Title: Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations
Authors: Kiel, C ×
Wohlgemuth, S
Rousseau, Frederic
Schymkowitz, Joost
Ferkinghoff-Borg, J
Wittinghofer, F
Serrano, L #
Issue Date: May-2005
Publisher: Academic Press
Series Title: Journal of Molecular Biology vol:348 issue:3 pages:759-775
Abstract: Considering the large number of putative Ras effector proteins, it is highly desirable to develop computational methods to be able to identify true Ras binding molecules. Based on a limited sequence homology. among members of the Ras association (RA) and Ras binding (RB) sub-domain families of the ubiquitin super-family, we have built structural homology models of Ras proteins in complex with different RA and RB domains, using the FOLD-X software. A critical step in our approach is to use different templates of Ras complexes, in order to account for the structural variation among the RA and RB domains. The homology models are validated by predicting the effect of mutating hot spot residues in the interface, and residues important for the specificity of interaction with different Ras proteins. The FOLD-X calculated energies of the best-modelled complexes are in good agreement with previously published experimental data and with new data reported here. Based on these results, we can establish energy thresholds above, or below which, we can predict with 96% confidence that a RA/RB domain will or will not interact with Ras. This study shows the importance of in depth structural analysis, high quality force-fields and modelling for correct prediction. Our work opens the possibility of genome-wide prediction for this protein family and for others, where there is enough structural information. (c) 2005 Elsevier Ltd. All rights reserved.
ISSN: 0022-2836
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Non-KU Leuven Association publications
× corresponding author
# (joint) last author

Files in This Item:

There are no files associated with this item.

Request a copy


All items in Lirias are protected by copyright, with all rights reserved.

© Web of science