πDMD Simulation as a Strategy for Refinement of AlphaFold2 Modeled Fuzzy Protein Complexes Structures

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 ordered proteins, such as 14-3-3γ, and proteins containing 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.