PyLasso: a PyMOL plugin to identify lassos.
Gierut, A. M., Niemyska, W., Dabrowski-Tumanski, P., Sułkowski, P., & Sulkowska, J. I. (2017).
Bioinformatics, 33(23), 3819-3821.
The exclusive effects of chaperonin on the behavior of the 52 knotted proteins
Zhao, Y., Dabrowski-Tumanski, P., Niewieczerzal, S., & Sulkowska, J. I. (2017).
PLoS Comput. Biol.
LassoProt: server to analyze biopolymers with lassos.
Dabrowski-Tumanski, P., Niemyska, W., Pasznik, P., & Sulkowska, J. I. (2016).
Nucleic acids research, 44(W1), W383-W389.
Methyl Transfer by Substrate Signaling from a Knotted Protein Fold
Christian, T., Sakaguchi, R., Perlinska, A. P., Lahoud, G., Ito, T., Taylor, E. A., ... & Hou, Y. M. (2016).
https://www.nature.com/articles/nsmb.3282
Complex lasso: new entangled motifs in proteins
Niemyska, W., Dabrowski-Tumanski, P., Kadlof, M., Haglund, E., Sułkowski, P., & Sulkowska, J. I. (2016)
Scientific reports, 6, 36895.
In search of functional advantages of knots in proteins
Dabrowski-Tumanski, P., Stasiak, A., & Sulkowska, J. I. (2016)
PloS one, 11(11), e0165986.
Prediction of the optimal set of contacts to fold the smallest knotted protein
Dabrowski-Tumanski, P., Jarmolinska, A. I., & Sulkowska, J. I. (2015)
Journal of Physics: Condensed Matter, 27(35), 354109
Connecting thermal and mechanical protein (un) folding landscapes.
Sun, L., Noel, J. K., Sulkowska, J. I., Levine, H., & Onuchic, J. N. (2014).
Biophysical journal, 107(12), 2950-2961.
KnotProt: a database of proteins with knots and slipknots.
Jamroz, M., Niemyska, W., Rawdon, E. J., Stasiak, A., Millett, K. C., Sułkowski, P., & Sulkowska, J. I. (2014).
Nucleic acids research, 43(D1), D306-D314.
Connecting termal and mechanical protein (un)folding landscapes
Sun, L., Noel, J. K., Sulkowska, J. I., Levine, H., & Onuchic, J. N. (2014).
Biophysical journal, 107(12), 2950-2961.
Structural and mechanistic basis of the fast metathesis initiation by six-coordinated ruthenium catalyst
Trzaskowski, B., & Grela, K. (2013)
Organometallics, 32(13), 3625-3630