Fig. 4: Molecular dynamics (MD) calculations of Cc1 and Cc display an inter-protein Gouy-Chapman conduit that is disrupted by phosphorylation.
From: Phosphorylation disrupts long-distance electron transport in cytochrome c
a, b Side view of the averaged sodium concentration map (M) at the X-axis plane dissecting both Cc1-Cc redox active sites (Cc and Y48pCMF Cc, respectively) facing each other at 3.2 nm separation taking the most external hydrogen atoms from the -CH3 distal pairs from each heme group, that is 4.2 nm taking the Fe-to-Fe distance. MD simulations were performed with explicit water (TIP3P solvent model) and 50 mM ionic concentration (NaCl) over 36 ns. Each contour line displays an increase of 0.15 M. (c–f) Side view of computed electrostatic potential with APBS76 from –1 kT/e (red) to 1 kT/e (blue) for Cc1-Cc pairs: Cc1-Cc (c), Cc1-Y48pCMF Cc in silico (d), Cc1-pY48 Cc (O-phospho-L-tyrosine) with charge –1 (e) and Cc1-pY48 Cc (O-phospho-L-tyrosine) with charge –2 (f). Ion concentration is 50 mM, pH 6.5. Each contour line displays an increase of 0.2 kT/e. g Virtualization of the Cc1-Cc system in 3D. Representation of the prism (blue) used to calculate the average concentration of sodium ions throughout the simulation. The image shows a single frame of the Cc1-Cc system depicting protein (cyan, translucent grey surface), heme groups (white with Iron atom in red), sodium ions (green spheres), and omitting water molecules. The closest backbone residues to the generated prism vertices are His18, Pro76, Lys79 and Ile85 of the Y48pCMF Cc, and Leu134, Leu94, Glu101 and Ala160 of Cc1. h Average sodium concentration over 36 ns in a 12.9 nm3 volume prism (prism dimensions for x, y, z = 15, 43, 20 units) centered between both heme groups of Cc and Cc1 for all systems. Volmap Tool Plugin 1.1 from VMD75 was used. i Derivation of binding kinetics from the BD computations of Cc1-Cc (red) and Cc1-Y48pCMF Cc (blue) complexes. For each computation, two curves are represented, corresponding to 4 independent pair-distances criteria for reaction, as reported previously65. Vertical lines correspond to the distances used as reaction criterion to estimate kon and ktrigger values. Source data are provided as a Source Data file.
