Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Proteins at solid interfaces and proteinic structures in simulations and experiment

2011/01/B/ST3/02190

Keywords:

proteins solids semiconductors nanoparticles virus capsids biosensors AFM

Descriptors:

  • 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: 8

Call: OPUS 1 - announced on 2011-03-15

Amount awarded: 390 000 PLN

Project start date (Y-m-d): 2011-12-01

Project end date (Y-m-d): 2014-11-30

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

Project status: Project settled

Equipment purchased [PL]

  1. 3 serwery, 3 UPS, macierz dyskowa (109 000 PLN)
  2. Breakout box (7 500 PLN)
  3. UVO cleaner (25 000 PLN)
  4. pudełko 40 złotych ostrzy AFM (4 000 PLN)
  5. Thermal K - moduł do kalibracji igieł (16 500 PLN)

Information in the final report

  • Publication in academic press/journals (18)
  • Articles in post-conference publications (1)
  • Book publications / chapters in book publications (1)
  1. Energy landscape and dynamics of proteins – an exact analysis of a simplified lattice model,
    Authors:
    M. Cieplak, J. R. Banavar
    Academic press:
    Physical Review E (Rapid Communication) (rok: 2013, tom: 88, strony: 040702(R)), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1103/PhysRevE.88.040702 - link to the publication
  2. Nanoindentation of 35 virus capsids in a molecular model: Relating Mechanical Properties to Structure
    Authors:
    M. Cieplak, M. O. Robbins
    Academic press:
    PLOS ONE (rok: 2013, tom: 8, strony: e63640), Wydawca: PLOS - Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0063640 - link to the publication
  3. Topological features in stretching of proteins
    Authors:
    M. Sikora, M. Cieplak
    Academic press:
    Biochemical Society Transactions (rok: 2013, tom: 41, strony: 519-522), Wydawca: Portland Press Limited, London
    Status:
    Published
    DOI:
    10.1042/BST20120289 - link to the publication
  4. Cystine plug and other novel mechanisms of large mechanical stability in dimeric proteins
    Authors:
    M. Sikora, M. Cieplak
    Academic press:
    Physical Review Letters (rok: 2012, tom: 109, strony: 208101), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1103/Phys. - link to the publication
  5. Unbinding and unfolding of adhesion protein complexes through stretching: interplay between shear and tensile mechanical clamps
    Authors:
    B. Różycki, Ł. Mioduszewski, M. Cieplak
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2014, tom: 82, strony: 3144-3153), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.24674 - link to the publication
  6. A multi-scale molecular dynamics study of micron-size supraparticle assembly from alkyl-coated 30 nm nanoparticles
    Authors:
    D. Thompson, M. Sikora, P. Szymczak, M. Cieplak
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2013, tom: 15, strony: 8132-8143), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c3cp50523e - link to the publication
  7. Amino acids and proteins at ZnO-water interfaces in molecular dynamics simulations
    Authors:
    D. Nawrocki, M. Cieplak
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2013, tom: 15, strony: 13628-13636), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c3cp52198b - link to the publication
  8. Denaturation of proteins near polar surfaces
    Authors:
    A. Starzyk, M. Cieplak
    Academic press:
    Journal of Chemical Physics (rok: 2011, tom: 135, strony: 235103), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4813854 - link to the publication
  9. Energy landscape and dynamics of an HP lattice model of proteins - The role of anisotropy
    Authors:
    Marek Cieplak, Jayanth R. Banavar
    Academic press:
    EPL (rok: 2013, tom: 104, strony: 58001), Wydawca: EDP Sciences, IOP Publishing, Italian Physical Society dla European Physical Society
    Status:
    Published
    DOI:
    10.1209/0295-5075/104/58001 - link to the publication
  10. Knotted proteins under tension
    Authors:
    M. Chwastyk, M. Cieplak
    Academic press:
    Israel J. Chem. (rok: 2014, tom: 54, strony: 1241-1249), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/ijch.201400004 - link to the publication
  11. Protein Unfolding by Biological Unfoldases: Insights from Modeling
    Authors:
    M. Wojciechowski, P. Szymczak, M. Carrion-Vazquez, M. Cieplak
    Academic press:
    Biophysics J. (rok: 2014, tom: 107, strony: 1661-1668), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bpj.2014.07.035 - link to the publication
  12. Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields
    Authors:
    G. Nawrocki, M. Cieplak
    Academic press:
    J. Phys. Chem. C (rok: 2014, tom: 118, strony: 12929-12943), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/jp5030558 - link to the publication
  13. Formation of cystine slipknots in dimeric proteins
    Authors:
    M. Sikora, M. Cieplak
    Academic press:
    PLOS ONE (rok: 2013, tom: 8, strony: e57443), Wydawca: PLOS - Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0057443 - link to the publication
  14. Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations
    Authors:
    G. Nawrocki, M. Cieplak
    Academic press:
    J. Chem. Phys. (rok: 2014, tom: 140, strony: 95101), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4866763 - link to the publication
  15. Proteins at air-water interfaces: a coarse-grained approach
    Authors:
    M. Cieplak, D. B. Allen, R. L. Leheny, D. H. Reich
    Academic press:
    Langmuir (rok: 2014, tom: 30, strony: 12888-96), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    brak - link to the publication
  16. Proteins in the electric field near the surface of mica
    Authors:
    A. Starzyk, M. Cieplak
    Academic press:
    Journal of Chemical Physics (rok: 2013, tom: 139, strony: 45102), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4813854 - link to the publication
  17. Structure-based analysis of thermodynamic and mechanical properties of cavity-containing proteins - case study of plant pathogenesis-related proteins of class 10
    Authors:
    M. Chwastyk, M. Jaskólski, M. Cieplak
    Academic press:
    FEBS Journal (rok: 2014, tom: 281, strony: 416-429), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1111/febs.12611 - link to the publication
  18. Theoretical tests of the mechanical protection strategy in protein nanomechanics
    Authors:
    M. Chwastyk, A. Galera, M. Sikora, A. Gomez-Sicilia, M. Carrion-Vazquez, M. Cieplak
    Academic press:
    Proteins (rok: 2013, tom: w druku, strony: w druku), Wydawca: Wiley
    Status:
    Accepted for publication
    DOI:
    w - link to the publication
  1. Mechanostability of proteins in structure based models
    Authors:
    M. Cieplak
    Conference:
    International Symposium on Biomechanics, (rok: 2012, ), Wydawca: Shanghai Scientific and Technological Literature Publishing House
    Data:
    konferencja listopad 2011
    Status:
    Published
  1. Mechanostability of virus capsids and their proteins in structure-based models
    Authors:
    M. Cieplak
    Book:
    Computational Methods to study the structure and dynamics of biomolecules and biomolecular processes - from bioinformatics to molecular quantum mechanics (rok: 2014, tom: -, strony: 295-315), Wydawca: Springer
    Status:
    Published

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