The nucleocapsid (N) protein of SARS-CoV-2 is known to participate in various host cellular processes, including interferon inhibition, RNA interference, apoptosis, and regulation of virus life cycles. Additionally, it has potential as a diagnostic antigen and/or immunogen. Our research focuses on examining structural changes caused by mutations in the N protein. We have modeled the complete tertiary structure of native and mutated forms of the N protein using Alphafold2. Notably, the N protein contains 3 disordered regions. The focus was on investigating the impact of mutations on the stability of the protein's dimeric structure based on binding free energy calculations (MM-PB/GB-SA) and RMSD fluctuations after MD simulations. The results demonstrated that 28 mutations out of 37 selected mutations analyzed, compared with wild-type N protein, resulted in a stable dimeric structure, while 9 mutations led to destabilization. Our results are important to understand the tertiary structure of the N protein dimer of SARS-CoV-2 and the effect of mutations on it, their behavior in the host cell, as well as for the research of other viruses belonging to the same genus additionally, to anticipate potential strategies for addressing this viral illness․

Starting from 1972, colchicine is known as the most useful drug for prevention of familial Mediterranean fever attacks. However, some patients do not respond to colchicine treatment, even taken in high doses. Despite the fact, that different hypotheses have been proposed, the molecular mechanisms of colchicine resistance are not completely clear. It is generally known, that colchicine binds β-tubulin and inhibits microtubules polymerization. The β-tubulin gene has SNPs, which lead to amino acid substitutions, and some of them are located in colchicine binding site (CBS). We have assumed, that this SNPs can affect tubulin-colchicine interaction and might be the reason for colchicine resistance. With this in mind, we modeled 7 amino acid substitutions in CBS, performed molecular dynamics simulations of tubulin-colchicine complex and calculated binding energies for every amino acid substitution. Thus, our study shows, that two amino acid substitutions in the β-tubulin, namely A248T and M257V, reduce binding energy for approximately 2-fold. Based on this, we assume, that these amino acid substitutions could be the reason for colchicine resistance. Thus, our study gives a new insight into colchicine resistance mechanism and provides information for designing colchicine alternatives, that could be effective for colchicine resistant patients.

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.

The study of the p53 protein and its interactions with other proteins is key to understanding the mechanisms by which p53 affects tumorigenesis. Mutations in the TP53 gene, which occur in approximately 50% of human cancers, often disrupt its function, highlighting its key role in tumorigenesis. Although structurally challenging due to the presence of unstructured regions, p53 has a well-documented role in DNA damage signaling and cancer progression. In this study, the interaction between p53 and 14-3-3γ monomers was studied using in silico methods. Using tertiary structure modeling, molecular dynamics, molecular docking, and virtual ligand screening, we identified small molecule compounds that can modulate the interaction of p53 with 14-3-3γ. Key findings of the study include identification of a ligand binding pocket in the p53‒14-3-3γ interaction interface, generation of full-length models of 14-3-3γ and p53 using in silico methods, and selection of potential protein–protein modulators with high affinity for the proteins under study.

Nipah virus (NiV) is a highly pathogenic zoonotic RNA virus that causes severe encephalitis, systemic vasculitis, and multiorgan damage in humans, with a case fatality rate of 40–75%. Among the viral factors implicated in NiV pathogenicity is the W protein, an intrinsically disordered product of the P gene. By binding to members of the 14-3-3 protein family, which regulate critical processes such as the cell cycle, apoptosis, and immune responses, W protein is thought to modulate host signaling pathways. Yet the molecular and structural basis of this interaction remains poorly understood. Here, we employed the AlphaFold 3 algorithm to predict 1000 models of the heterotetrameric complex formed by W protein dimers and the 14-3-3σ dimer. Candidate structures were filtered according to two structural criteria—potential disulfide bond formation between Cys421 residues of the W dimer, and preservation of interactions between phosphorylated Ser449 (Sep449) and residues Arg56, Arg129, and Tyr130 in the 14-3-3σ binding site. Nine models that satisfied these criteria were further refined and evaluated by molecular dynamics (MD) simulations in the OpenMM environment. Following 100-ns MD simulations, three models were selected for extended microsecond-scale simulations to assess their stability over extended timescales. The simulations indicated that all three complexes remained stable over the simulated timescales and displayed structural features consistent with interactions involving intrinsically disordered proteins. Among them, one model (Model 3) showed the most favorable combination of structural and energetic features. Our findings support the structural feasibility of the proposed interaction and demonstrate that the modeled heterotetrameric complex is capable of adopting stable conformations. These results provide a basis for further in silico studies and exploratory small-molecule screening aimed at modulating this protein–protein interaction in the context of viral host–pathogen interactions.