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Interdomain allosteric communication in Rad50 protein and its role in genome maintence by Mre11 complex

2016/21/B/NZ1/02847

Keywords

Descriptors

  • NZ1_3: Biofizyka
  • NZ1_2: Biochemia
  • ST5_16: Chemia biologiczna

Panel

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

Host institution

Uniwersytet Wrocławski, Wydział Biotechnologii

Voivodeship: dolnośląskie

Other projects carried out by the institution »

Principal investigator (from the host institution)

prof. Artur Krężel

Number of co-investigators in the project: 7

Call

OPUS 11 – announced on 2016-03-15

Amount awarded
1 478 920 PLN
Project start date
2017-01-12
Project end date
2020-11-11
Project duration
46 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.

Equipment purchased [PL]

  1. 2 zestawy komputerowe do analizy danych i obliczeń.
  2. Spektrofluorymetr do pomiaru czasu zaniku fluorescencji. Cost: 350 000 PLN

Information in the final report

Publication in academic press/journals (14)

  1. Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation

    Authors:
    Józef B. Tran, Michał Padjasek, Artur Krężel
    Academic press:
    International Journal of Molecular Sciences (year: 2022, volume: 23, pages: 11140), Publisher: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms231911140 – link to the publication

  2. Optimized allosteric inhibition of engineered protein tyrosine phosphatases with an expanded palette of biarsenical small molecules

    Authors:
    Samuel Korntner, Adam Pomorski, Artur Krężel, Anthony C. Bishop
    Academic press:
    Bioorganic and Medicinal Chemistry (year: 2018, volume: 26, pages: 2610-2620), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bmc.2018.04.026 – link to the publication

  3. Chemometrics-assisted optimization of liquid chromatography-quadrupole-time-of-flight mass spectrometry analysis for targeted metabolomics

    Authors:
    Manuel David Peris-Díaz, Olga Rodak, Shannon R. Sweeney, Artur Krężel, Enrique Sentandreu
    Academic press:
    Talanta (year: 2019, volume: 199, pages: 380-387), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.talanta.2019.02.075 – link to the publication

  4. Fluorescent probes for selective protein labeling in lysosomes: a case of alpha-galactosidase A

    Authors:
    Cornelius Bohl, Adam Pomorski, Susanne Seemann, Anne-Marie Knospe, Chaonan Zheng, Artur Krężel, Arndt Rolfs, Jan Lukas
    Academic press:
    The FASEB Journal (year: 2017, volume: 31, pages: 5258-5267), Publisher: Federation of American Societies for Experimental Biology
    Status:
    Published
    DOI:
    10.1096/fj.201700058RRRR – link to the publication

  5. Phytochelatins as a Dynamic System for Cd(II) Buffering from the Micro- to Femtomolar Range

    Authors:
    Joanna Wątły, Marek Łuczkowski, Michał Padjasek, Artur Krężel
    Academic press:
    Inorganic Chemistry (year: 2021, volume: 60, pages: 4657-4675), Publisher: American Chemical Society (ACS)
    Status:
    Published
    DOI:
    10.1021/acs.inorgchem.0c03639 – link to the publication

  6. Molar absorption coefficients and stability constants of Zincon metal complexes for determination of metal ions and bioinorganic applications

    Authors:
    Anna Kocyła, Adam Pomorski, Artur Krężel
    Academic press:
    Journal of Inorganic Biochemistry (year: 2017, volume: 176, pages: 53-65), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jinorgbio.2017.08.006 – link to the publication

  7. Reactivity of Cu(II)-, Zn(II)- and Fe(II)-Thiosemicarbazone Complexes with Glutathione and Metallothionein: from Stability over Dissociation to Transmetallation

    Authors:
    Alice Santoro, Bertrand Vileno, Òscar Palacios, Manuel David Peris-Díaz, Gilles Riegel, Christian Gaiddon, Artur Krężel, Peter Faller
    Academic press:
    Metallomics (year: 2019, volume: 11, pages: 994-1004), Publisher: Royal Chemical Society
    Status:
    Published
    DOI:
    10.1039/C9MT00061E – link to the publication

  8. Mass Spectrometry-Based Structural Analysis of Cysteine-Rich Metal-Binding Sites in Proteins with MetaOdysseus R Software

