Mechanistic Studies of CRISPR-Medicated Bacterial Immunity

CRISPR 治疗的细菌免疫机制研究

• 批准号: 9067452
• 负责人: Rakhi Rajan
• 金额: $ 21.94万
• 依托单位: UNIVERSITY OF OKLAHOMA
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至 2017-09-05
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9067452
• 关键词: Address; Benchmarking; Binding; Biological Models; Biological Process; Biology; Catalysis; Centers of Research Excellence; Charge; Clustered Regularly Interspaced Short Palindromic Repeats; Communities; Computing Methodologies; Data; Development; Disease; Electrostatics; Environment; Enzymes; Goals; Homologous Gene; Immunity; Instruction; Ions; Knowledge; Leucine Zippers; Measurement; Methodology; Methods; Modeling; N-terminal; Nature; Oklahoma; Peptide Fragments; Peripheral; Postdoctoral Fellow; Protein Engineering; Proteins; Protocols documentation; Psychological Techniques; Qualifying; Regulation; Research; Residual state; Role; Sampling; Sodium Chloride; Solvents; Structure; Supercomputing; Surface; Techniques; Testing; Theoretical Studies; Titrations; Validation; Variant; Work; antigen antibody binding; base; computer cluster; computing resources; driving force; graduate student; improved; inhibitor/antagonist; insight; method development; molecular dynamics; novel strategies; post-doctoral training; protein folding; protonation; research study; response; simulation; structural biology; theories; thermostability; tool; villin

Electrostatic phenomena are ubiquitous in biological processes such as protein folding, binding, and catalysis. Our current knowledge of electrostatic effects on protein stability is mainly derived from protein engineering experiments and theoretical studies using static-structure based Poisson-Boltzmann calculations. However, while macroscopic measurements often cannot isolate electrostatic effects from others, the accuracy of theoretical predictions is limited by the lack of explicit treatment of protein dielectric response, conformational dynamics and effects due to residual structures in the unfolded state. As a result, despite two decades of research, important questions such as how and to what extent electrostatic interactions modulate protein stability have not been adequately answered. The lack of accurate means to predict electrostatic contributions not only hampers fundamental understanding of protein stability but also poses a roadblock for advancing computational protein design. The objectives of this application are to 1) advance atomic-level studies of pH-dependent phenomena by further developing continuous constant pH molecular dynamics and related methodologies, and 2) improve quantitative prediction and detailed understanding of electrostatic modulation of protein stability by studying several model systems including the N-terminal domain of ribosomal L9 protein, villin headpiece subdomain, leucine zipper, and meso-, thermoand hyper thermophilic variants of peripheral subunit binding domain. The proposed method development will provide the structural biology community with powerful tools for studying a wide range of electrostatic phenomena in biology. The insights gained in the application studies are expected to shift the native-centric paradigm of protein stability and function and transform the static-structure based view of protein electrostatics. They will also help establish general principles for computational protein design.

静电现象在生物学过程中无处不在，例如蛋白质折叠，结合和 催化。我们目前对静电对蛋白质稳定性影响的了解主要来自蛋白质 使用基于静态结构的Poisson-Boltzmann的工程实验和理论研究 计算。但是，尽管宏观测量通常无法从 其他的，理论预测的准确性受到蛋白质介电的明确处理的限制 响应，构象动力学和效果是由于未折叠状态的残留结构引起的。因此， 尽管进行了二十年的研究，但重要的问题，例如如何以及在何种程度上进行静电 相互作用调节蛋白质稳定性尚未得到充分回答。缺乏准确的手段 预测静电贡献不仅会阻碍对蛋白质稳定性的基本理解，还可以 为推进计算蛋白设计的障碍构成了障碍。此应用程序的目标是 1）通过进一步发展连续恒定pH，对pH依赖性现象进行预先原子级研究 分子动力学和相关方法，以及2）改进定量预测和详细的预测 通过研究多种模型系统，包括 核糖体L9蛋白，villin头饰子域的N末端结构域，亮氨酸拉链和中，中，热和 外周亚基结合结构域的多嗜热变体。提出的方法开发 将为结构生物学社区提供强大的工具，用于研究广泛的静电 生物学现象。申请研究中获得的见解有望改变以天然为中心 蛋白质稳定性和功能的范式，并改变基于静态结构的蛋白质视图 静电。它们还将帮助建立计算蛋白设计的一般原则。