Membrane localization and dynamics of geranylgeranylated Rab5 hypervariable region

The small GTPase Rab5 is a key regulator of endosomal trafficking processes and a marker for the early endosome. The C-terminal hypervariable region (HVR) of Rab5 is post-translationally modified at residues Cys212 and Cys213 to accommodate two geranylgeranyl anchors (C20 carbon chain length) in order to associate Rab5 with the membrane. The structural role of the HVR regarding protein-early endosome membrane recruitment is not resolved due to its high degree of flexibility and lack of crystallographic information. Here, full-atomistic and coarse-grained molecular dynamics simulations of the truncated Rab5 HVR206–215 in three model membranes of increasing complexity (pure phospholipid bilayer, ternary membrane with cholesterol, six-component early endosome) were performed. Specific electrostatic interactions between the HVR206–215 Arg209 residue and the phosphate group of the inositol ring of PI(3)P were detected. This shows that PI(3)P acts as a first contact site of protein recruitment to the early endosome. The free energy change of HVR206–215 extraction from the bilayer was largest for the physiological negatively charged membrane. 5μs coarse-grained simulations revealed an active recruitment of PI(3)P to the HVR206–215 supporting the formation of Rab5- and PI(3)P enriched signaling platforms. [Display omitted] •Membrane structure is only locally perturbed by HVR anchoring.•HVR conformational space is not associated with membrane composition.•Formation of persistent electrostatic and hydrogen bonding HVR-PI(3)P interaction•HVR lateral diffusion is slowed down with increasing cholesterol as well as PI(3)P fraction.