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Information of the project and the call

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Multiscale and multiphase molecular dynamics of disordered proteins and proteinceous liquid droplets

2018/31/B/NZ1/00047

Keywords:

molecular dynamics inytrinsically disordered proteins proteinaceous droplets gluten neurodegeneration

Descriptors:

  • NZ1_3: Biophysics
  • NZ1_1: Molecular biology
  • NZ1_4: Structural biology

Panel:

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

Host institution :

Instytut Fizyki Polskiej Akademii Nauk

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Mateusz Chwastyk 

Number of co-investigators in the project: 7

Call: OPUS 16 - announced on 2018-09-14

Amount awarded: 1 159 400 PLN

Project start date (Y-m-d): 2019-07-24

Project end date (Y-m-d): 2024-07-23

Project duration:: 36 months (the same as in the proposal)

Project status: Pending project

Project description

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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 (19)
  • Book publications / chapters in book publications (1)
  1. Pseudo-improper-dihedral model for intrinsically disordered proteins
    Authors:
    Ł. Mioduszewski, B. Różycki, M. Cieplak
    Academic press:
    J. Chem. Theor. Comput. (rok: 2020, tom: 16, strony: 4726-4733), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jctc.0c00338 - link to the publication
  2. Rhizobium etli has two L-asparaginases with low sequence identity but similar structure and catalytic center
    Authors:
    J. I. Loch, P. Worsztynowicz, J. Sliwiak, M. Grzechowiak, B. Imiolczyk, K. Pokrywka, M. Chwastyk, M. Gilski, M. Jaskolski
    Academic press:
    ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (rok: 2023, tom: 79, strony: 775-791), Wydawca: INT UNION CRYSTALLOGRAPHY2 ABBEY SQ, CHESTER CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S2059798323005648 - link to the publication
  3. The role of cavities in biological structures
    Authors:
    Ł. Mioduszewski, Karol Wołek, and Mateusz Chwastyk
    Academic press:
    Acta Physica Polonica A (rok: 2024, ), Wydawca: POLISH ACAD SCIENCES INST PHYSICSAL LOTNIKOW 32-46, PL-02-668 WARSAW, POLAND
    Status:
    Accepted for publication
    DOI:
    brak - link to the publication
  4. Conformational biases of alpha-synuclein and formation of transient knots
    Authors:
    M. Chwastyk, M. Cieplak
    Academic press:
    J. Phys. Chem. B (rok: 2020, tom: 124, strony: 45615), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b08481 - link to the publication
  5. Mechanical unfolding of proteins - A comparative nonequilibrium molecular dynamics study
    Authors:
    V. V. Mykuliak, M. Sikora, J. J. Booth, M. Cieplak, D. V. Shalashilin, V. P. Hytonen
    Academic press:
    Biophys. J. (rok: 2020, tom: 119, strony: 939-949), Wydawca: Biophysical Society
    Status:
    Published
    DOI:
    10.1016/j.bpj.2020.07.030 - link to the publication
  6. Network of inter-basin traffic in intrinsically disordered PUMA protei
    Authors:
    B. R. H. de Aquino, M. Cieplak
    Academic press:
    EPL (rok: 2020, tom: 132, strony: 28002), Wydawca: European Physical Society
    Status:
    Published
    DOI:
    10.1209/0295-5075/132/28002 - link to the publication
  7. Preface to the JPCM special issue on droplets and vesicles
    Authors:
    Marek Cieplak,Rui D M Travasso
    Academic press:
    Journal of Physics: Condensed Matter (rok: 2022, tom: 34, strony: 30401), Wydawca: IOP Publishing
    Status:
    Published
    DOI:
    10.1088/1361-648X/ac2f6f - link to the publication
  8. Transient knots in intrinsically disordered proteins and neurodegeneration
    Authors:
    M. Cieplak, M. Chwastyk, Ł. Mioduszewski, B. R. H. de Aquino
    Academic press:
    Progress in Mol. Biol. and Translational Sci. (rok: 2020, tom: 174, strony: 79-103), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/bs.pmbts.2020.03.003. - link to the publication
  9. Viscoelastic properties of wheat gluten in a molecular dynamics study
    Authors:
