Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Influence of knotted structure on function of proteins and protein structure prediction

2012/07/E/NZ1/01900

Keywords:

knotted proteins function of proteins prediction protein structure evolution computer simulation

Descriptors:

  • NZ1_3: Biophysics
  • NZ2_7: Bioinformatics
  • ST1_6: Topology

Panel:

NZ1 - Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution :

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Joanna Sułkowska 

Number of co-investigators in the project: 5

Call: SONATA BIS 2 - announced on 2012-09-15

Amount awarded: 1 480 077 PLN

Project start date (Y-m-d): 2013-08-29

Project end date (Y-m-d): 2020-01-28

Project duration:: 77 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Software - oprogramowanie (3 300 PLN)
  2. komputery stacjonarne (2 szt.) (11 000 PLN)
  3. wielordzeniowe jednostki obliczeniowe (10 szt.) (80 000 PLN)
  4. Software - oprogramowanie (2 000 PLN)
  5. dodatkowe dyski (1 836 PLN)
  6. switch, UPS, dyski (10 000 PLN)

Information in the final report

  • Publication in academic press/journals (24)
  • Book publications / chapters in book publications (2)
  1. Complex lasso: new entangled motifs in proteins
    Authors:
    W Niemyska, P Dabrowski-Tumanski, M Kadlof, E Haglund, P Sułkowski, JI Sulkowska
    Academic press:
    Scientific Reports (rok: 2016, tom: 6, strony: 45301), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/srep36895 - link to the publication
  2. DCA-MOL - a PyMOL plugin to analyze direct evolutionary couplings
    Authors:
    AI Jarmolinska, Q Zhou, JI Sulkowska, F Morcos
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2019, tom: 59, strony: 625-629), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jcim.8b00690 - link to the publication
  3. Determining Critical Amino Acid contacts for knotted protein
    Authors:
    P. Dabrowski-Tumanski, S. Niewieczerzal and J. I. Sulkowska
    Academic press:
    TASK Quarterly (rok: 2014, tom: 18 No 3, strony: 323–337), Wydawca: Scientific Bulletin of the Academic Computer Center in Gdansk
    Status:
    Published
    DOI:
    brak - link to the publication
  4. GapRepairer – repair structures with topological care
    Authors:
    AI Jarmolinska*, M Kadlof*, P Dabrowski-Tumanski, JI Sulkowska
    Academic press:
    Bioniformatics (rok: 2018, tom: 34, strony: 3300–3307), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty334 - link to the publication
  5. Genus trace reveals the topological complexity and domain structure of biomolecules
    Authors:
    S Zajac, C Geary, E Andersen, P Dabrowski-Tumanski, JI Sulkowska, P Sułkowski
    Academic press:
    Scientifical Reports (rok: 2018, tom: 8, strony: 45300), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-018-35557-3 - link to the publication
  6. Proteins' knotty problems
    Authors:
    AI Jarmolinska, AP Perlinska, R Runkel, B Trefz, P Virnau, JI Sulkowska
    Academic press:
    J Mol Biol. (rok: 2018, tom: 43, strony: 244-257), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.012 - link to the publication
  7. Current approaches to disentangle the mystery of knotted protein folding
    Authors:
    P Dabrowski-Tumanski, M Sklodowski, JI Sulkowska
    Academic press:
    TASK Quarterly (rok: 2016, tom: 20, strony: 361–371), Wydawca: Scientific Bulletin of the Academic Computer Center in Gdansk
    Status:
    Published
    DOI:
    10.17466/tq2016/20.4/f - link to the publication
  8. Knotting and unknotting proteins in the chaperonin cage: effects of the excluded volume
    Authors:
    Szymon Niewieczerzal, Joanna I Sulkowska
    Academic press:
    PloS One (rok: 2017, tom: 10, strony: 23), Wydawca: PloS One
    Status:
    Published
    DOI:
    10.1371/journal.pone.0176744 - link to the publication
  9. LinkProt: database collecting information about biological links
    Authors:
    P Dabrowski-Tumanski*, AI Jarmolinska*, W Niemyska*, E Rawdon, KC Millett, JI Sulkowska
    Academic press:
    Nucleic Acids Res. (rok: 2016, tom: 45, strony: 243-249), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw976 - link to the publication
  10. Methyl Transfer by Substrate Signaling from a Knotted Protein Fold
    Authors:
    T Christian*, R Sakaguchi*, AP Perlinska*, G Lahoud, T Ito, EA Taylor, S Yokoyama, JI Sulkowska, Ya-Ming Hou
    Academic press:
    Nature Structure & Molecular Biology (rok: 2016, tom: 23, strony: 941-948), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/nsmb.3282 - link to the publication
  11. The APS-bracket - a topological tool to classify lasso proteins, RNAs and other tadpole-like structures.
    Authors:
    P Dabrowski-Tumanski, JI Sulkowska
    Academic press:
    Reactive and Functional Polymers (rok: 2018, tom: 132, strony: 19-25), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.reactfunctpolym.2018.09.005 - link to the publication
  12. The exclusive effects of chaperonin on the behavior of the 52 knotted proteins
