Volume 10, Issue 1 (2019)                   JMBS 2019, 10(1): 85-92 | Back to browse issues page

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Monsefi M, Erfan-Niya H, Ghadari R. Molecular Dynamics Simulation of Influences of Solvent Ionic Concentration on the Binding of MUC1–G Peptide and Anti-MUC1 Aptamer. JMBS 2019; 10 (1) :85-92
URL: http://biot.modares.ac.ir/article-22-15864-en.html
1- Chemical Engineering Department, Faculty of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran
2- Chemical Engineering Department, Faculty of Chemical & Petroleum Engineering, University of Tabriz, Tabriz, Iran, Faculty of Chemical & Petroleum Engineering, University of Tabriz, 29 Bahman Boulevard, Tabriz, Iran. Postal Code: 5166616471 , herfan@tabrizu.ac.ir
3- Organic & Biochemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
Abstract:   (6198 Views)
Aims: 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.
Materials and Methods: 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.
Findings: 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. Conclusion: 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.
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Article Type: Research Paper | Subject: Agricultural Biotechnology
Received: 2017/04/4 | Accepted: 2017/11/15 | Published: 2019/03/16

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