πDMD simulation as a strategy for refinement of AlphaFold2 modeled fuzzy protein complex structures
- Authors: Muradyan N.G.1, Sargsyan A.A.1,2, Arakelov V.G.1, Paronyan A.K.1,2, Arakelov G.G.1,2, Nazaryan K.B.1,2
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Affiliations:
- Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA)
- Russian–Armenian University
- Issue: Vol 59, No 2 (2025)
- Pages: 277–287
- Section: СТРУКТУРНО-ФУНКЦИОНАЛЬНЫЙ АНАЛИЗ БИОПОЛИМЕРОВИ ИХ КОМПЛЕКСОВ
- URL: https://edgccjournal.org/0026-8984/article/view/682882
- DOI: https://doi.org/10.31857/S0026898425020095
- EDN: https://elibrary.ru/GFYXKD
- ID: 682882
Cite item
Abstract
Disordered proteins are of great interest due to their structural features, as they do not have well-defined three-dimensional structures. These proteins, often called intrinsically disordered proteins or regions, play critical roles in various cellular processes and are associated with the development of a number of diseases. Our in silico research focused on the investigation of protein complexes that include both the ordered protein, such as 14-3-3γ, and proteins with intrinsically disordered regions, such as nucleocapsid (N) of SARS-CoV-2 and p53. Our findings demonstrate that complexes modeled by AlphaFold2 and refined using discrete molecular dynamics simulations acquire assembled structures in disordered regions. After refinement, the modeled complexes exhibit a degree of structural assembly that addresses a key challenge in studying disordered proteins – their propensity to evade stable conformations.
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About the authors
N. G. Muradyan
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA)
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, YerevanA. A. Sargsyan
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA); Russian–Armenian University
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, Yerevan; YerevanV. G. Arakelov
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA)
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, YerevanA. K. Paronyan
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA); Russian–Armenian University
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, Yerevan; YerevanG. G. Arakelov
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA); Russian–Armenian University
Author for correspondence.
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, Yerevan; YerevanK. B. Nazaryan
Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA); Russian–Armenian University
Email: g_arakelov@mb.sci.am
Laboratory of Computational Modeling of Biological Processes
Armenia, Yerevan; YerevanReferences
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