The trajectory was analyzed for the B-factor calculation. The RMSD of

The trajectory was analyzed for the B-factor calculation. The RMSD of the sensitive regions with respect to the starting conformation was compared for the WT and MT structures during the course of the simulations. The RMSD was found to increase as a function of time for MT c.35G.A (p.G12D) when compared with WT and MT c.38G.A (p.G13D) (Figure 2A). By monitoring the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?34, we found that the GTP-I-BRD9 site binding pocket in the c.35G.A (p.G12D) protein was more open than that of the WT and c.38G.A (p.G13D) proteins (Figure 2B). The results of calculating the B-factors for each residue 12926553 at the sensitive sites (P-Potential of Mean Force (PMF) SimulationsTo explore the free energy profiles for the process of GTP binding with wild-type KRAS and its mutants (c.35G.A (p.G12D) and c.38G.A (p.G13D)), PMF simulations were performed using umbrella-sampling MD simulations [48]. The PMF is defined as the potential that gives an average force over all the configurations of a given system [49]. It generated a series of configurations along a reaction coordinate, after which umbrellasampling was used to restrain these conformations within the sampling windows. The total number of windows for each complex structure was approximately 30, depending on the initial structure of each ?system. Each window was separated by 1.0 A, covering the ??reaction coordinates from ,8 A to 40 A. The biasing force constant applied in the different windows of the umbrella sampling ?was 10.0 kcal/(mol.A2). The selected conformations for each window were first equilibrated for 100 ps and then kept for 1 ns for production sampling. The frequency of the data collection was set to 1 ps, which was identical to that of the time step of umbrellasampling MD. After the umbrella-sampling MD simulations were finished for each system, the data collected from the separate simulation frames were combined along the reaction coordinates. These data were then used to calculate the PMF for the entire binding process using the weighted histogram analysis method (WHAM) [50,51].Results Madrasin Molecular Modeling and Structural Analysis of Human KRASHuman KRAS-GTP models were constructed using the published crystal structure (PDB Id: 3GFT) as the template (Figure 1). The sensitive sites were located at the regions that participate in the GTP hydrolysis. This includes the P-loop (phosphate-binding loop, amino acids 10?6), which binds the cphosphate of GTP, and switch I (amino acids 32?8) and II (amino acids 60?7), which regulate binding to the KRASFigure 1. Molecular modeling of Human KRAS. The structure contains three sensitive sites: the P-loop (green), the switch I region (blue) and the switch II (red). The GTP and 15755315 the Mg2+ ion are shown by ball-and-stick representations. doi:10.1371/journal.pone.0055793.gComputational Analysis of KRAS MutationsFigure 2. The molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites (P-loop, switch I and II regions) of WT, G12D and G13D structures with respect to the initial conformation during the course of the simulation; (B) the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?4 for WT, G12D, and G13D, respectively. doi:10.1371/journal.pone.0055793.gloop, switch I and II regions) revealed that the atomic fluctuations of c.35G.A (p.G12D) mutant were significant at the switch II and P-loop regions when compared with.The trajectory was analyzed for the B-factor calculation. The RMSD of the sensitive regions with respect to the starting conformation was compared for the WT and MT structures during the course of the simulations. The RMSD was found to increase as a function of time for MT c.35G.A (p.G12D) when compared with WT and MT c.38G.A (p.G13D) (Figure 2A). By monitoring the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?34, we found that the GTP-binding pocket in the c.35G.A (p.G12D) protein was more open than that of the WT and c.38G.A (p.G13D) proteins (Figure 2B). The results of calculating the B-factors for each residue 12926553 at the sensitive sites (P-Potential of Mean Force (PMF) SimulationsTo explore the free energy profiles for the process of GTP binding with wild-type KRAS and its mutants (c.35G.A (p.G12D) and c.38G.A (p.G13D)), PMF simulations were performed using umbrella-sampling MD simulations [48]. The PMF is defined as the potential that gives an average force over all the configurations of a given system [49]. It generated a series of configurations along a reaction coordinate, after which umbrellasampling was used to restrain these conformations within the sampling windows. The total number of windows for each complex structure was approximately 30, depending on the initial structure of each ?system. Each window was separated by 1.0 A, covering the ??reaction coordinates from ,8 A to 40 A. The biasing force constant applied in the different windows of the umbrella sampling ?was 10.0 kcal/(mol.A2). The selected conformations for each window were first equilibrated for 100 ps and then kept for 1 ns for production sampling. The frequency of the data collection was set to 1 ps, which was identical to that of the time step of umbrellasampling MD. After the umbrella-sampling MD simulations were finished for each system, the data collected from the separate simulation frames were combined along the reaction coordinates. These data were then used to calculate the PMF for the entire binding process using the weighted histogram analysis method (WHAM) [50,51].Results Molecular Modeling and Structural Analysis of Human KRASHuman KRAS-GTP models were constructed using the published crystal structure (PDB Id: 3GFT) as the template (Figure 1). The sensitive sites were located at the regions that participate in the GTP hydrolysis. This includes the P-loop (phosphate-binding loop, amino acids 10?6), which binds the cphosphate of GTP, and switch I (amino acids 32?8) and II (amino acids 60?7), which regulate binding to the KRASFigure 1. Molecular modeling of Human KRAS. The structure contains three sensitive sites: the P-loop (green), the switch I region (blue) and the switch II (red). The GTP and 15755315 the Mg2+ ion are shown by ball-and-stick representations. doi:10.1371/journal.pone.0055793.gComputational Analysis of KRAS MutationsFigure 2. The molecular dynamics trajectories for: (A) Comparison of the RMSD plots of the sensitive sites (P-loop, switch I and II regions) of WT, G12D and G13D structures with respect to the initial conformation during the course of the simulation; (B) the pocket distances between the mass center of residues 12?3 and the mass center of residues 32?4 for WT, G12D, and G13D, respectively. doi:10.1371/journal.pone.0055793.gloop, switch I and II regions) revealed that the atomic fluctuations of c.35G.A (p.G12D) mutant were significant at the switch II and P-loop regions when compared with.