IN SILICO STRUCTURAL CHARACTERIZATION AND MOLECULAR DYNAMICS OF TRYPANOSOMA RANGELI GP63: INSIGHTS FROM ALPHAFOLD MODELING

Resumo

The Trypanosoma rangeli surface metalloprotease GP63 (TrGP63) holds diagnostic relevance due to its cross-reactivity with Trypanosoma cruzi homologs. However, its structural characterization remains limited. This study aimed at the in silico structural characterization of TrGP63, employing computational modeling and molecular dynamics (MD) simulations to validate the protein's dynamic behavior. Three-dimensional prediction was performed using AlphaFold, and the model's quality was assessed by confidence metrics (pLDDT > 90; pTM = 0.95) and stereochemical analysis (PROCHECK). Conformational stability was investigated through 25 ns MD simulations (GROMACS, GROMOS57a4 force field). The generated model exhibited high accuracy and identified the conserved catalytic motif HEXXH. The MD simulations demonstrated the structural stability of TrGP63. Radius of Gyration (Rg) and Root-Mean-Square Deviation (RMSD) analyses indicated rapid system accommodation and maintenance of an equilibrated conformational state. Fluctuation analysis (RMSF) revealed rigidity in the central domains, including the catalytic site, and greater flexibility in the C-terminal region. These results provide the first molecular dynamics-validated structural model of TrGP63. Furthermore, structural and electrostatic divergences, specifically its predominantly neutral catalytic cleft and less conserved C-terminal region, suggest distinct substrate specificities. Consequently, these regions are prime targets for designing species-specific epitopes, facilitating the accurate differential diagnosis of Chagas disease.