Profile
Leader
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Profile
Prof. Joanna Sułkowska
e-mail: j.sulkowska@cent.uw.edu.pl
phone: +48 22 55 43675
room: 04.43
ORCID: 0000-0003-2452-0724
SCOPUS ID: 9242724100
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
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Selected publications
- Bruno da Silva F., Gabrovšek B., Korpacz M., Luczkiewicz K., Niewieczerzal S., Sikora M., Sulkowska J.I.
Knots and θ-Curves Identification in Polymeric Chains and Native Proteins Using Neural Networks
(2024) Macromolecules, 57 (9), pp. 4599 – 4608
DOI: 10.1021/acs.macromol.3c02479
- Gren B.A., Antczak M., Zok T., Sulkowska J.I., Szachniuk M.
Knotted artifacts in predicted 3D RNA structures
(2024) PLoS Computational Biology, 20 (6 JUNE), art. no. e1011959
DOI: 10.1371/journal.pcbi.1011959
- Dabrowski-Tumanski P., Goundaroulis D., Stasiak A., Rawdon E.J., Sulkowska J.I.
Theta-curves in proteins
(2024) Protein Science, 33 (9), art. no. e5133
DOI: 10.1002/pro.5133
- Rubach P., Sikora M., Jarmolinska A.I., Perlinska A.P., Sulkowska J.I.
AlphaKnot 2.0: A web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models
(2024) Nucleic Acids Research, 52 (W1), pp. W187 – W193
DOI: 10.1093/nar/gkae443
- Tubiana L., Alexander G.P., Barbensi A., Buck D., Cartwright J.H.E., Chwastyk M., Cieplak M., Coluzza I., Čopar S., Craik D.J., Di Stefano M., Everaers R., Faísca P.F.N., Ferrari F., Giacometti A., Goundaroulis D., Haglund E., Hou Y.-M., Ilieva N., Jackson S.E., Japaridze A., Kaplan N., Klotz A.R., Li H., Likos C.N., Locatelli E., López-León T., Machon T., Micheletti C., Michieletto D., Niemi A., Niemyska W., Niewieczerzal S., Nitti F., Orlandini E., Pasquali S., Perlinska A.P., Podgornik R., Potestio R., Pugno N.M., Ravnik M., Ricca R., Rohwer C.M., Rosa A., Smrek J., Souslov A., Stasiak A., Steer D., Sułkowska J., Sułkowski P., Sumners D.W.L., Svaneborg C., Szymczak P., Tarenzi T., Travasso R., Virnau P., Vlassopoulos D., Ziherl P., Žumer S.
Topology in soft and biological matter
(2024) Physics Reports, 1075, pp. 1 – 137
DOI: 10.1016/j.physrep.2024.04.002
- Sikora M., Klimentova E., Uchal D., Sramkova D., Perlinska A.P., Nguyen M.L., Korpacz M., Malinowska R., Nowakowski S., Rubach P., Simecek P., Sulkowska J.I.
Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model
(2024) Protein Science, 33 (7), art. no. e4998
DOI: 10.1002/pro.4998
- Perlinska A.P., Sikora M., Sulkowska J.I.
Everything AlphaFold tells us about protein knots
(2024) Journal of Molecular Biology, 436 (19), art. no. 168715
DOI: 10.1016/j.jmb.2024.168715
- Niemyska W., Mukherjee S., Gren B.A., Niewieczerzal S., Bujnicki J.M., Sulkowska J.I.
Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology
(2024) Journal of Molecular Biology, 436 (6), art. no. 168455
DOI: 10.1016/j.jmb.2024.168455
- Zayats V., Sikora M., Perlinska A.P., Stasiulewicz A., Gren B.A., Sulkowska J.I.
Conservation of knotted and slipknotted topology in transmembrane transporters
(2023) Biophysical Journal, 122 (23), pp. 4528 – 4541
DOI: 10.1016/j.bpj.2023.10.031
- Perlinska A.P., Nguyen M.L., Pilla S.P., Staszor E., Lewandowska I., Bernat A., Purta E., Augustyniak R., Bujnicki J.M., Sulkowska J.I.
Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens
(2023) Frontiers in Molecular Biosciences, 10, art. no. 1223830
DOI: 10.3389/fmolb.2023.1223830
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