Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

Delete all

Predicting affinity of ligands to RNA. The case of an aminoglycoside-sensing riboswitch.

2017/26/M/NZ1/00827

Keywords:

RNA riboswitch aminoglycosides molecular dynamics enhanced sampling methods

Descriptors:

  • NZ2_8: Computational biology
  • NZ1_4: Structural biology
  • NZ1_3: Biophysics

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):

prof. Joanna Trylska 

Number of co-investigators in the project: 7

Call: HARMONIA 9 - announced on 2017-06-14

Amount awarded: 560 000 PLN

Project start date (Y-m-d): 2018-04-20

Project end date (Y-m-d): 2023-12-19

Project duration:: 68 months (the same as in the proposal)

Project status: Project completed

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (6)
  • Articles in post-conference publications (1)
  1. Towards catalytic antibiotics: redesign of aminoglycosides to catalytically disable bacterial ribosomes
    Authors:
    Boris Smolkin, Alina Khononov, Tomasz Pieńko, Michal Shavit, Valery Belakhov, Joanna Trylska, Timor Baasov
    Academic press:
    ChemBioChem (rok: 2019, tom: 20, strony: 247-259), Wydawca: Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
    Status:
    Published
    DOI:
    10.1002/cbic.201800549 - link to the publication
  2. Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection
    Authors:
    Piotr Chyży, Marta Kulik, Suyong Re, Yuji Sugita, Joanna Trylska
    Academic press:
    Front. Mol. Biosci. (rok: 2021, tom: 8, strony: 633130), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2021.633130 - link to the publication
  3. Thermal stability of peptide nucleic acid complexes
    Authors:
    Maciej Jasiński, Joanna Miszkiewicz, Michael Feig, Joanna Trylska
    Academic press:
    J. Phys. Chem. B (rok: 2019, tom: 123, strony: 8168-8177), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b05168 - link to the publication
  4. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides
    Authors:
    Marta Kulik, Takaharu Mori, Yuji Sugita, Joanna Trylska
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46(19), strony: 9960-9970), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky833 - link to the publication
  5. Molecular dynamics in multi-dimensional space explains how mutations affect the association path of neomycin to a riboswitch
    Authors:
    Piotr Chyży, Marta Kulik, Ai Shinobu, Suyong Re, Yuji Sugita, Joanna Trylska
    Academic press:
    Proceedings of the National Academy of Sciences of the USA (rok: 2024, tom: 121(15), strony: e2317197121), Wydawca: National Academy of Sciences
    Status:
    Published
    DOI:
    10.1073/pnas.2317197121 - link to the publication
  6. Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques
    Authors:
    Filip Leonarski, Maciej Jasiński, Joanna Trylska
    Academic press:
    Biochimie (rok: 2019, tom: 156, strony: 22-32), Wydawca: Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM)
    Status:
    Published
    DOI:
    10.1016/j.biochi.2018.09.005 - link to the publication
  1. Can we predict a riboswitch activity with different ligands by calculations?
    Authors:
    Marta Kulik, Takaharu Mori, Yuji Sugita, Joanna Trylska
    Conference:
    24th Annual Meeting of the RNA Society (rok: 2019, ), Wydawca: RNA Society
    Data:
    konferencja June 11-16
    Status:
    Published

O Narodowym Centrum Nauki

Finansowanie nauki

Współpraca zagraniczna

Centrum prasowe

Deklaracja dostępności
Przetwarzanie danych osobowych
Polityka cookies

Partnerzy