Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Computational studies of the disulfide-bond role in proteins.

2019/35/D/ST4/03156

Keywords:

disulfide bonds protein structure protein function molecular dynamics

Descriptors:

  • ST4_004:
  • ST4_001:
  • ST4_003:

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Instytut Fizyki Polskiej Akademii Nauk

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Paweł Krupa 

Number of co-investigators in the project: 3

Call: SONATA 15 - announced on 2019-09-16

Amount awarded: 399 420 PLN

Project start date (Y-m-d): 2020-06-10

Project end date (Y-m-d): 2024-06-09

Project duration:: 48 months (the same as in the proposal)

Project status: Project settled

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 (8)
  • Book publications / chapters in book publications (1)
  1. A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta
    Authors:
    Pamela Smardz, Midhun Mohan Anila, Paweł Rogowski, Mai Suan Li, Bartosz Różycki, Pawel Krupa
    Academic press:
    International Journal of Molecular Sciences (rok: 2024, tom: 25, strony: 6698), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms25126698 - link to the publication
  2. A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta
    Authors:
    Pamela Smardz, Midhun Mohan Anila, Paweł Rogowski, Mai Suan Li, Bartosz Różycki, Pawel Krupa
    Academic press:
    International Journal of Molecular Sciences (rok: 2024, tom: 25, strony: 6698), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms25126698 - link to the publication
  3. Why does the herpes simplex 1 virus-encoded UL49.5 protein fail to inhibit the TAP-dependent antigen presentation?
    Authors:
    N Karska, I Zhukov, AD Lipińska, S Rodziewicz-Motowidło, P Krupa
    Academic press:
    Biochimica et Biophysica Acta (BBA) - Biomembranes (rok: 2023, tom: 1865, strony: 184200), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbamem.2023.184200 - link to the publication
  4. Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies
    Authors:
    Natalia H Rogoża, Magdalena A Krupa, Pawel Krupa*, Adam K Sieradzan
    Academic press:
    Molecules (rok: 2024, tom: 29, strony: 1919), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules29091919 - link to the publication
  5. Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role
    Authors:
    P. Krupa, G. La Penna, M.S. Li
    Academic press:
    International Journal of Molecular Sciences (rok: 2023, tom: 24, strony: 12698), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms241612698 - link to the publication
  6. Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment
    Authors:
    Pamela Smardz, Adam K. Sieradzan, Paweł Krupa
    Academic press:
    J. Phys. Chem. B (rok: 2022, tom: J. Phys. Chem. B 2022, 126, 33, 6240–6249, strony: 6240–6249), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c04718 - link to the publication
  7. Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role
    Authors:
    P. Krupa, G. La Penna, M.S. Li
    Academic press:
    International Journal of Molecular Sciences (rok: 2023, tom: 24, strony: 12698), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms241612698 - link to the publication
  8. Multilayered Computational Framework for Designing Peptide Inhibitors of HVEM-LIGHT Interaction
    Authors:
    Piotr Ciura, Pamela Smardz, Marta Spodzieja, Adam K. Sieradzan, and Pawel Krupa
    Academic press:
    Journal of Physical Chemistry B (rok: 2024, tom: 1, strony: 1), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.4c02255 - link to the publication
  1. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking
    Authors:
    Magdalena A. Krupa, Paweł Krupa
    Book:
    Protein-Protein Docking (Part of the book series: Methods in Molecular Biology (MIMB, volume 2780)) (rok: 2024, tom: 2780, strony: 27-41), Wydawca: Humana New York, NY (Springer Protocols)
    Status:
    Published
    DOI:
    10.1007/978-1-0716-3985-6_3 - link to the publication

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