Journal
METHODS
Volume 49, Issue 2, Pages 181-188Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymeth.2009.04.004
Keywords
Flexibility/rigidity; Topological network representation; Ribosome; Exit tunnel; Antibiotics
Funding
- DFG [SFB 579]
- Goethe-University, Frankfurt
- Heinrich-Heine-University, Dusseldorf
- Hessian Science Program
- Frankfurt International Graduate School for Science (FIGSS)
- Otto-Stern-School in Frankfurt
- McGill University's Bellairs Research Institute, Barbados
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RNA structures are highly flexible biomolecules that can undergo dramatic conformational changes required to fulfill their diverse functional roles. Constraint counting on a topological network representation of an RNA structure can provide very efficiently detailed insights into the intrinsic flexibility characteristics of the biomolecule. In the network, vertices represent atoms and edges represent covalent and strong non-covalent bonds and angle constraints. Initially, the method has been successfully applied to identify rigid and flexible regions in proteins. Here, we present recent progress in extending the approach to RNA structures. As a case study, we analyze stability characteristics of the ribosomal exit tunnel and relate these findings to the tunnel's active role in co-translational processes. (c) 2009 Elsevier Inc. All rights reserved.
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