Role of the arginine finger in Ras.RasGAP revealed by QM/MM calculations.
In the Ras.Ras.GAP complex, hydrolysis of guanosine triphosphate is strongly accelerated GAP as compared to Ras alone. This is largely attributed to the arginine finger R789(GAP) pointing to AlF(x) in the transition state analogue. We performed QM/MM simulations where triphosphate was treated using the quantum mechanical method of density functional theory, while the protein complex and water environment were described classically using MD. Compared to Ras, the crucial electron shift, bond stretching and distortion towards an eclipsed gamma-to-beta orientation are much more pronounced. The arginine finger is shown to act by displacing water out of the binding niche. The resulting enhanced electrostatic field catalyses the cleavage step.
te Heesen
Henrik
H
Department of Biophysics, ND 04 North, University of Bochum, D-44780, Bochum, Germany.
Gerwert
Klaus
K
Schlitter
Jürgen
J
D001120:Arginine / Q000737:chemistry*; D002384:Catalysis; D019295:Computational Biology; D006160:Guanosine Triphosphate / Q000378:metabolism; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008958:Models, Molecular; D011487:Protein Conformation; D055672:Static Electricity; D013329:Structure-Activity Relationship; D020703:ras GTPase-Activating Proteins / Q000737:chemistry*; D018631:ras Proteins / Q000737:chemistry* / Q000378:metabolism
D020703:ras GTPase-Activating Proteins; D006160:Guanosine Triphosphate; D001120:Arginine; D018631:ras Proteins