NDLI: Exploring the Structure Space of Wildtype Ras Guided by Experimental Data

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Exploring the Structure Space of Wildtype Ras Guided by Experimental Data

Content Provider	ACM Digital Library
Author	Clausen, Rudy Shehu, Amarda
Abstract	The Ras enzyme mediates critical signaling pathways in cell proliferation and development by transitioning between GTP- (active) and GDP-bound (inactive) states. Many cancers are linked to specific Ras mutations affecting its conformational switching between active and inactive states. A detailed understanding of the sequence-structure-function space in Ras is missing. In this paper, we provide the first steps towards such an understanding. We conduct a detailed analysis of X-ray structures of wildtype and mutant variants of Ras. We embed the structures onto a low-dimensional structure space by means of Principal Component Analysis (PCA) and show that these structures are energetically feasible for wildtype Ras. We then propose a probabilistic conformational search algorithm to further populate the structure space of wildtype Ras. The algorithm explores a low-dimensional map as guided by the principal components obtained through PCA. Generated conformations are rebuilt in all-atom detail and energetically refined through Rosetta in order to further populate the structure space of wildtype Ras with energetically-feasible structures. Results show that a variety of novel structures are revealed, some of which reproduce experimental structures not subjected to the PCA but withheld for the purpose of validation. This work is a first step towards a comprehensive characterization of the sequence-structure space in Ras, which promises to reveal novel structures not probed in the wet laboratory, suggest new mutations, propose new binding sites, and even elucidate unknown interacting partners of Ras.
Starting Page	756
Ending Page	763
Page Count	8
File Format	PDF
ISBN	9781450324342
DOI	10.1145/2506583.2506706
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-09-22
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Energy surface Structure space Stable structures Ras Probabilistic search Multiscaling Principal components
Content Type	Text
Resource Type	Article

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