Root Mean Square Deviation Lab Report

Root mean square deviation (RMSD):
The root mean square deviation (RMSD) is a measure of structural differences that are observed on superimposition of two protein structures at a different time points i.e. current position and previous position. The RMSD values for backbone atoms of each residue were calculated for entire trajectory to see the evolution of structure with time. The RMSD plot is shown in Supplementary Figure S7 where timestep is plotted on X-axis while RMSD (Å) is plotted on Y-axis. The blue and red curve depicts the RMSD plot of wild type (WT) and mutant (MT) protein respectively. It can be seen from the figure that RMSD curve for mutant protein is moving in a narrow window of ~3.0 Å with a rise in peak at ~15 to 16 ns. Visual inspection of the trajectory in VMD (visual molecular dynamics) showed that during this time period the electrostatic loop undergo conformational change. Especially a small helical part of this loop achieved random coil conformation but quickly reverted back
The red-white-blue spectrum represents high-moderate-low RMSF values i.e. substructures having red colour are more dynamic, substructures with white colour are moderately dynamic and substructures with blue colour are least dynamic. Careful inspection of the colour coded protein structure for wild type dimer revealed that both the electrostatic loop region and zinc binding loop regions show greater conformational flexibility as compared to rest of the structure. Interestingly, these substructures i.e. the electrostatic loop region and zinc binding loop region showed a greater degree of rigidity (Figure 6C) in mutant dimer as compared to wild type dimer. Additionally, other regions such as the Greek-key β-barrel structure which enjoins the active site also showed less flexibility in mutant