Figure 5
Analysis of RMSD, RMSF, Rg, and H bonds of native and five mutants of MCM6 over 50 ns simulation. (A) RMSD values of Cα atoms of native and mutant structures. (B) RMSF values of Cα atoms of native and mutant structures. (C) Calculation of Rg, which is represented as a time-dependent change during the simulation. (D) Calculation of H-bonds represented as a time-depend. The color scheme is as follows: native (blue), I123S mutant (red), V456M mutant (green), D463G mutant (violet), R602H mutant (yellow), and R633W mutant (orange). A 50 ns molecular dynamics (MD) simulation was performed using the "Desmond v6.3 Program" in Schrodinger 2020-3 under the Linux framework49. The simulation was performed following the three-site transferrable intermolecular potential (TIP3P) water model50. An orthorhombic box shape with a 10 Å distance from the center was used to maintain a specific volume, and Na+ and Cl- were added to neutralize the whole system with a salt concentration of 0.15 M. An OPLS3e force field was applied51.
