Figure 5
From: Three distinct regions of cRaf kinase domain interact with membrane
Two dimensional radial distribution function, g2D(r), of phosphorous atoms of PA (A) and PC (B) around specific atoms of the basic cluster residues. Nξ atom of K399 and Nδ atom of R391, R398 and R401 were used. The g2D(r) is averaged over all four peptides in the cRaf simulation, cRaf αC-Pept. The different colors show convergence using time-blocks 600–700 ns (black), 700–800 ns (red), 800–900 ns (blue), and 900 to 1000 ns (green). (C) Histogram of tres (residence time of PA around individual residues of the cRaf basic cluster). tres is calculated using Eq. 1. A surface “groove” formed by basic cluster residues e.g. R391 and R398 is shown in surface representation with the following color scheme: blue (+), red (−) and white (all hydrophobic) and green (all other amino acids). The phosphate of POPA is shown in red (oxygen) and tan (phosphorous) vdW spheres. (D) Multivalent salt-bridge interaction between a single PA lipid and two residues (R391 and R398) from the basic cluster.
