CeNT
herb

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
 
Prof. Joanna Sułkowska
email: j.sulkowska@cent.uw.edu.pl
phone: +48 22 55 43675
room: 04.43
Strona internetowa: http://jsulkowska.cent.uw.edu.pl/


Group Leader:
Prof. Joanna Sułkowska


Lab Manager:
Michał Tyras, MSc

Postdoctoral Fellows:
Fernando Bruno da Silva, PhD
Anna Kluza, PhD
Mariusz Możajew, PhD
Szymon Niewieczerzal, PhD

programmists:
Agata Perlińska
PhD Paweł Rubach

Students:

Iwona Lewandowska

Maciej Sikora

Mai Lan Nguyen

Mateusz Fortunka

Jacek Płonka

Julia Sosinska

Dominika Krason

Magdalena Osełka

Julia Sikroska

Julia Kamysz

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
AlphaKnot 2.0: A web server for the visualization of proteins’ knotting and a database of knotted AlphaFold-predicted models
Rubach P., Sikora M., Jarmolińska A.I., Perlinska A.P., Sulkowska J.I.
Nucleic Acids Research, 52 (W1), pp. W187 - W193
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods
Wanda Niemyska, Paweł Rubach, Bartosz A Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J Rawdon, Joanna I Sułkowska
Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W44–W50
Lasso Proteins—Unifying Cysteine Knots and Miniproteins
Bartosz Ambroży Greń, Paweł Dąbrowski-Tumański, Wanda Niemyska Joanna Ida Sułkowska
Polymers, 13(22), 3988
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
Vasilina Zayats, Agata P. Perlinska, Aleksandra I. Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I. Sulkowska
PLoS Computational Biology, 17(10), e1009502.
Knot_pull—python package for biopolymer smoothing and knot detection.
Jarmolinska, A. I., Gambin, A., & Sulkowska, J. I.
Bioinformatics, 36(3), 953-955.
Genus for biomolecules
Rubach, P., Zajac, S., Jastrzebski, B., Sulkowska, J. I., & Sułkowski, P.
Nucleic acids research, 48(D1), D1129-D1135.
Mg2+-Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study
Kałek, M., Perlińska, A., Sułkowska, J. (2020)
ACS Catalysis (10), 8058-8068
Topoly: Python package to analyze the topology of polymers
Dabrowski-Tumanski, P., Rubach, P., Niemyska, W., Gren, B. A., & Sulkowska, J. I.
Briefings in Bioinformatics
The Folding of Knotted Proteins: Distinguishing the Distinct behavior of Shallow and Deep Knots
Piejko, M., Niewieczerzal, S., & Sulkowska, J. I.
Israel Journal of Chemistry, 60(7), 713-724
On folding of entangled proteins: knots, lassos, links and theta-curves
Sulkowska, J. I.
Current opinion in structural biology, 60, 131-141
A Guide to Targeting the Endocannabinoid System in Drug Design
Stasiulewicz, A., Znajdek, K., Grudzień, M., Pawiński, T., & Sulkowska, J. I.
International journal of molecular sciences, 21(8), 2778
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Perlinska, A. P., Stasiulewicz, A., Nawrocka, E. K., Kazimierczuk, K., Setny, P., & Sulkowska, J. I.
PLoS computational biology, 16(5), e1007904
A novel de novo mutation p.Ala428Asp in KRT5 gene as a cause of localized epidermolysis bullosa simplex
Stawczyk-Macieja, M., Wertheim-Tysarowska, K., Jakubowski, R., Szczerkowska-Dobosz, A., Krygier, M., Wilkowska, A., . . . & Nowicki, R. (2019).
Experimental Dermatology
KnotProt 2.0: a database of proteins with knots and other entangled structures
Dabrowski-Tumanski, P., Rubach, P., Goundaroulis, D., Dorier, J., Sułkowski, P., Millett, K. C., . . . Sułkowska, J. I. (2019).
Nucleic Acids Research, 47(D1), D367-D375
Proteins’ Knotty Problems
Jarmolinska, A. I., Perlinska, A. P., Runkel, R., Trefz, B., Ginn, H. M., Virnau, P., & Sulkowska, J. I. (2019).
Journal of Molecular Biology, 431(2), 244-257
DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings
Jarmolinska, A. I., Zhou, Q., Sulkowska, J. I., & Morcos, F.
Journal of Chemical Information and Modeling, 59(2), 625-629
Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function
Dabrowski-Tumanski, P., Gren, B., & Sulkowska, J. I.
Polymers, 11(4), 707
Defining and detecting links in chromosomes
Niewieczerzal, S., Niemyska, W., & Sulkowska, J. I.
Scientific reports, 9(1), 1-10.
PconsFam: An interactive database of structure predictions of Pfam families
Lamb, J., Jarmolinska, A. I., Michel, M., Menéndez-Hurtado, D., Sulkowska, J. I., & Elofsson, A.
Journal of molecular biology, 431(13), 2442-2448.
PyLink: a PyMOL plugin to identify links
Gierut, A. M., Dabrowski-Tumanski, P., Niemyska, W., Millett, K. C., & Sulkowska, J. I.
Bioinformatics, 35(17), 3166-3168.
Supercoiling in a protein increases its stability
Niewieczerzał, S., & Sulkowska, J. I.
Physical review letters, 123(13), 138102.
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
Genus trace reveals the topological complexity and domain structure of biomolecules
Zając, S., Geary, C., Andersen, E. S., Dabrowski-Tumanski, P., Sulkowska, J. I., & Sułkowski, P.
Scientific Reports, 8(1)
Dominant ELOVL1 mutation causes neurological disorder with ichthyotic keratoderma, spasticity, hypomyelination and dysmorphic features
Kutkowska-Kazmierczak, A., Rydzanicz, M., Chlebowski, A. (2018)
Journal of Medical Genetics
Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways
Rydzewski, J., Jakubowski, R., Nowak, W., & Grubmüller, H.
Journal of Chemical Theory and Computation, 14(6), 2843-2851
Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel
Dabrowski-Tumanski, P., Piejko, M., Niewieczerzal, S., Stasiak, A., & Sulkowska, J. I.
The Journal of Physical Chemistry B, 122(49), 11616-11625
The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures
Dabrowski-Tumanski, P., & Sulkowska, J. I.
Reactive and Functional Polymers, 132, 19-25.
Entangled Proteins: Knots, Slipknots, Links, and Lassos
Sułkowska, J. I., & Sułkowski, P.
The Role of Topology in Materials, Springer
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.
To Tie or Not to Tie? That Is the Question
Dabrowski-Tumanski, P., & Sulkowska, J.
Polymers, 9(12), 454.
Transmembrane helix connectivity in Orai1 controls two gates for calcium-dependent transcription
Frischauf, I., Litviňuková, M., Schober, R., Zayats, V., Svobodová, B., Bonhenry, D., . . . Schindl, R.
Science Signaling, 10(507).
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