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