    Authors:
    Manuel David Peris-Diaz
    Academic press:
    Journal of Proteome Reserach (year: 2021, volume: 20, pages: 776-785), Publisher: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jproteome.0c00651 – link to the publication

  9. InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information

    Authors:
    Józef Ba Tran, Artur Krężel
    Academic press:
    Journal of Proteome Research (year: 2021, volume: 20, pages: 1889-1901), Publisher: American Chemical Society (ACS)
    Status:
    Published
    DOI:
    10.1021/acs.jproteome.0c00906 – link to the publication

  10. Galvanization of Protein–Protein Interactions in a Dynamic Zinc Interactome

    Authors:
    Anna Kocyła, Józef Tran, Artur Krężel
    Academic press:
    Trends in Biochem Sciences (year: 2021, volume: 46, pages: 64-79), Publisher: Cell Press / Elsevier
    Status:
    Published
    DOI:
    10.1016/j.tibs.2020.08.011 – link to the publication

  11. Metal Exchange in the Interprotein ZnII-Binding Site of the Rad50 Hook Domain: Structural Insights into CdII-Induced DNA-Repair Inhibition

    Authors:
    Michał Padjasek, Maciej Maciejczyk, Michał Nowakowski, Olga Kerber, Maciej Pyrka, Wiktor Koźmiński, Artur Krężel
    Academic press:
    Chemistry - A European Journal (year: 2020, volume: 26, pages: 3297 – 3313), Publisher: Wiley
    Status:
    Published
    DOI:
    10.1002/chem.201904942 – link to the publication

  12. Formation of highly stable multinuclear AgnSn clusters in zinc fingers disrupts their structure and function

    Authors:
    Katarzyna Kluska, Manuel D. Peris-Dıiaz, Dawid Płonka, Alexander Moysa, Michał Dadlez, Aurelien Deniaud, Wojciech Bal, Artur Krężel
    Academic press:
    Chemical Communications (year: 2020, volume: 56, pages: 1329--1332), Publisher: Royal Chemical Society
    Status:
    Published
    DOI:
    10.1039/c9cc09418k – link to the publication

  13. Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains

    Authors:
    Michał Padjasek, Anna Kocyła, Katarzyna Kluska, Olga Kerber, Józef Ba Tran, Artur Krężel
    Academic press:
    Journal of Inorganic Biochemistry (year: 2020, volume: 204, pages: 110955), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jinorgbio.2019.110955 – link to the publication

  14. An Extremely Stable Interprotein Tetrahedral Hg(Cys)4 Core Formed in the Zinc Hook Domain of Rad50 Protein at Physiological pH

    Authors:
    Marek Łuczkowski, Michał Padjasek, Józef B. Tran, Lars Hemmingsen, Olga Kerber, Jelena Habjanič, Eva Freisinger, Artur Krężel
    Status:
    Accepted for publication

Articles in post-conference publications (26)

  1. Investigation of zinc hook domain of Rad50 from S. cerevisiae - spectroscopic stability studies of minimal and full domain length peptides interactions with Zn(II)

    Authors:
    Józef Tran, Michał Padjasek, Artur Krężel
    Conference:
    24-th Polish Peptide Symposium (year: 2017, pages: 142), Publisher: Uniwersytet Gdański
    Date:
    conference 3-7.09
    Status:
    Published

  2. Bisarsenowe sondy fluorescencyjne - Chemia na pomoc biologii

    Authors:
    Adam Pomorski
    Conference:
    60 Zjazd Naukowy Polskiego Towarzystwa Chemicznego (year: 2017, pages: 525), Publisher: Politechnika Wrocławska
    Date:
    conference 17-21.09
    Status:
    Published

  3. Structural and energetic factors that control zinc protein domains stability and function

    Authors:
    Justyna Adamczyk, Anna Kocyła, Michał Padjasek, Katarzyna Kluska, Artur Krężel
    Conference:
    24-th Polish Peptide Symposium (year: 2017, pages: 40), Publisher: Uniwersytet Gdański
    Date:
    conference 3-7.09
    Status:
    Published

  4. How proteins match Zn(II) affinity with their functions? Relations between thermodynamics and free zinc status

    Authors:
    Adam Pomorski, Agnieszka drozd, Katarzyna Kluska, Justyna Adamczyk, Anna Kocyła, Artur Krężel
    Conference:
    International Society for Zinc in Biology ISZB 5-th meeting (year: 2017, pages: 46), Publisher: UCLAN
    Date:
    conference 18-22.06
    Status:
    Published

