Modeling Ribosomal Control, Function and Assembly

描述（由申请人提供）：核糖体是众所周知的抗生素、遗传病和抗癌药物的靶点，但其实际作用机制尚未详细了解。不同状态的核糖体的许多结构的可用性现在为实现揭示trna和mRNA的易位，蛋白质延伸以及30S亚基蛋白组分在16S RNA支架上的组装所涉及的步骤的总体目标提供了重要的机会。该项目建立在先前成功的基础上：1)用于识别组装过程中的中间体的实验足迹实验；2)通过对结构进行粗粒化计算蛋白质和rna的重要大结构域运动，表示为弹性网络，通过正常模式分析揭示结构运动。因此，计算整个核糖体结构的运动变得可行，从而产生有关各种成分如何相互作用或相互作用的信息，并将运动可视化。通过采用混合粗粒度方法，揭示了结构内部结合位点、活性位点和铰链处的大结构域运动和复杂的原子细节。对预测的构象变化和功能机制的验证将来自实验数据，如FRET和单分子实验。对于30S核糖体亚基组装，将利用这些强大的计算来开发组装中间体的分子模型，以生成与表明构象变化的新修饰实验一致的结构。这种创新的实验和计算的协调将提高两组研究的效用。对核糖体结构动力学的广泛模拟，结合各种已知的结构、生化和序列保护数据，有望产生关于这种核糖核蛋白机器如何运作的重要的新分子细节，为新的治疗方法开辟前景。

DESCRIPTION (provided by applicant): The ribosome is a well-known target for antibiotics, genetic diseases, and anti-cancer drugs, but its actual mechanism of action is not yet understood in detail. The availability of a number of structures of the ribosome in different states now presents an important opportunity to achieve the overall goals to unravel the steps involved in the translocation of the tRNAs and mRNA, protein elongation, and the assembly of the 30S subunit protein components onto the 16S RNA scaffold. The project is built upon previous successes in 1) experimental foot printing experiments for identifying intermediates in the assembly process and 2) computing the important large domain motions of proteins and RNAs by coarse-graining the structures, represented as an elastic network, revealing the structural motions through normal mode analysis. Thus it becomes feasible to compute the motions of the entire ribosome structure, yielding information about how the various components engage together or in opposition, as well as visualizing the motions. By adopting a mixed coarse-grained approach, the large domain motions and at the same time the intricate atomic details at binding sites, active sites, and hinges are revealed within the structure. Validation of the predicted changes in conformation and suggested mechanisms of function will come from experimental data such as FRET and single molecule experiments. For the 30S ribosomal subunit assembly, molecular models will be developed for assembly intermediates by utilizing these robust computations to generate structures consistent with new modification experiments indicating conformational changes. This innovative coordination of experiments and computations will enhance the utility of both groups of studies. Extensive simulations of the structural dynamics of the ribosome, combined with the various known structural, biochemical, and sequence conservation data are expected to yield important new molecular details of how this ribonucleo-protein machine functions, opening prospects for new therapeutic approaches.