Software for Homology Modeling of Ribosomes

描述(申请人提供)：在基因组学时代，序列数据库的指数增长是由于人们希望了解基本的大分子结构机制，以及这些结构如何与细胞中的寡核苷酸、蛋白质和代谢物相互作用。然而，在可用的相应3D结构的数量上存在巨大的差异。目前确定三维结构的实验方法，如X射线结晶学和核磁共振，可能会很麻烦和有问题，需要巨大的时间投资和受过这些技术培训的专家团队。为了解决这些问题，开发了软件工具来模拟大分子复合体，但它们仍然是初级的，因为它们的计算仍然非常昂贵，它们不能模拟非常大的大分子结构，如核糖体，它们没有统一到一个单一的平台，并且到目前为止还没有得到严格的评估。在此Fast Track SBIR应用程序中，DNA Software，Inc.计划扩展现有3D同源结构预测平台的功能。我们目前的原型软件RNA-123专注于RNA，它已经可以通过基于序列的同源建模准确地预测5S rRNA大小(~120个核苷酸长)的分子的三维结构。该软件的工程化和功能扩展将使研究人员第一次能够研究整个核糖体的结构机制。RNA-123将使在目前不存在晶体结构的情况下对致病细菌核糖体进行建模成为可能，从而及时地利用它们来开发新型合理设计的RNA靶向药物。这一目标将通过七个具体目标(第一阶段的目标1-3和第二阶段的目标1-4)来实现：目标1.1：设计现有的三维预测技术RNA-123，并扩展其能力，以便能够预测较大序列和复合体的三维结构。目的1.2：以已知的大肠杆菌16S rRNA的三维晶体结构为模板，预测嗜热葡萄球菌16S rRNA的三维结构，反之亦然。目的1.3：通过评估在Aim 1.2中预测的16S rRNA结构来测试在Aim 1.1中开发的软件。目的2.1：扩展在第一阶段开发的软件的功能，以允许对细菌或真核核糖体大小的蛋白质-RNA复合体进行同源建模。目的2.2：预测和评估已知的完整核糖体(70S)和核糖体亚基(30S和50S)的结构，以测试在第一阶段和第二阶段的AIMS 1中开发的软件。目标2.3：预测的大肠杆菌16S rRNA突变体的三维结构与其生物学活性的相关性。目的2.4：预测临床上重要的两种病原菌铜绿假单胞菌和金黄色葡萄球菌核糖体的三维结构。这笔赠款将对整个科学界产生长期影响，因为一旦RNA-123的功能扩展到能够对整个核糖体进行同源建模，它就可以很容易地对生物聚合物、DNA和碳水化合物以及它们相互之间的复合体、RNA和类药物小分子进行建模。RNA-123将使科学家能够使用可用的最新、最准确的生物信息学工具，对全人类产生直接影响。 与公共卫生相关：RNA-123将是一个有价值的生物信息学工具，促进公共和私人社区的研究人员的工作。科学家将能够对蛋白质数据库中没有结构数据的大分子三维结构进行建模，以便更好地指导他们在实验室中的研究工作，从而节省时间和不必要的费用。该项目的结果将是加快开发合理设计的针对具有生物医学和生物防御意义的病原菌的新型RNA靶向药物。

DESCRIPTION (provided by applicant): The exponential growth of sequence databases in the genomics era was promoted by the desire to understand fundamental macromolecular structural mechanisms, and how these structures interact with oligonucleotides, proteins and metabolites in a cell. However, a huge discrepancy in the number of corresponding 3D structures available exists. Current experimental methods of 3D structure determination, such as X-ray crystallography and Nuclear Magnetic Resonance, can be cumbersome and problematic, requiring a huge time investment as well as a team of experts that are trained in these techniques. To address these concerns software tools were developed to model macromolecular complexes, but they are rudimentary in that they are still very computationally expensive, they cannot model very large macromolecular structures such as the ribosome, they are not unified into a single platform, and they have not been critically evaluated to date. In this Fast Track SBIR application DNA Software, Inc. proposes to extend the functionality of an existing 3D homology structure prediction platform. Our current prototype software, RNA-123, has focused upon RNA and it can already accurately predict the 3D structures of molecules the size of 5S rRNA (~120 nucleotides long) using sequence-based homology modeling. The engineering and extension of the functionality of this software will enable a researcher, for the very first time, to study the structural mechanisms of a whole ribosome. RNA-123 will make it possible to model pathogenic bacterial ribosomes, where no crystal structures currently exist, to exploit them in a timely manner to develop new classes of rationally designed RNA-targeted drugs. This objective will be accomplished in seven specific aims (aims 1-3 in Phase I and aims 1-4 in Phase II): Aim 1.1: Engineer existing 3D prediction technology, RNA-123, and extend its capabilities to allow for the prediction of 3D structures of larger sequences and complexes. Aim 1.2: Predict the 3D structure of 16S rRNA of T. Thermophilus by using the known 3D crystal structure of 16S rRNA of E. coli as a template and vice versa. Aim 1.3: Test the software developed in aim 1.1 by assessing the 16S rRNA structures predicted in aim 1.2. Aim 2.1: To extend the capabilities of the software developed in phase 1 to allow homology modeling of protein-RNA complexes the size of a bacterial or eukaryotic ribosome. Aim 2.2: Predict and evaluate structures for the known complete ribosomes (70S) and ribosomal subunits (30S and 50S) to test the software developed in aims 1 of phase I and II. Aim 2.3: Correlation of predicted 3D structures of E. coli's 16S rRNA mutants with their biological activity. Aim 2.4: Predict 3D structure of the complete ribosomes of P.aeruginosa, and S. aureus, 2 clinically important pathogens. This grant will have long-term effects on the scientific community as a whole, because once the functionality of RNA-123 is extended to be able to homology model an entire ribosome, it can be easily adapted to model biopolymers, DNA, and carbohydrates as well as their complexes with each other, RNA, and drug-like small molecules. RNA-123 will enable scientists with the latest, most accurate bioinformatics tool available, having an immediate impact on all of humanity. PUBLIC HEALTH RELEVANCE: RNA-123 will be a valuable bioinformatics tool, facilitating the work of researchers in both the public and private communities. Scientists will be able to model macromolecular 3-Dimensional structures, having no structural data in the Protein Data Bank, in silico, to better direct their research efforts in the laboratory, thereby saving time and needless expense. The result of this project will be to speed the development of new classes of rationally designed RNA-targeted drugs against pathogenic bacteria having bio-medical and bio-defense implications.