Coarse-graining the nano-machine ribosome to elucidate its functional dynamics

Ozge Kurkcuoglu, Pemra Doruker*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Coarse-grained computational techniques can provide information on conformational dynamics of the supramolecule ribosome, for which full-atom approaches become computationally demanding. Elastic network models and coarse-grained molecular dynamics simulations are the most commonly used methods for simple descriptions of the biomolecular structure. Usually, an amino acid or a nucleotide residue is represented by a single node, and simplified potential energy functions are used for interacting nodes. These approaches have been successful in reproducing the micro-to-milliseconds dynamics information, such as the experimentally observed ratchet-like rotation of the ribosomal subunits. Furthermore, they have provided insights on the structure-dynamicsfunction relationship of the ribosomal complex. This review summarizes various coarsegraining approaches on the nano-machine and recent studies that focus on its different functional sites.

Original languageEnglish
Title of host publicationRibosomes
Subtitle of host publicationMolecular Structure, Role in Biological Functions and Implications for Genetic Diseases
PublisherNova Science Publishers, Inc.
Number of pages14
ISBN (Print)9781624176982
Publication statusPublished - Mar 2013


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