Figure 4.

Probe binding analysis. Density of probes in the single-probe (A) and mixed-probe simulations (B) projected onto the respective PSTM of G12D K-Ras catalytic domain in OS2. A contour level of $\le -RT\ln \frac{s}{c_0}=-1.8$ was used in both maps, where c₀ = 2.8 M and 0.4 M is the bulk concentration of probes in the single- and mixedprobe simulations, respectively, and s is the calculated molar concentration at the surface. The inset in (B) shows projection of the coordinates of two Ras-bound ligands on the PSTM: 2-(1H-indol-3-ylmethyl)-1H-imidazo[4,5-c]pyridine (PDB ID 4EPV) that binds at p1 (yellow) and S-adenosylmethionine (4YNM) that targets p4 (red). (C) Probability density profile of the seven probe molecules as a function of distance from the center of mass of the catalytic domain of K-Ras. The probability, p(r), of finding a probe between r and r+dr shown in part C was normalized using ${\displaystyle {\int }_0^{\infty }4}\pi r^{2}p(r)\text{d}r=1$