  5. Insight into the cellular buffering mechanism through structural characterization of partially-depleted methallothionein 2

    Authors:
    Manuel David Peris-Díaz, Dominika Wojewska, Agnieszka Drozd, Artur Krężel
    Conference:
    11-th International Biometals Symposium (year: 2018, pages: 63), Publisher: University of Ottawa
    Date:
    conference 15-19.07
    Status:
    Published

  6. Beyond classical binding sites in zinc proteins - biophysical overview of zinc hook, zinc clasp and altred zinc fingers

    Authors:
    Anna Kocyła, Michał Padjasek, Katarzyna Kluska, Justyna Adamczyk, Olga Kerber, Józef Tran, Artur Krężel
    Conference:
    Eurobic 14 (year: 2018, pages: abstrakt 188), Publisher: University of Birmingham
    Date:
    conference 26-30.08
    Status:
    Published

  7. Wpływ sposobu koordynacji oraz powinowactwa jonów Zn(II) na komórkową funkcję metalobiałek

    Authors:
    Katarzyna Kluska, Anna Kocyła, Olga Kerber, Józef Tran, Michał Padjasek, Manuel Peris-Díaz, Artur Krężel
    Conference:
    62 Zjazd PTChem Warszawa (year: 2019, pages: S02-12), Publisher: Politechnika Warszawska
    Date:
    conference 2019-09-02 - 2019-09-06
    Status:
    Published

  8. Relationship between the architecture of zinc coordination and zinc binding affinity in proteins-insights into zinc regulation

    Authors:
    Katarzyna Kluska, Olga Kerber, Adam Pomorski, Anna Kocyła, Michał Padjasek, Józef Tran, Manuel Peris-Diáz, Justyna Adamczyk, Artur Krężel
    Conference:
    61 Zjazd Naukowy Polskiego Towarzystwa Chemicznego (year: 2018, pages: S01-2), Publisher: Uniwersytet Jagielloński
    Date:
    conference 17-21.09
    Status:
    Published

  9. How proteins match Zn(II) affinity to fit their function? Relationship between thermodynamics and free zinc status

    Authors:
    Michał Padjasek, Anna Kocyła, Katarzyna Kluska, Justyna Adamczyk, Manuel David Peris Díaz, Artur Krężel
    Conference:
    11-th International Biometals Symposium (year: 2018, pages: 39), Publisher: University of Ottawa
    Date:
    conference 15-19.07
    Status:
    Published

  10. Biophysical characterization of Rad50 zinc hook domain from thermophilic archeon Thermoplasma acidophilum

    Authors:
    Olga Kerber, Artur Krężel
    Conference:
    43-rd FEBS Congress (year: 2018, pages: 437), Publisher: FEBS
    Date:
    conference 7-12.07
    Status:
    Published

  11. Składanie białek z wykorzystaniem peptydowych motywow dimeryzujących zależnych od jonow Zn(II)

    Authors:
    Anna Kocyła, Artur Krężel
    Conference:
    62 Zjazd PTChem Warszawa (year: 2019, pages: S15-6), Publisher: Politechnika Warszawska
    Date:
    conference 2019-09-02 - 2019-09.06
    Status:
    Published

  12. Deciphering Cd(II) ion's impact on intermolecular Zn(II)-binding site of Rad50 zinc hook domain

    Authors:
    Michał Padjasek, Artur Krężel
    Conference:
    25-th Polish Peptide Symosium (year: 2019, pages: 106), Publisher: Uniwersytet Medyczny we Wrocławiu
    Date:
    conference 2019-09-08 - 2019-08-12
    Status:
    Published

  13. Insight into Rad50's phosphorylation – stability and Zn(II) binding

    Authors:
    Józef Tran, Michał Padjasek, Artur Krężel
    Conference:
    25-th Polish Peptide Symosium (year: 2019, pages: 121), Publisher: Uniwersytet Medyczny we Wrocławiu
    Date:
    conference 2019-09-08 - 2019-09-12
    Status:
    Published

  14. Insights into the origin of weakly bound Zn(II) ion in metallothionein proteins from computational modeling

    Authors:
    Manuel David Peris-Díaz, Artur Krężel
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 195), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

