Computational study of a transition state analog of phosphoryl transfer in the Ras–RasGAP complex: AlF x versus MgF 3 –
- 29 July 2005
- journal article
- Published by Springer Nature in Journal of Molecular Modeling
- Vol. 11 (6) , 503-508
- https://doi.org/10.1007/s00894-005-0259-4
Abstract
The structures of the complexes between Ras•GDP bound to RasGAP in the presence of three probable γ-phosphate analogs (AlF3, AlF 4 − and MgF 3 − ) for the transition state (TS) of the hydrolysis of guanosine triphosphate (GTP) by the Ras-RasGAP enzymes have been modeled by quantum mechanical—molecular mechanical (QM/MM) calculations. These simulations contribute to the dispute on the nature of the TS in the hydrolysis reaction, since medium resolution X-ray crystallography cannot discern among stereochemically similar isoelectronic species (e.g., AlF3 or MgF 3 − ). The optimized geometry for each structure has been found starting from experimental coordinates of one of them (PDBID: 1WQ1). Direct comparison of the experimental and computed geometry configurations in the immediate vicinity of the active site suggests that MgF 3 − is the most likely candidate for the phosphate analog in the experimental structure.Keywords
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