Interaction of Heavy Metals with 7S Soybean Globulin: Molecular Dynamics Study

Abstract

Molecular dynamics (MD) simulations were performed to examine the structural and dynamic effects of Cd²⁺ and Co³⁺ binding on 7S soybean globulin. Using a 200 ns simulation at 300 K with GROMACS and the CHARMM General Force Field, key structural parameters—including root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and root-mean-square fluctuations (RMSF)—were analyzed to assess protein stability, flexibility, and compactness under varying metal ion concentrations. The results of the MD simulation indicate: i) at low metal concentrations, the protein maintained structural stability with minimal deviations; ii) increasing metal ion concentrations induced distinct structural changes in the protein structure depending on the ion type; iii) lower metal concentrations primarily affected specific regions of the α-subunit, whereas higher concentrations influenced both the α- and β-subunits; iv) fluctuations in secondary structure elements—α-helices, 3₁₀-helices, and β-strands—suggested potential destabilization, particularly in systems with high metal concentrations; v) α-helical content remained stable throughout the simulation, a slight decrease in β-sheet content was observed at higher metal concentrations. This suggests that heavy metal binding may have a destabilizing effect on β-sheet structures, altering the overall conformation of 7S globulin. These insights are valuable for the development of protein-based nanomaterials for heavy metal detection and sorption.