Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations.
Rab5a is currently a most interesting target because it is responsible for regulating the early endosome fusion in endocytosis and possibly the budding process. We utilized longtime-scale molecular dynamics simulations to investigate the internal motion of the wild-type Rab5a and its A30P mutant. It was observed that, after binding with GTP, the global flexibility of the two proteins is increasing, while the local flexibility in their sensitive sites (P-loop, switch I and II regions) is decreasing. Also, the mutation of Ala30 to Pro30 can cause notable flexibility variations in the sensitive sites. However, this kind of variations is dramatically reduced after binding with GTP. Such a remarkable feature is mainly caused by the water network rearrangements in the sensitive sites. These findings might be of use for revealing the profound mechanism of the displacements of Rab5a switch regions, as well as the mechanism of the GDP dissociation and GTP association.
Wang
Jing-Fang
JF
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. jfwang@gordonlifescience.org
Chou
Kuo-Chen
KC
D001120:Arginine / Q000737:chemistry / Q000235:genetics; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D006160:Guanosine Triphosphate / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011392:Proline / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary; D020696:rab5 GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics
D006160:Guanosine Triphosphate; D001120:Arginine; D011392:Proline; D020696:rab5 GTP-Binding Proteins