ArticleNucleic acids research2008
Revealing unique properties of the ribosome using a network based analysis.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Review
- Network theory reveals principles of spliceosome structure and dynamics.Structure (London, England : 1993) · 2022Article
- Modeling the ribosome as a bipartite graph.PloS one · 2022Article
- Evolution of ribosomal protein network architectures.Scientific reports · 2021Article
- Network theory of the bacterial ribosome.PloS one · 2020Article
- Eigenvector centrality for characterization of protein allosteric pathways.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis.Turkish journal of biology = Turk biyoloji dergisi · 2018Article
- Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins.Genome biology and evolution · 2017Article
- Network-based approaches in drug discovery and early development.Clinical pharmacology and therapeutics · 2013Review
- Secondary structure and domain architecture of the 23S and 5S rRNAs.Nucleic acids research · 2013Article
- Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains.PloS one · 2013Article
- Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues.In silico pharmacology · 2013Article
- Article
- Prediction of protein-binding areas by small-world residue networks and application to docking.BMC bioinformatics · 2011Article
- Structural signatures of antibiotic binding sites on the ribosome.Nucleic acids research · 2010Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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