Fig 1.
Alignment of 3D predicted structure (colored blue) and the corresponding experimentally solved structures from PDB database (colored red) for the 5 ssRNA aptamers used in this study.
Each structure was labeled by its PDB ID, nucleotides (nt) number, and the calculated RMSD values (in Angstrom).
Table 1.
The results for the selection of ssRNA candidates from Protein Data Bank database.
Fig 2.
Starting configuration of the MD simulation of the 1XWP model.
The aptamer molecule (colored blue) was solvated in water (colored red) and the system was neutralized with 14 sodium ions (colored yellow).
Fig 3.
(A-E) The evolution of RMSDs towards time for the aptamer structures with respect to the first structure (time 0). (F) RMSDs evolution of 2EVY-RC after the simulation was extended to 200 ns. It can be seen that the RMSD becomes stagnant after 170 ns.
Fig 4.
The overlays of 3D predicted structure (colored blue) and the corresponding experimentally solved structures from the PDB database (colored red) for the five aptamers at 0, 20, 40, 60, 80, and 100 ns during the MD simulation.
Table 2.
The summary of RMSD values at different time points throughout the MD simulation of the aptamer models corresponding to its crystal structures from the PDB database.
Fig 5.
Comparison of the representative structure of aptamer model (RC-Cl, light blue) with their corresponding structure before simulation (RC, blue), after 100ns simulation (RC-last, dark green), representative of reference structure (Ref-Cl, light green), crystal structure (Ref, red), and structure of reference structure after 100ns simulation (Ref-last, orange).
The RMSD of each alignment was written at the bottom of the structure (in Angstrom).