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

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MONSEFI M.; Erfan Niya H.; GHADARI R.

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Journal: JOURNAL OF BIOTECHNOLOGY Year:2019 | Volume:10 | Issue:1 Page(s): 85-92

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Title

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

Author(s)

MONSEFI M. | Erfan Niya H. | GHADARI R. | Issue Writer Certificate

Keywords

Molecular dynamics simulationQ1

Peptide–Q1

aptamer bindingQ1

MUC1Q1

AptasensorQ1

Abstract

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 & 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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APA: Copy

MONSEFI, M., Erfan Niya, H., & GHADARI, R.. (2019). Molecular Dynamics Simulation of Influences of Solvent Ionic Concentration on the Binding of MUC1– G Peptide and Anti-MUC1 Aptamer. JOURNAL OF BIOTECHNOLOGY, 10(1 ), 85-92. SID. https://sid.ir/paper/231232/en

Vancouver: Copy

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. JOURNAL OF BIOTECHNOLOGY[Internet]. 2019;10(1 ):85-92. Available from: https://sid.ir/paper/231232/en

IEEE: Copy

M. MONSEFI, H. Erfan Niya, and R. GHADARI, “Molecular Dynamics Simulation of Influences of Solvent Ionic Concentration on the Binding of MUC1– G Peptide and Anti-MUC1 Aptamer,” JOURNAL OF BIOTECHNOLOGY, vol. 10, no. 1 , pp. 85–92, 2019, [Online]. Available: https://sid.ir/paper/231232/en

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