Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Specificity in detection of PTCs in mRNA by NMD and its network, insights from cancer perspective and cross-linking (XL-MS)

2020/36/C/NZ2/00108

Keywords:

mRNA premature termination codons NMD eukaryotic release factors exon junction complex cross-linking molecular modeling molecular dynamics

Descriptors:

  • NZ2_008:
  • NZ2_007:
  • NZ2_010:

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Uniwersytet Gdański, Międzynarodowe Centrum Badań nad Szczepionkami Przeciwnowotworowymi

woj. pomorskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Umesh Kalathiya 

Number of co-investigators in the project: 2

Call: SONATINA 4 - announced on 2019-12-16

Amount awarded: 604 075 PLN

Project start date (Y-m-d): 2020-12-01

Project end date (Y-m-d): 2024-01-31

Project duration:: 38 months (the same as in the proposal)

Project status: Project settled

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 (11)
  1. The Elephant Evolved p53 Isoforms that Escape MDM2-Mediated Repression and Cancer
    Authors:
    Padariya, M., Jooste, M. L., Hupp, T., Fåhraeus, R., Vojtesek, B., Vollrath, F., Kalathiya, U., & Karakostis, K
    Academic press:
    Molecular biology and evolution (rok: 2022, tom: 39(7), strony: msac149), Wydawca: Oxford University Press on behalf of the Society for Molecular Biology and Evolution
    Status:
    Published
    DOI:
    10.1093/molbev/msac149 - link to the publication
  2. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
    Authors:
    Kalathiya, U., Padariya, M., Faktor, J., Coyaud, E., Alfaro, J. A., Fahraeus, R., Hupp, T. R., Goodlett, D. R.
    Academic press:
    Biomolecules (rok: 2021, tom: 11(3), strony: 382), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom11030382 - link to the publication
  3. Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations.
    Authors:
    Padariya, M., Kote, S., Mayordomo, M., Dapic, I., Alfaro, J., Hupp, T., Fahraeus, R., Kalathiya, U.
    Academic press:
    Computational and structural biotechnology journal (rok: 2021, tom: 19, strony: 5072–5091), Wydawca: ELSEVIER
    Status:
    Published
    DOI:
    10.1016/j.csbj.2021.09.006 - link to the publication
  4. In Vitro Cross-Linking MS Reveals SMG1–UPF2–SMG7 Assembly as Molecular Partners within the NMD Surveillance
    Authors:
    Padariya, M.; Vojtesek, B.; Hupp, T.; Kalathiya, U.
    Academic press:
    International Journal of Molecular Sciences (rok: 2024, tom: 25, strony: 3182), Wydawca: mdpi
    Status:
    Published
    DOI:
    10.3390/ijms25063182 - link to the publication
  5. Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the 'Regulatory Loop'
    Authors:
    Padariya, M., Fahraeus, R., Hupp, T., Kalathiya, U.
    Academic press:
    International journal of molecular sciences (rok: 2021, tom: 22(23), strony: 12744), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms222312744 - link to the publication
  6. Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade
    Authors:
    Lisowska, M., Lickiss, F., Gil-Mir, M., Huart, A. S., Trybala, Z., Way, L., Hernychova, L., Krejci, A., Muller, P., Krejcir, R., Zhukow, I., Jurczak, P., Rodziewicz-Motowidło, S., Ball, K., Vojtesek, B., Hupp, T., Kalathiya, U.
    Academic press:
    Frontiers in microbiology (rok: 2022, tom: 13, strony: 875556), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmicb.2022.875556 - link to the publication
  7. Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)
    Authors:
    Kalathiya, U., Padariya, M., Faktor, J., Coyaud, E., Alfaro, J. A., Fahraeus, R., Hupp, T. R., Goodlett, D. R.
    Academic press:
    Biomolecules (rok: 2021, tom: 11(3), strony: 382), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom11030382 - link to the publication
  8. The Binding Specificity of PAB1 with Poly(A) mRNA, Regulated by Its Structural Folding
    Authors:
    Padariya, M., Kalathiya, U
    Academic press:
    Biomedicines (rok: 2022, tom: 10(11), strony: 2981), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biomedicines10112981 - link to the publication
  9. Identification of novel interferon responsive protein partners of human leukocyte antigen A (HLA-A) using cross-linking mass spectrometry (CLMS) approach
    Authors:
    Singh, A., Padariya, M., Faktor, J., Kote, S., Mikac, S., Dziadosz, A., Lam, T. W., Brydon, J., Wear, M. A., Ball, K. L., Hupp, T., Sznarkowska, A., Vojtesek, B., Kalathiya, U
    Academic press:
    Scientific reports (rok: 2022, tom: 12(1), strony: 19422), Wydawca: Nature Portfolio
    Status:
    Published
    DOI:
    10.1038/s41598-022-21393-z - link to the publication
  10. Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations.
    Authors:
    Padariya, M., Kote, S., Mayordomo, M., Dapic, I., Alfaro, J., Hupp, T., Fahraeus, R., Kalathiya, U.
    Academic press:
    Computational and structural biotechnology journal (rok: 2021, tom: 19, strony: 5072–5091), Wydawca: ELSEVIER
    Status:
    Published
    DOI:
    10.1016/j.csbj.2021.09.006 - link to the publication
  11. Molecular Determinants and Specificity of mRNA with Alternatively-Spliced UPF1 Isoforms, Influenced by an Insertion in the 'Regulatory Loop'
    Authors:
    Padariya, M., Fahraeus, R., Hupp, T., Kalathiya, U.
    Academic press:
    International journal of molecular sciences (rok: 2021, tom: 22(23), strony: 12744), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms222312744 - link to the publication

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