Molecular Dynamics Simulation of Influences of Solvent Ionic Concentration on the Binding of MUC1–G Peptide and Anti-MUC1 Aptamer

Molecular insights into the analyte-bioreceptor interactions play a vital role in the efficacy of designing biosensors. Biosensors that utilize aptamers as bioreceptors are highly efficient with high specificity and reusability. Aptasensors can be used in a variety of conditions of in vivo or in vitro. The aim of this study was to study the changes in the solvent conditions of the binding of MUC1-G peptide and the anti-MUC1 aptamer. The molecular dynamics simulation method has been used to investigate the change of molecular interactions due to selective variations in solvent conditions. The results can be used to reflect a variety of environments, in which the aptasensor utilizes anti-MUC1 S2.2 aptamer as a bioreceptor and MUC1–G peptide as a biomarker. Based on the calculated binding energies, the medium containing 0.10M NaCl and anti-MUC1 S2.2 aptamer demonstrates the highest affinity toward the MUC1-G peptide among the studied concentrations of NaCl, and the arginine amino acid has a key role in the aptamer–peptide binding. The results of MD simulation indicated that the increase in the concentration of NaCl in the interaction environment leads to a decrease in binding energies; therefore, the binding affinity of the anti-MUC1 aptamer to MUC1-G peptide decreases. Insights from present modeling demonstrate the selectiveness and sensitivity to solvent conditions, which should be considered in the development of biosensors.