✦ LIBER ✦

Molecular dynamics simulations of the Ras:Raf and Rap:Raf complexes

✍ Scribed by Jun Zeng; Herbert R. Treutlein; Thomas Simonson

Publisher: John Wiley and Sons
Year: 1999
Tongue: English
Weight: 471 KB
Volume: 35
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19990401)35:1<89::aid-prot9>3.0.co;2-s

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✦ Synopsis

The protein Raf is an immediate downstream target of Ras in the MAP kinase signalling pathway. The complex of Ras with the Ras-binding domain (RBD) of Raf has been modelled by homology to the (E30D,K31E)-Rap1A:RBD complex, and both have been subjected to multiple molecular dynamics simulations in solution. While both complexes are stable, several rearrangements occur in the Ras:RBD simulations: the RBD loop 100-109 moves closer to Ras, Arg73 in the RBD moves towards Ras to form a salt bridge with Ras-Asp33, and Loop 4 of the Ras switch II region shifts upwards toward the RBD. The Ras:RBD interactions (including the RBD-Arg73 interaction) are consistent with available NMR and mutagenesis data on the Ras: RBD complex in solution. The Ras switch II region does not interact directly with the RBD, although indirect interactions exist through the effector domain and bridging water molecules. No large-scale RBD motion is seen in the Ras:RBD complex, compared to the Rap:RBD complex, to suggest an allosteric activation of Raf by Ras. This may be because the Raf kinase domain (whose structure is unknown) is not included in the model.

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