The main objective of this project is to determine the kinetics and energetics of binding of various ligands to the ribosome. These ligands include aminoglycoside antibiotics and their derivatives, elongation factors EF-Tu and EF-G and their proposed mutants. Timely and specific binding of these molecules is essential for the proper peptide formation in translation of the genetic code. EF-Tu and EF-G are crucial for, respectively, incorporating the aminoacylated tRNAs into the ribosome and for translocating both the tRNAs and mRNA after the peptide bond formation. Many antibiotics interfere with the binding of elongation factors, hinder the incorporation of the aminoacylated tRNA or inhibit functional conformational changes of the ribosome. The knowledge of what interactions govern the ligand encounter and binding with the ribosome will aid our understanding of the bi-molecular association, translation and inhibitory properties of antibiotics. The research will allow to propose experiments involving mutations of residues that prevent elongation factor binding and experiments suggesting derivatives of antibiotics that make their binding more specific. The effect of flexibility of ligands and the ribosome on association will be assessed. The techniques to study the energetics, thermodynamics, and kinetics of binding will include: molecular dynamics, Brownian dynamics and Poisson-Boltzmann implicit solvent models. Current simulation techniques will be extended and modified in order to enable the detailed studies of large macromolecular assemblies with over 200,000 atoms. The influence of long-range electrostatic steering will be investigated. The electrostatic similarity among the diffusing factors and complementarity with the ribosome binding site will be analyzed. The effect of flexibility of ligands and the ribosome on association will be assessed and the simulation methods will be extended to account for internal motions of the diffusing molecules. The project will promote international collaborative research between University of California at San Diego and Warsaw University in Poland. Blocking the ribosome function is important in curing many diseases, therefore, predictions of new molecules interfering with the ribosome are needed and this project will help to suggest them. The understanding of the mechanism governing the diffusion of molecules toward the ribosome could help in proposing novel antibiotics that bind stronger. This project will also help propose modifications of ribosome factors which hinder their correct association with the ribosome and prevent proper ribosome function.
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