MD simulations of the PbINP dimer. A) Two PbINP monomers were aligned via their tyrosine ladders prior to the start of the MD simulation. Waters allowed to equilibrate at the dimerization interface prior to the start of the simulation are shown as red and white spheres. B) Final scene from the 10-ns simulation showing exclusion of waters from the dimerization interface. C) The Cα RMSD (nm) of the PbINP dimer was plotted as a function of time (ns). The plots are of either the dimer starting from the hydrated interface (red line) or the energy-minimized average dimer simulated at the elevated temperature of 298 K (green line). A plot of the Cα RMSD (nm) of the PbINP monomer (black line) run at the elevated temperature of 298 K was also plotted as a function of time (ns). D) The number of side-chain hydrogen bonds formed during the simulation was plotted as a function of time (ns).
Garnham et al. BMC Structural Biology 2011 11:36 doi:10.1186/1472-6807-11-36