    Authors:
    Y Zhao*, S Niewieczerzal*, P Dabrowski-Tumanski*, JI Sulkowska
    Academic press:
    PLoS Computational Biology (rok: 2018, tom: 14, strony: e1005970), Wydawca: PloS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1005970 - link to the publication
  13. The exclusive effects of chaperonin on the behavior of the 52 knotted proteins
    Authors:
    Y Zhao, S Niewieczerzal, P Dabrowski-Tumanski, JI Sulkowska
    Academic press:
    Plos Computational Biology (rok: 2018, tom: 14(3), strony: e1005970), Wydawca: PloS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1005970 - link to the publication
  14. To Tie or Not to Tie? That Is the Question
    Authors:
    P Dabrowski-Tumanski, JI Sulkowska
    Academic press:
    Polymers (rok: 2017, tom: 9, strony: 454-474), Wydawca: Multidisciplinary Digital Publishing Institute
    Status:
    Published
    DOI:
    10.3390/polym9090454 - link to the publication
  15. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting From the Ribosome Exit Channel
    Authors:
    P Dabrowski-Tumanski, M Piejko, S Niewieczerzal, S Stasiak, JI Sulkowska
    Academic press:
    The Journal of Physical Chemistry B (rok: 2018, tom: 122, strony: 11616-11625), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.8b07634 - link to the publication
  16. Defining and detecting links in chromosomes
    Authors:
    S Niewieczerzal, W Niemyska, JI Sulkowska
    Academic press:
    Scientific Reports (rok: 2019, tom: 9, strony: 11753), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41598-019-47999-4 - link to the publication
  17. LassoProt: server to analyze biopolymers with lassos
    Authors:
    P Dąbrowski-Tumanski, W Niemyska, P Pasznik, JI Sulkowska
    Academic press:
    Nucleic Acids Res (rok: 2016, tom: 44, strony: 383-389), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkw308 - link to the publication
  18. Molecular dynamics and structural comparison approach to understanding the role of the knots in proteins
    Authors:
    AP Perlinska, JM Macnar, JI Sulkowska
    Academic press:
    TASK Quarterly (rok: 2016, tom: 20, strony: 373-381), Wydawca: Scientific Bulletin of the Academic Computer Center in Gdansk
    Status:
    Published
    DOI:
    10.17466/tq2016/20.4/h - link to the publication
  19. In search of functional advantages of knots in proteins
    Authors:
    P Dabrowski-Tumanski, A Stasiak, JI Sulkowska
    Academic press:
    PloS One (rok: 2016, tom: 2, strony: 45305), Wydawca: PloS One
    Status:
    Published
    DOI:
    10.1371/journal.pone.0165986 - link to the publication
  20. KnotProt: a database of proteins with knots and slipknots
    Authors:
    M. Jamroz, W. Niemyska, EJ Rawdon, A. Stasiak, KC Millett, P. Sułkowski, JI Sulkowska
    Academic press:
    Nucleic Acids Res. (rok: 2015, tom: 43, strony: D306-D314), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gku1059 - link to the publication
  21. PconsFam: An interactive database of structure predictions of Pfam families
    Authors:
    J Lamb, AI Jarmolinska, M Michel, D Menendez Hurtado, JI Sulkowska, A Elofsson
    Academic press:
    Journal of Molecular Biology (rok: 2019, tom: 431, strony: 2442-2448), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmb.2019.01.047 - link to the publication
  22. PyLasso – a PyMOL plugin to identify lassos
    Authors:
    Aleksandra Gierut, Wanda Niemyska, Pawel Dabrowski-Tumanski, Piotr Sułkowski, and Joanna I. Sulkowska
    Academic press:
    Bioinformatics (rok: 2017, tom: 33, strony: 3819–3821), Wydawca: Oxford
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btx493 - link to the publication
  23. KnotGenome: A server to analyze entanglements of chromosomes
    Authors:
    JI Sulkowska, S Niewieczerzal, AI Jarmolinska, JT Siebert, P Virnau, W Niemyska
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, strony: 17-24), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky511 - link to the publication
  24. KnotProt 2.0: A database of proteins with knots and other entangled structures
    Authors:
    P Dabrowski-Tumanski, P Rubach, D Goundaroulis, J Dorier, P Sułkowski, KC Millett, EJ Rawdon, A Stasiak, JI Sulkowska
    Academic press:
    Nucleic Acid Research (rok: 2019, tom: 47, strony: D367–D375), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky1140 - link to the publication
  1. Entangled Proteins: Knots, Slipknots, Links, and Lassos
    Authors:
    P Sulkowski, JI Sulkowska
    Book:
    The Role of Topology in Materials (rok: 2018, tom: 189, strony: 201-226), Wydawca: Sringer
    Status:
    Published
    DOI:
    link to the publication
  2. TrmD: A Methyl Transferase for tRNA Methylation With m1G37
    Authors:
    Ya-MIng Hou, Ryuma Matsubara, Ryuichi Takase, Isao Masuda, Joanna I. Sulkowska
    Book:
    The Enzyme (rok: 2017, tom: 41, strony: 89-115), Wydawca: Elsevier
    Status:
    Published
    DOI:
    link to the publication

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