Revealing unique properties of the ribosome using a network based analysis

@article{citeulike:3000842, abstract = {The ribosome is a complex molecular machine that offers many potential sites for functional interference, therefore representing a major target for antibacterial drugs. The growing number of high-resolution structures of ribosomes from different organisms, in free form and in complex with various ligands, provides unique data for structural and comparative analyses of RNA structures. We model the ribosome structure as a network, where nucleotides are represented as nodes and intermolecular interactions as edges. As shown previously for proteins, we found that the major functional sites of the ribosome exhibit significantly high centrality measures. Specifically, we demonstrate that mutations that strongly affect ribosome function and assembly can be distinguished from mild mutations based on their network properties. Furthermore, we observed that closeness centrality of the rRNA nucleotides is highly conserved in the bacteria, suggesting the network representation as a comparative tool for the ribosome analysis. Finally, we suggest a global topology perspective to characterize functional sites and to reveal the unique properties of the ribosome. 10.1093/nar/gkn433}, author = {David-Eden, Hilda and Mandel-Gutfreund, Yael }, citeulike-article-id = {3000842}, doi = {http://dx.doi.org/10.1093/nar/gkn433}, journal = {Nucl. Acids Res.}, keywords = {analysis, modelling, network, ribosome, structure}, month = {July}, pages = {gkn433+}, posted-at = {2008-07-15 04:45:46}, priority = {2}, title = {Revealing unique properties of the ribosome using a network based analysis}, url = {http://dx.doi.org/10.1093/nar/gkn433}, year = {2008} }

TY - JOUR ID - citeulike:3000842 L3 - citeulike-article-id:3000842 TI - Revealing unique properties of the ribosome using a network based analysis JF - Nucl. Acids Res. SP - gkn433 N2 - The ribosome is a complex molecular machine that offers many potential sites for functional interference, therefore representing a major target for antibacterial drugs. The growing number of high-resolution structures of ribosomes from different organisms, in free form and in complex with various ligands, provides unique data for structural and comparative analyses of RNA structures. We model the ribosome structure as a network, where nucleotides are represented as nodes and intermolecular interactions as edges. As shown previously for proteins, we found that the major functional sites of the ribosome exhibit significantly high centrality measures. Specifically, we demonstrate that mutations that strongly affect ribosome function and assembly can be distinguished from mild mutations based on their network properties. Furthermore, we observed that closeness centrality of the rRNA nucleotides is highly conserved in the bacteria, suggesting the network representation as a comparative tool for the ribosome analysis. Finally, we suggest a global topology perspective to characterize functional sites and to reveal the unique properties of the ribosome. 10.1093/nar/gkn433 KW - analysis KW - modelling KW - network KW - ribosome KW - structure AU - David-Eden, Hilda AU - Mandel-Gutfreund, Yael PY - 2008/07/14/ UR - http://dx.doi.org/10.1093/nar/gkn433 ER -