Sandbox 208: Difference between revisions

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GDI binds the Rab molecule via three interaction sites:

'''GDI-Rab Binding Platform (RBP)''', with bêta strands e1 and e3 and helix C, which form a separate binding site. It appears to be essential structural element, forming a number of interactions with the C-terminus and switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.

*'''GDI-Rab Binding Platform (RBP)''', with bêta strands e1 and e3 and helix C, which form a separate binding site. It appears to be essential structural element, forming a number of interactions with the C-terminus and switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.

'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)''', located in the cleft between domain I and domain II, which coordinates the flexible extended C-terminus of Rab. It is formed by residues 93-112 from domain I and 226-235 from domain II and reprent a hydrophobic cavity on the surface of the protein located between the GDI domains. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms.

*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)''', located in the cleft between domain I and domain II, which coordinates the flexible extended C-terminus of Rab. It is formed by residues 93-112 from domain I and 226-235 from domain II and reprent a hydrophobic cavity on the surface of the protein located between the GDI domains. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms.

'''Domain II of GDI or Lipid Binding Site''', consisting solely of alpha helices D, E, H and F of domain II, which form a prenyl-lipid binding pocket, exhibiting an open conformation and accomodating the prenyl moiety of a modified Rab if present. K145 (on GDI) may play an important role in formation of lipid-binding cavity by functionning as a spreader that keeps helices D and E appart.

*'''Domain II of GDI or Lipid Binding Site''', consisting solely of alpha helices D, E, H and F of domain II, which form a prenyl-lipid binding pocket, exhibiting an open conformation and accomodating the prenyl moiety of a modified Rab if present. K145 (on GDI) may play an important role in formation of lipid-binding cavity by functionning as a spreader that keeps helices D and E appart.

Additional minor contacts involve the N-terminus and C-terminus of GDI, as well as the Mobile Effector Loop (MEL). C-terminus of Rab molecules must be located in the vicinity of the MEL that is necessary for interaction with target membranes.

Sandbox 208: Difference between revisions

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@@ Line 19: / Line 19: @@
 GDI binds the Rab molecule via three interaction sites:
-'''GDI-Rab Binding Platform (RBP)''', with bêta strands e1 and e3 and helix C, which form a separate binding site. It appears to be essential structural element, forming a number of interactions with the C-terminus and switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.
+*'''GDI-Rab Binding Platform (RBP)''', with bêta strands e1 and e3 and helix C, which form a separate binding site. It appears to be essential structural element, forming a number of interactions with the C-terminus and switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.
-'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)''', located in the cleft between domain I and domain II, which coordinates the flexible extended C-terminus of Rab. It is formed by residues 93-112 from domain I and 226-235 from domain II and reprent a hydrophobic cavity on the surface of the protein located between the GDI domains. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms.
+*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)''', located in the cleft between domain I and domain II, which coordinates the flexible extended C-terminus of Rab. It is formed by residues 93-112 from domain I and 226-235 from domain II and reprent a hydrophobic cavity on the surface of the protein located between the GDI domains. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms.
-'''Domain II of GDI or Lipid Binding Site''', consisting solely of alpha helices D, E, H and F of domain II, which form a prenyl-lipid binding pocket, exhibiting an open conformation and accomodating the prenyl moiety of a modified Rab if present. K145 (on GDI) may play an important role in formation of lipid-binding cavity by functionning as a spreader that keeps helices D and E appart.
+*'''Domain II of GDI or Lipid Binding Site''', consisting solely of alpha helices D, E, H and F of domain II, which form a prenyl-lipid binding pocket, exhibiting an open conformation and accomodating the prenyl moiety of a modified Rab if present. K145 (on GDI) may play an important role in formation of lipid-binding cavity by functionning as a spreader that keeps helices D and E appart.
 Additional minor contacts involve the N-terminus and C-terminus of GDI, as well as the Mobile Effector Loop (MEL). C-terminus of Rab molecules must be located in the vicinity of the MEL that is necessary for interaction with target membranes.