ASSOCIATION OF ELONGATION FACTORS AND ANTIBIOTICS WITH THE RIBOSOME

描述(申请人提供)：本项目的主要目标是确定各种配体与核糖体结合的动力学和能量学。这些配体包括氨基糖苷类抗生素及其衍生物、延伸因子EF-Tu和EF-G及其建议的突变体。这些分子的及时和特定结合对于遗传密码翻译过程中正确的多肽形成是必不可少的。EF-Tu和EF-G分别对于将氨酰化的tRNAs整合到核糖体中以及在多肽键形成后tRNAs和mRNAs的移位起关键作用。许多抗生素干扰延伸因子的结合，阻碍氨基酰化的tRNA的掺入，或抑制核糖体的功能性构象变化。了解什么相互作用控制着配体与核糖体的相遇和结合，将有助于我们理解抗生素的双分子结合、翻译和抑制特性。这项研究将允许提出涉及阻止延伸因子结合的残基突变的实验，以及建议使其结合更具特异性的抗生素衍生物的实验。将评估配体和核糖体的灵活性对结合的影响。研究结合的能量学、热力学和动力学的技术包括：分子动力学、布朗动力学和泊松-玻尔兹曼隐含溶剂模型。目前的模拟技术将被扩展和修改，以便能够详细研究具有超过20万个原子的大分子组装。研究了远程静电转向的影响。分析扩散因子之间的静电相似性以及与核糖体结合部位的互补性。将评估配体和核糖体的灵活性对结合的影响，并将扩展模拟方法以考虑扩散分子的内部运动。该项目将促进加州大学圣地亚哥分校和波兰华沙大学之间的国际合作研究。阻断核糖体的功能在许多疾病的治疗中是重要的，因此，需要预测新的分子干扰核糖体，这个项目将有助于建议它们。对控制分子向核糖体扩散的机制的理解可能有助于提出结合更强的新型抗生素。该项目还将帮助提出修改核糖体因子的建议，这些修改阻碍了核糖体与核糖体的正确结合，并阻碍了核糖体的正常功能。

DESCRIPTION (provided by applicant): 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.