Volume 10, Issue 1 (2019)
JMBS 2019, 10(1): 85-92 |
Back to browse issues page
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
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 ,
3- Organic & Biochemistry Department, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
Abstract: (6715 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 theaptasensor 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 S2.2aptamer 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 .
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
Findings: Based on the calculated binding energies, the medium containing 0.10M NaCl and anti-MUC1 S2.2
Article Type: Research Paper |
Subject:
Agricultural Biotechnology
Received: 2017/04/4 | Accepted: 2017/11/15 | Published: 2019/03/16
Received: 2017/04/4 | Accepted: 2017/11/15 | Published: 2019/03/16
References
1. Mehrotra P. Biosensors and their applications - a review. J Oral Biol Craniofac Res. 2016;6(2):153-9.
https://doi.org/10.1016/j.jobcr.2015.12.002 [Link] [DOI:10.1016/j.jobcr.2015.12.002]
2. Jain KK. The handbook of biomarkers. New York: Springer Science & Business Media; 2010. [Link] [DOI:10.1007/978-1-60761-685-6]
3. Nath S, Mukherjee P. MUC1: A multifaceted oncoprotein with a key role in cancer progression. Trends Mol Med. 2014;20(6):332-42. [Link] [DOI:10.1016/j.molmed.2014.02.007]
4. Yamaguchi T, Yokoyama Y, Ebata T, Matsuda A, Kuno A, Ikehara Y, et al. Verification of WFA-sialylated MUC1 as a sensitive biliary biomarker for human biliary tract cancer. Ann Surg Oncol. 2016;23(2):671-7. [Link] [DOI:10.1245/s10434-015-4878-4]
5. Prakash JS, Rajamanickam K. Aptamers and their significant role in cancer therapy and diagnosis. Biomedicines. 2015;3(3):248-69. [Link] [DOI:10.3390/biomedicines3030248]
6. Ku TH, Zhang T, Luo H, Yen TM, Chen PW, Han Y, et al. Nucleic acid aptamers: An emerging tool for biotechnology and biomedical sensing. Sensors (Basel). 2015;15(7):16281-313. [Link] [DOI:10.3390/s150716281]
7. Wang K, He MQ, Zhai FH, He RH, Yu YL. A novel electrochemical biosensor based on polyadenine modified aptamer for label-free and ultrasensitive detection of human breast cancer cells. Talanta. 2017;166:87-92. [Link] [DOI:10.1016/j.talanta.2017.01.052]
8. Rhinehardt KL, Srinivas G, Mohan RV. Molecular dynamics simulation analysis of anti-MUC1 aptamer and mucin 1 peptide binding. J Phys Chem B. 2015;119(22):6571-83. [Link] [DOI:10.1021/acs.jpcb.5b02483]
9. Rhinehardt K, Mohan R, Srinivas G, Kelkar A. Analysis and understanding of aptamer and peptide molecular interactions: Application to mucin 1 (Muc1) aptasensor. 2nd International Symposium on Physics and Technology of Sensors (ISPTS), 7-10 March, 2015, Pune, India. Piscataway: IEEE; 2015. [Link] [DOI:10.1109/ISPTS.2015.7220133]
10. Ferreira CS, Matthews CS, Missailidis S. DNA aptamers that bind to MUC1 tumour marker: Design and characterization of MUC1-binding single-stranded DNA aptamers. Tumour Biol. 2006;27(6):289-301. [Link] [DOI:10.1159/000096085]
11. Kikin O, D'Antonio L, Bagga PS. QGRS Mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 2006;34(Web Server Issue):W676-82. [Link]
12. Jokar M, Safaralizadeh MH, Hadizadeh F, Rahmani F, Kalani MR. Apta-nanosensor preparation and in vitro assay for rapid Diazinon detection using a computational molecular approach. J Biomol Struct Dyn. 2017;35(2):343-53. [Link] [DOI:10.1080/07391102.2016.1140594]
13. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406-15. [Link] [DOI:10.1093/nar/gkg595]
14. Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, et al. Automated 3D structure composition for large RNAs. Nucleic Acids Res. 2012;40(14):e112. [Link] [DOI:10.1093/nar/gks339]
15. Dokurno P, Bates PA, Band HA, Stewart LM, Lally JM, Burchell JM, et al. Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition. J Mol Biol. 1998;284(3):713-28. [Link] [DOI:10.1006/jmbi.1998.2209]
16. Pichinuk E, Benhar I, Jacobi O, Chalik M, Weiss L, Ziv R, et al. Antibody targeting of cell-bound MUC1 SEA domain kills tumor cells. Cancer Res. 2012;72(13):3324-36. [Link] [DOI:10.1158/0008-5472.CAN-12-0067]
17. DeLano WL. Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography. 2002; 40(1):82-92. [Link]
18. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham III TE, DeBolt S et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun. 1995;91(1-3):1-41. [Link] [DOI:10.1016/0010-4655(95)00041-D]
19. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1995;117(19):5179-97. [Link] [DOI:10.1021/ja00124a002]
20. Li LJ. Simultaneous detection of organic and inorganic substances in a mixed aqueous solution using a microwave dielectric sensor. Prog Electromagn Res C. 2010;14:163-71. [Link] [DOI:10.2528/PIERC10051308]
21. Kesimer M, Sheehan JK. Analyzing the functions of large glycoconjugates through the dissipative properties of their absorbed layers using the gel-forming mucin MUC5B as an example. Glycobiology. 2008;18(6):463-72. [Link] [DOI:10.1093/glycob/cwn024]
22. Humphrey W, Dalke A, Schulten K. VMD: Visual molecular dynamics. J Mol Graph. 1996;14(1):33-8. [Link] [DOI:10.1016/0263-7855(96)00018-5]
23. Vilar S, Cozza G, Moro S. Medicinal chemistry and the Molecular Operating Environment (MOE): Application of QSAR and molecular docking to drug discovery. Curr Top Med Chem. 2008;8(18):1555-72. [Link] [DOI:10.2174/156802608786786624]
24. Lobanov MIu, Bogatyreva NS, Galzitskaia OV. Radius of gyration is indicator of compactness of protein structure. Mol Biol (Mosk). 2008;42(4):701-6. [Russian] [Link]
25. Kong HY, Byun J. Nucleic acid aptamers: New methods for selection, stabilization, and application in biomedical science. Biomol Ther (Seoul). 2013;21(6):423-34. [Link] [DOI:10.4062/biomolther.2013.085]
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |