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

2018/31/B/NZ1/00047

Keywords

Descriptors

  • NZ1_3: Biofizyka
  • NZ1_1: Biologia molekularna
  • NZ1_4: Biologia strukturalna

Panel

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

Host institution

Instytut Fizyki PAN

Voivodeship: 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
2019-07-24
Project end date
2024-07-23
Project duration
60 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 (18)

  1. 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. (year: 2020, volume: 174, pages: 79-103), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/bs.pmbts.2020.03.003. – link to the publication

  2. Proteins at curved fluid-fluid interfaces in a coarse-grained model

    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    J. Phys. Condens. Matter (year: 2020, volume: 32, pages: 404003), Publisher: Institute of Physics
    Status:
    Published
    DOI:
    10.1088/1361-648X/ab94f6 – link to the publication

  3. Protein droplets in systems of disordered homopeptides and the amyloid glass phase

    Authors:
    Ł. Mioduszewski, M. Cieplak
    Academic press:
    Phys. Chem. Chem. Phys. (year: 2020, volume: 22, pages: 15592-15599), Publisher: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/D0CP01635G – link to the publication

  4. Pseudo-improper-dihedral model for intrinsically disordered proteins

    Authors:
    Ł. Mioduszewski, B. Różycki, M. Cieplak
    Academic press:
    J. Chem. Theor. Comput. (year: 2020, volume: 16, pages: 4726-4733), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jctc.0c00338 – link to the publication

  5. Preface to the JPCM special issue on droplets and vesicles

    Authors:
    Marek Cieplak,Rui D M Travasso
    Academic press:
    Journal of Physics: Condensed Matter (year: 2022, volume: 34, pages: 30401), Publisher: IOP Publishing
    Status:
    Published
    DOI:
    10.1088/1361-648X/ac2f6f – link to the publication

  6. Viscoelastic properties of wheat gluten in a molecular dynamics study

    Authors:
    Łukasz Mioduszewski, Marek Cieplak
    Academic press:
    PLOS Computational Biology (year: 2021, volume: 17, pages: e1008840), Publisher: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1008840 – link to the publication

  7. 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. (year: 2020, volume: 7, pages: 591381), Publisher: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2020.591381 – link to the publication

  8. Nascent Folding of Proteins Across the Three Domains of Life

    Authors:
    Mateusz Chwastyk, Marek Cieplak
    Academic press:
    Frontiers in Molecular Biosciences (year: 2021, volume: 8, pages: 692230), Publisher: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2021.692230 – link to the publication

  9. 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 (year: 2023, volume: 284, pages: 108611), Publisher: ELSEVIER
    Status:
    Published
    DOI:
    10.1016/j.cpc.2022.108611 – link to the publication

  10. 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 (year: 2023, volume: 10, pages: 1106599), Publisher: Frontiers Media S.A.
    Status:
    Published
    DOI:
    10.3389/fchem.2022.1106599 – link to the publication

  11. 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 (year: 2023, volume: 79, pages: 775-791), Publisher: INT UNION CRYSTALLOGRAPHY2 ABBEY SQ, CHESTER CH1 2HU, ENGLAND
    Status:
    Published
    DOI:
    10.1107/S2059798323005648 – link to the publication

  12. 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. (year: 2020, volume: 2, pages: 13242), Publisher: American Physical Society
    Status:
    Published
    DOI:
    10.1103/PhysRevResearch.2.013242 – link to the publication

  13. Conformational biases of alpha-synuclein and formation of transient knots

    Authors:
    M. Chwastyk, M. Cieplak
    Academic press:
    J. Phys. Chem. B (year: 2020, volume: 124, pages: 46345), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b08481 – link to the publication

  14. Network of inter-basin traffic in intrinsically disordered PUMA protei

    Authors:
    B. R. H. de Aquino, M. Cieplak
    Academic press:
    EPL (year: 2020, volume: 132, pages: 28002), Publisher: European Physical Society
    Status:
    Published
    DOI:
    10.1209/0295-5075/132/28002 – link to the publication

  15. 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 (year: 2021, volume: 29, pages: 46033), Publisher: Cell Press
    Status:
    Published
    DOI:
    10.1016/j.str.2021.01.006 – link to the publication

  16. 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. (year: 2020, volume: 119, pages: 939-949), Publisher: Biophysical Society
    Status:
    Published
    DOI:
    10.1016/j.bpj.2020.07.030 – link to the publication

  17. The role of cavities in biological structures

    Authors:
    Ł. Mioduszewski, Karol Wołek, and Mateusz Chwastyk
    Status:
    Accepted for publication

  18. 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
    Status:
    Accepted for publication

Book publications / chapters in book publications (1)

  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 (year: 2022, volume: 2340, pages: 105-120), Publisher: Springer
    Status:
    Published

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