  15. Biophysical properties of Rad50 zinc hook domain

    Authors:
    Olga Kerber, Artur Krężel
    Conference:
    25-th Polish Peptide Symosium (year: 2019, pages: 82), Publisher: Uniwersytet Medyczny we Wrocławiu
    Date:
    conference 2019-09-08 - 2019-09-12
    Status:
    Published

  16. Regulacja i deregulacja funkcji białek cynkowych - Walka dobrego z dobrym i złym

    Authors:
    Artur Krężel
    Conference:
    64 Zjazd Naukowy PTChem (year: 2022, pages: 113), Publisher: UMCS
    Date:
    conference 11-16.09
    Status:
    Published

  17. Metal-binding properties of the eukaryotic Rad50 hook domain variants – insights into the sequence-stability relationship

    Authors:
    Olga Kerber, Artur Krężel
    Conference:
    16-th European Biological Inorganic Chemistry Conference (year: 2022, pages: MM44), Publisher: EuroBIC-16
    Date:
    conference 17-21.07
    Status:
    Published

  18. Metal-coupled folding as the driving force for zinc proteins function - insight into sequence-structure-stability relationships in zinc finger, hook and clasp domains

    Authors:
    Olga Kerber, Michał Padjasek, Józef B. Tran, Katarzyna Kluska, Anna Kocyła, Artur Krężel
    Conference:
    17-th Naples Workshop on Bioactive Peptides (year: 2022, pages: O 29), Publisher: 17-th Naples Workshop on Bioactive Peptides
    Date:
    conference 16-18.06
    Status:
    Published

  19. Relationships of the structural and zinc buffering properties of human metallothioneins

    Authors:
    Manuel D. Peris-Diaz, Agnieszka Drozd, Dominika Wojewska, Roman Guran, Adam Pomorski, Ondriej Zitka, Vojtech Adam, Artur Krężel
    Conference:
    The 6-th Meeting of International Society for Zinc Biology (year: 2019, pages: 28), Publisher: Kyoto University
    Date:
    conference 2019-09-06 - 2019-09-13
    Status:
    Published

  20. Phosphorylation in zinc hook domain of Rad50 protein - stability and architecture Investigation

    Authors:
    Józef Tran, Michał Padjasek, Artur Krężel
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 108), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

  21. Zinc Hook Domain – Puzzling Rad50 Interprotein Zn(II) Binding Site with Many Faces

    Authors:
    Józef Tran, Olga Kerber, Michał Padjasek, Maciej Maciejczyk, Marek Łuczkowski, Tomasz Kochańczyk, Artur Krężel
    Conference:
    19th International Conference on Biological Inorganic Chemistry (year: 2019, pages: 237), Publisher: University of Zurich
    Date:
    conference 2019-08-11 - 2019-08-16
    Status:
    Published

  22. Sequence-structure-stability relations in zinc hook, zinc clasp and altered zinc finger protein domains

    Authors:
    Katarzyna Kluska, Olga Kerber, Anna Kocyła, Józef Tran, Michał Padjasek, Artur Krężel
    Conference:
    International Symposium on Metal Complexes (year: 2019, pages: 46338), Publisher: University of Debrecen
    Date:
    conference 2019-06-11 - 2019-06-14
    Status:
    Published

  23. Metal dependent folding of a naturally altered zinc finger domains – insight into coordination mode, stability and function

    Authors:
    Katarzyna Kluska, Artur Krężel
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 110), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

  24. Relationship of the structural and zinc buffering properties of human metallothioneins

    Authors:
    Artur Krężel, Manuel David Peris-Díaz, Agnieszka Drozd, Dominika Wojewska, Roman Guran, Adam Pomorski, Ondrej Zitka, Vojtech Adam
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 151), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

  25. Biophysical characterization of Rad50 zinc hook domain from various thermophilic organisms

    Authors:
    Olga Kerber, Katarzyna Kluska, Artur Krężel
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 111), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

  26. Effect of silver ions on zinc fingers structure and function – spectroscopic and stability studies

    Authors:
    Katarzyna Kluska, Dawid Płonka, Olga Kerber, Wojciech Bal, Artur Krężel
    Conference:
    7-th International Symposium on Metallomics (year: 2019, pages: 109), Publisher: Politechnika Warszawska
    Date:
    conference 2019-06-30 - 2019-07-03
    Status:
    Published

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Graphic design and implementation: Jakub Piotrowski