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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Structure-based dynamical models of large and complex biomolecular systems

2014/15/B/ST3/01905

Keywords:

molecular dynamics coarse-grained models protein complexes stretching of proteins virus capsids proteasomes protein adsorption

Descriptors:

  • ST3_17: Other related subjects
  • NZ1_3: Biophysics

Panel:

ST3 - Condensed matter physics: structure, electronic properties, fluids, nanosciences, biological physics

Host institution :

Instytut Fizyki PAN

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Marek Cieplak 

Number of co-investigators in the project: 6

Call: OPUS 8 - announced on 2014-09-15

Amount awarded: 678 540 PLN

Project start date (Y-m-d): 2015-07-14

Project end date (Y-m-d): 2018-10-13

Project duration:: 39 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. 5 serwerow do obliczen (125 000 PLN)

Information in the final report

  • Publication in academic press/journals (17)
  1. Criteria for folding in structure-based models of proteins
    Authors:
    K. Wołek, M. Cieplak
    Academic press:
    J. Chem. Phys. (rok: 2016, tom: 144, strony: 185102), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4948783 - link to the publication
  2. Disordered peptide chains in an a-C-based coarse-grained model
    Authors:
    Ł. Mioduszewski, M. Cieplak
    Academic press:
    Phys. Chem. Chem. Phys (rok: 2018, tom: 20, strony: 19057-19070), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c8cp03309a - link to the publication
  3. Structural fluctuations and thermal stability of proteins in crowded environments: effects of the excluded volume
    Authors:
    A. Starzyk, M. Wojciechowski, M. Cieplak
    Academic press:
    Physical Biology (rok: 2016, tom: 13, strony: 66002), Wydawca: Institute of Physics (UK)
    Status:
    Published
    DOI:
    10.1088/1478-3975/13/6/066002 - link to the publication
  4. Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A
    Authors:
    B. Różycki, M. Cieplak
    Academic press:
    Molecular Biosystems (rok: 2016, tom: 12, strony: 3589-3599), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c6mb00606j - link to the publication
  5. Structural changes in barley protein LTP1 isoforms at air-water interfaces
    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    Langmuir (rok: 2017, tom: 33, strony: 4769-4780), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.langmuir.7b00791 - link to the publication
  6. The volume of cavities in proteins and virus capsids
    Authors:
    M. Chwastyk, M. Jaskólski, M. Cieplak
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2016, tom: 84, strony: 1275-1286), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25076 - link to the publication
  7. Topological transformations in proteins: effects of heating and proximity of an interface
    Authors:
    Y. Zhao, M. Chwastyk, M. Cieplak
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 39851), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/srep39851 - link to the publication
  8. AFM studies of morphological properties of selected organometallic compounds based on 8-Hydroxyquinoline
    Authors:
    A. Aamoum. P. Plóciennik, J. Strzelecki, A. Korcala, H. Bougharraf, M. Bakasse, Y. Boughaleb, A. Zawadzka
    Academic press:
    Optical and Quantum Electronics (rok: 2018, ), Wydawca: Springer
    Status:
    Submitted
    DOI:
    brak - link to the publication
  9. Dual binding mode in cohesin-dockerin complexes as assessed through stretching studies
    Authors:
    M. Wojciechowski, M. Cieplak
    Academic press:
    J. Chem. Phys. (rok: 2016, tom: 145, strony: 134102), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4963693 - link to the publication
  10. Proteins at the air-water interface in a lattice model
    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    J. Chem. Phys. (rok: 2018, tom: 148, strony: 94704), Wydawca: Americam Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.5017789 - link to the publication
  11. Self-assembly of model proteins into virus capsid
    Authors:
    K. Wołek, M. Cieplak
    Academic press:
    J. Phys.: Cond. Matter (rok: 2017, tom: 47, strony: 474003), Wydawca: IOPscience
    Status:
    Published
    DOI:
    10.1088/1361-648X/aa9351 - link to the publication
  12. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module
    Authors:
    M. Wojciechowski, B. Różycki, Pham D. Q. Huy, M. S. Li, E. A. Bayer, M. Cieplak
    Academic press:
    Sci. Reports (rok: 2018, tom: 8, strony: 5051), Wydawca: Springer-Nature
    Status:
    Published
    DOI:
    10.1038/s41598-018-23380-9 - link to the publication
  13. Proteins at air-water and oil-water interfaces in an all-atom model
    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    Phys. Chem. Chem. Phys. (rok: 2017, tom: 19, strony: 25197-25206), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C7CP03829A - link to the publication
  14. Unfolding knots by proteasome-like systems: simulations of the behavior of folded and neurotoxic proteins
    Authors:
    M. Wojciechowski, A. Gomez-Sicilia, M. Carrion-Vazquez, M. Cieplak
    Academic press:
    Molecular Biosystems (rok: 2016, tom: 12, strony: 2700-2712), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c6mb00214e - link to the publication
  15. Combining the MARTINI and structure-based coarse-grained approaches for the molecular dynamics studies of conformational transitions in proteins
    Authors:
    A. Poma, M. Cieplak, P. E. Theodorakis
    Academic press:
    J. Chem. Theory Comp. (rok: 2017, tom: 13, strony: 1366-1374), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.6b00986 - link to the publication
  16. Stability of structurally entangled protein dimers
    Authors:
    Y. Zhao, M. Cieplak
    Academic press:
    Proteins (rok: 2018, tom: 86, strony: 945-955), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25526 - link to the publication
  17. Structural entanglements in protein complexes
    Authors:
    Y. Zhao, M. Chwastyk, M. Cieplak
    Academic press:
    J. Chem. Phys. (rok: 2017, tom: 146, strony: 225102), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4985221 - link to the publication

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