58
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.
