1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Molecular Insight into the Adsorption of Tobramycin Specific Aptamer on Graphene Sheet
Paper ID : 1457-ICB10
Authors:
Hamed Zahraee1, Zahra Khoshbin *2, Mohammad Reza Bozorgmehr3
1گزوه زیست شناسی، دانشکده علوم، دانشگاه فردوسی مشهد، ایران
2گروه شیمی دارویی، دانشکده داروسازی، دانشگاه علوم پزشکی مشهد، ایران
3گروه شیمی، دانشکده علوم پایه، دانشگاه آزاد اسلامی، مشهد، ایران
Abstract:
Aptasensors are biosensors based on aptamers as the bio-recognition [1-3]. Graphene is a two-dimensional carbon sheet, attractive for the design of fluorescence and electrochemical aptasensors [4]. Graphene provides some anchorage sites for aptamers; hence, we theoretically study the adsorption behavior of the tobramycin-specific aptamer on graphene by molecular dynamics (MD) simulation to provide a molecular confirmation on the aptamer adsorption by graphene, suitable for the design of graphene-based aptasensors. To have an initial aptamer (PDB ID: 1LC4) configuration, 25 ns MD simulation was done using GROMACS 2018.4 [5,6] with CHARMM36-jul2021 force field. The output was added to a simulation box containing a graphene sheet, and 190 ns MD simulation was performed. The decrease in the RMSD fluctuations proved the steady adsorption of the aptamer on the sheet (Fig. 1). The RMSF analysis proved the higher flexibility of the nucleotides at the 3´-region in comparison with that at the 5´-region (Fig. 2). Indeed, the aptamer adsorption was first happened through its 5´-region, and then, its 3´-end, in accordance with the distance between the center of mass (COM) of each nucleotide and graphene along the Z-axis (Fig. 3). Mean squared displacement (MSD) parameter reflected the adsorption behavior of the aptamer (Fig. 4), a potent anchoring of the aptamer on the graphene surface after the simulation. The free energy landscape (FEL) proved that the aptamer-graphene complex was energetically favorable (Fig. 5). The reduced density gradient (RDG) analysis clarified that the hydrogen bonding and van der Waals interactions played an important role in the aptamer adsorption on graphene (Fig. 6). Finally, the output observation by PyMOL software [7] illustrated that the aptamer was first adsorbed through its 5´-region, and then, its 3´-region, and finally, its structure was completely located on the graphene surface.
Keywords:
Adsorption; Aptamer; Graphene; Molecular dynamics simulation; Tobramycin
Status : Paper Accepted (Poster Presentation)