ASSOCIATION OF ELONGATION FACTORS AND ANTIBIOTICS WITH THE RIBOSOME

本计画的主要目标是确定各种配体结合的动力学和能量学 到核糖体。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及其提出的突变体。 这些分子的及时和特异性结合对于翻译中正确的肽形成至关重要 遗传密码的一部分EF-Tu和EF-G分别对整合氨酰化的tRNA至关重要 进入核糖体，并在肽键形成后转运tRNA和mRNA。许多 抗生素干扰延伸因子的结合，阻碍氨基酰化的 tRNA或抑制核糖体的功能构象变化。了解什么样的相互作用 控制配体的遭遇和与核糖体的结合将有助于我们理解双分子 抗生素的缔合、翻译和抑制性质。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和实验 这表明抗生素的衍生物使它们的结合更特异。配体柔性的影响 并评估核糖体的结合。 研究结合的能量学、热力学和动力学的技术将包括： 动力学、布朗动力学和泊松-玻尔兹曼隐式溶剂模型。当前模拟 技术将得到扩展和修改，以便能够详细研究大分子 拥有超过20万个原子的集合体将研究远程静电转向的影响。 扩散因子间的静电相似性及与核糖体结合位点的互补性 将被分析。将评估配体和核糖体的柔性对缔合的影响， 模拟方法将扩展到考虑扩散分子的内部运动。 该项目将促进加州大学旧金山分校和美国加州大学旧金山分校之间的国际合作研究。 迭戈和华沙大学在波兰。 阻断核糖体功能在治疗许多疾病中很重要，因此， 干扰核糖体的分子是必需的，这个项目将有助于提出它们。的 了解分子向核糖体扩散的机制有助于 提出了结合力更强的新型抗生素。该项目还将有助于提出核糖体的修饰 阻碍它们与核糖体正确结合并阻止核糖体正常功能的因子。

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.