    Łukasz Mioduszewski, Marek Cieplak
    Academic press:
    PLOS Computational Biology (rok: 2021, tom: 17, strony: e1008840), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1008840 - link to the publication
  10. Cohesin-dockerin code in cellulosomal binding modes and its allosteric regulation by proline isomerization
    Authors:
    A. M. Vera, A. Galera-Prat, M. Wojciechowski,B. Różycki, D. V. Laurents, M. Carrion-Vazquez, M. Cieplak, P. Tinnefeld
    Academic press:
    Structure (rok: 2021, tom: 29, strony: 45302), Wydawca: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.str.2021.01.006 - link to the publication
  11. The networks of the inter-basin traffic in intrinsically disordered proteins
    Authors:
    B. R. H. de Aquino, M. Chwastyk, Ł. Mioduszewski, M. Cieplak
    Academic press:
    Phys. Rev. Res. (rok: 2020, tom: 2, strony: 13242), Wydawca: American Physical Society
    Status:
    Published
    DOI:
    10.1103/PhysRevResearch.2.013242 - link to the publication
  12. Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: Fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
    Authors:
    Ł. Mioduszewski, J. Bednarz, M. Chwastyk, M. Cieplak
    Academic press:
    Computer Physics Communications (rok: 2023, tom: 284, strony: 108611), Wydawca: ELSEVIER
    Status:
    Published
    DOI:
    10.1016/j.cpc.2022.108611 - link to the publication
  13. Nascent Folding of Proteins Across the Three Domains of Life
    Authors:
    Mateusz Chwastyk, Marek Cieplak
    Academic press:
    Frontiers in Molecular Biosciences (rok: 2021, tom: 8, strony: 692230), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2021.692230 - link to the publication
  14. Proteins at curved fluid-fluid interfaces in a coarse-grained model
    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    J. Phys. Condens. Matter (rok: 2020, tom: 32, strony: 404003), Wydawca: Institute of Physics
    Status:
    Published
    DOI:
    10.1088/1361-648X/ab94f6 - link to the publication
  15. The coexistence region in the Van der Waals fluid and the liquid-liquid phase transitions
    Authors:
    Dinh Quoc Huy Pham, Mateusz Chwastyk, Marek Cieplak
    Academic press:
    Frontiers in Chemistry (rok: 2023, tom: 10, strony: 1106599), Wydawca: Frontiers Media S.A.
    Status:
    Published
    DOI:
    10.3389/fchem.2022.1106599 - link to the publication
  16. Protein dynamics in tight tunnels
    Authors:
    M. Wojciechowski, M. Chwastyk
    Academic press:
    Acta Physica Polonica A (rok: 2024, ), Wydawca: POLISH ACAD SCIENCES INST PHYSICSAL LOTNIKOW 32-46, PL-02-668 WARSAW, POLAND
    Status:
    Submitted
    DOI:
    brak - link to the publication
  17. Properties of cavities in biological structures - a survey of the Protein Data Bank
    Authors:
    M. Chwastyk, E. Panek, J. Malinowski, M. Jaskólski, M. Cieplak
    Academic press:
    Front. Mol. Biosci. (rok: 2020, tom: 7, strony: 591381), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2020.591381 - link to the publication
  18. Protein droplets in systems of disordered homopeptides and the amyloid glass phase
    Authors:
    Ł. Mioduszewski, M. Cieplak
    Academic press:
    Phys. Chem. Chem. Phys. (rok: 2020, tom: 22, strony: 15592-15599), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/D0CP01635G - link to the publication
  19. The GōMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes
    Authors:
    L. F. Cofas-Vargas, R. A. Moreira, S. Poblete, M. Chwastyk, A. B. Poma
    Academic press:
    Acta Physica Polonica A (rok: 2024, ), Wydawca: POLISH ACAD SCIENCES INST PHYSICSAL LOTNIKOW 32-46, PL-02-668 WARSAW, POLAND
    Status:
    Accepted for publication
    DOI:
    brak - link to the publication
  1. Contact-Based Analysis of Aggregation of Intrinsically Disordered Proteins
    Authors:
    Marek Cieplak, Łukasz Mioduszewski, Mateusz Chwastyk
    Book:
    Methods in Molecular Biology - Computer Simulations of Aggregation of Proteins and Peptides (rok: 2022, tom: 2340, strony: 105-120), Wydawca: Springer
    Status:
    Published

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