Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session I

4-POS Board 4 Exploring Alternative Signaling Pathways between Decoding Center of Bacterial Ribosome and Active Site of EF-Tu – tRNA – GDP Complex Basak Akdas , Ozge Kurkcuoglu Levitas. Istanbul Technical University, Istanbul, Turkey. Supramolecule ribosome, responsible for protein synthesis, consists of small and large subunits, respectively called 30S and 50S in bacteria. During protein synthesis, communication of distant functional sites on the complex is maintained via signal transmission throughout the structure, such as between the decoding center (DC) on 30S decoding the genetic code and elongation factor (EF) Tu assisting aminoacyl-transfer RNA (tRNA) 1 . Revealing major and minor communication pathways between functional sites is critical to understand the allosteric mechanisms employed by the complex for a successful translation. In this study, Yen’s Algorithm 2 is employed with the elastic network approach 3 on Thermus Thermophilus ribosome structure to reveal twenty shortest paths between DC and EF-Tu. The ribosome structure is represented as a network of nodes and edges. Nodes are placed at alpha-carbon and phosphor atoms of residues, and lengths of edges are calculated based on atom-atom interactions. Major and minor signaling pathways exist between DC and GTPase center of EF-Tu and pass through functional regions such as Sarcin-Ricin Loop (SRL), aminoacyl-tRNA 1 and intersubunit bridge B2a, which was proposed to bear an important role in enzymatic steps of translation 4 . These findings suggest important hints for understanding functional activities of the ribosome and identifying new target sites for drug design. [1] Schmeing, T.M.; Voorhees, R M.; Kelley, A.C.; Gao, Y.-G.; Murphy, F.V. IV; Weir, J.R.; Ramakrishnan, V. Science, 2009, 326(5953), 688. [2] Yen, J.Y. Management Science, 1971, 17, 712. [3] Kurkcuoglu, O.; Turgut, O.T.; Cansu, S.; Jernigan, R.L.; Doruker, P. Biophysical Journal, 2009, 97, 1178. [4] Kipper, K.; Hetenyi, C.; Sild, S.; Remme, J.; Liiv, A. J Molecular Biology, 2009, 385, 405.

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