Computational Insights into the Structural Dynamics of the E Protein’s DIII Domain in Brazilian Yellow Fever Virus: Implications of Amino Acid Variations on Protein Plasticity and Potential Impact on Vaccine Efficacy

During 2016–2019, Brazil witnessed one of the largest yellow fever virus (YFV) outbreaks. Experimental studies suggested that the epitope recognized by vaccine-specific mAb 411 is strongly associated with the EDIII domain of the E protein. This prompted us to analyze the global protein sequences of the YFV-EDIII domain to explore the conserved mutations that modulate the domain structure. Through comprehensive computational analysis combining sequence alignment, stability prediction, and molecular dynamics simulations, we characterized structural and functional consequences of mutations exclusive to Brazilian strains. Multiple sequence alignments of 223 publicly available YFV protein sequences revealed four prevalent mutations in the EDIII domain: V318A, K331R, I335 M, and I344 V, occurring in more than 65% of the analyzed sequences. Notably, V318A and I335 M mutations were found exclusively in Brazilian strains, while K331R and I344 V showed broader geographic distributions but higher prevalence in South American isolates. Thermodynamic stability predictions using multiple computational approaches revealed that individual mutations, particularly V318A, consistently demonstrated destabilizing effects, with predicted ΔΔG values ranging from −0.43 to −5.40 kcal/mol. Molecular dynamics analysis suggests that the mutations significantly changed the conformational rearrangement and folding of the YFV-EDIII domain at positions 310–312, 315, 321, and 342. In conclusion, our study demonstrates that the four prevalent mutations in Brazilian YFV strains represent a sophisticated example of compensatory evolution, where the virus has optimized its structural stability through a strategic combination of individual substitutions. Therefore, we hypothesized that the significant conformational rearrangement and folding of the YFV-EDIII domain due to mutation would affect the binding of antibodies despite not analyzing virus–antibody interactions.