Figure 4

Analysis of the β barrel shape. (a) Example of a mean cylinder axis (orange) and of a set of cylinders (blue) describing the cavity interior of the SH3 β barrel. The SH3 structure is drawn in cartoon, with β strands colored in yellow. The cylinder axis origin is in the middle of cylinder. (b,c) Mean length of the β barrel obtained along MD simulations, as the position difference between the two extreme cylinders. The length was calculated for WT (black), L28A (red) and L28P (green) sequences, in simulations based on the sets full (b) and reduced (c) of NMR restraints. (d-f) Profiles of β barrel inner cavity described by cylinder radii plotted as interlaced values obtained from the runs. The corresponding MD simulations are based on the sets full (d), reduced (e) and random (f) of NMR restraints. The profiles are plotted along the coordinate of the slabs on the cylinder axis (Additional file 1), the axis origin being set at the middle of the cylinder axis drawn in plot (a).