Computational study of a transition state analog of phosphoryl transfer in the Ras-RasGAP complex: AlF(x) versus MgF3-.
J Mol Model
; 11(6): 503-8, 2005 Nov.
Article
en En
| MEDLINE
| ID: mdl-16052311
The structures of the complexes between Ras*GDP bound to RasGAP in the presence of three probable gamma-phosphate analogs (AlF3, AlF4- and MgF3-) 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 MgF3-). 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 MgF3- is the most likely candidate for the phosphate analog in the experimental structure.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Fosfatos
/
Proteínas ras
/
Proteínas Activadoras de ras GTPasa
Idioma:
En
Revista:
J Mol Model
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2005
Tipo del documento:
Article
Pais de publicación:
Alemania