Molecular Dynamic Simulations (MDS) of Putative Ribozyme in presence of MgCl2

It is a known phenomenon from earlier reports [26,27] that ribozyme should have a Mg⁺² ion in its active state in its active conformation. To check whether the predicted RNA regulatory element has similar property and shows an interaction with Mg⁺² ion in its minimum energy confirmation and how this Mg⁺² ion helps in its stabilizing the folding kinetics, we performed 100ns MD simulation in presence of 5mM, 10mM and 25mM MgCl₂ concentrations using Desmond (D.E. Shaw Research) with same parameters mentioned earlier. All MD simulations were performed on HP ProLiant SL390s workstation equipped with 2 Intel Quad core processors and 1 Nvidia tesla M2090 GPUs with 4190 Mb memory. After successful completion of MD simulations all the essential quality parameters were analyzed and RMSD, RMSF were calculated along with the interactions of putative ribozyme and Mg⁺² ions during the entire length of MD simulations. All the plots were generated using the Desmond 3.2 analysis tools. Structural analysis, images and movies were generated using Pymol (Delano Scientific).