Sandbox 208: Difference between revisions

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== Catalytic mechanism ==
== Catalytic mechanism ==


In the GDI domain I, the four helices A, C I and N forme a bundle. Helix I and the loop adjacent to the helix C belong to RBP and make direct contact with the globular core domain of the Rab molecule upon its binding. This relatively low affinity binding is followed by interaction of the initially disordered C-terminus with the hydrophobic patch of the CCR. Rab binding may promote the rearrangement of the GDI helices by pushing helix I toward the GDI core, whereas the loop following helix C is pushed away from the core, resulting in displacement of helices C and N. The displaced helices C and N make direct contact with domain II of GDI and appear to induce a conformationnal change, resulting in structural reorganization of domain II. The majority of GDI domain II (helices E, H, G and F) retains its structure upon Rab binding. This stabilizes the interaction of domain II of GDI with the membrane over the buried genranylgaranyl moities. However, there is a change in its orientation relative to domain I, and helix D is not tighly packed within domain II anymore. The side chain of Phe192 located in helix G flips and pushes the loop following helix D away, stabilizing the pocket in the open conformation. A conformational change leads to opening of the hydrophobic cavity between helices D and E in domain II and facilitate extraction of the geranylgeranyl lipid from the bilayer. Solvent exposure presumably is the reason for the moderate affinity of GDI to unprenylated Rab: the increase affinity of GDI to Rab upon prenyl group binding might be due to the Rab lipid moiety filling the open hydrophobic lipid binding pocket in GDI, diminishing the solvent exposed hydrophobic surfaces of the GDI-Rab complex. The large increase in affinity of GDI to Rab upon prenyl group binding appears to be the driving force for the membrane extraction process.
Initially, Rab is anchored to a target membrane via its lipid moieties. After interactions with its effectors, it returns to the GDP bound form. There is a primary recognition between Rab and GDI: the GTPase domain of Rab is recognized by GDI. GDI binds to Rab via the RBP, forming a low affinity complex. Then, the Rab conserved C terminal AXA box is recognized and bound by the GDI CCR, increasing the complex affinity. Interactions between CCR and the hydrophobic residues of the AXA box lead to a conformation change of the domain II. The GDI lipid binding pocket opens. It is located in the vicinity of the Rab lipid anchor, leading to a favorable situation for lipid transfer. Firstly, the first extracted lipid initially binds to the superficial lipid binding site leading to the formation of a transient high affinity complex still anchored in the membrane. Secondly, this complex is converted into a soluble complex by coordinating transfer of the GDI-bound lipid into the buried binding site. This event facilitates flipping of the second lipid from the membrane to the surface binding site. Thus, a high affinity Rab-GDI complex is formed and released from the membrane.  
GDI transports and then mediates the delivery of prenylated Rab to another target membrane. GDI leads to the docking of RAb via a protein interaction with the protein GDF. The docked complex undergoes a conformational change. This leads to the transfer of the first and then the second geranylgeranyl moiety into the membrane and subsequently to the release of the Rab C-terminus from the CBR.
Finally, the Rab protein enters its functional cycle whereas GDI is released into the cytosol.


= Disease =
= Disease =
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