Structure and Dynamics of Ribonucleic Acids

核糖体是由蛋白质和核糖核酸分子组成的小颗粒，负责细胞内蛋白质的合成。各种各样的实验方法正在提供关于这种粒子结构的信息。哈维博士正在开发计算机建模方法，以便将这些信息整合到核糖体和其他核糖核蛋白复合体的模型中。根据可获得的数据，这些程序能够产生低分辨率或高分辨率的模型。分辨率最低的“简洁”模型只确定了主要亚结构的位置，如单个蛋白质和RNA茎，但没有更详细的信息；另一个极端是全原子模型。还建立了混合分辨率的模型，对大多数结构和全原子细节只在有足够信息的情况下才有简洁的模型。这些程序产生了一系列模型，所有这些模型都与实验数据一致，并提供了关于结构不同部分的不确定性的定量陈述，这应该有助于指导未来的实验研究。这项研究将涉及对方法的扩展和改进，包括更强大的能量最小化算法、蒙特卡罗算法和全原子模型的分子动力学模拟。它还描述了在大肠杆菌核糖体、真核小核糖核蛋白、RNaseP和四膜虫核酶中的应用。

The ribosome is a small particle composed of molecules of proteins and ribonucleic acid which is responsible for the synthesis of proteins in the cell. A wide variety of experimental methods are providing information on the structure of this particle. Dr. Harvey is developing computer modeling methods for integrating that information into models for the ribosome and for other ribonucleoprotein complexes. The procedures are capable of producing low or high resolution models, depending on the available data. The lowest resolution "succinct" models identify only the locations of the principal substructures, such as individual proteins and RNA stems, but no more detailed information; at the other extreme are all-atom models. Models of mixed resolution are also produced, with succinct models for most of the structure and all-atom detail only where sufficient information exists. These procedures produce a range of models, all consistent with the experimental data and provide quantitative statements about the uncertainties in various parts of the structure, which should be useful in guiding future experimental studies. The study will involve extensions and improvements to the methodology, including more powerful algorithms for energy minimization, Monte Carlo, and molecular dynamics simulations on all-atom models. It also describes applications to the E. coli ribosome, eukaryotic small nuclear ribonucleoproteins, RNase P, and the Tetrahymena ribozyme.