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.

静电现象在生物过程中普遍存在，例如蛋白质折叠、结合和 催化。我们目前关于静电对蛋白质稳定性影响的知识主要来源于蛋白质 使用基于静态结构的泊松玻尔兹曼进行工程实验和理论研究 计算。然而，虽然宏观测量通常无法将静电效应与 其他人，理论预测的准确性因缺乏对蛋白质电介质的明确处理而受到限制 响应、构象动力学和展开状态下残余结构的影响。因此， 尽管进行了二十年的研究，诸如静电如何以及程度如何等重要问题仍然存在。 相互作用调节蛋白质稳定性尚未得到充分解答。缺乏准确的手段 预测静电贡献不仅妨碍对蛋白质稳定性的基本理解，而且 为推进计算蛋白质设计设置了障碍。该应用程序的目标是 1) 通过进一步发展连续恒定pH值，推进pH依赖性现象的原子水平研究 分子动力学和相关方法，2）改进定量预测和详细 通过研究几个模型系统来了解蛋白质稳定性的静电调节，包括 核糖体 L9 蛋白的 N 端结构域、绒毛头亚结构域、亮氨酸拉链以及内消旋、热和 外周亚基结合域的超嗜热变体。所提出的方法开发 将为结构生物学界提供研究各种静电的强大工具 生物学中的现象。在应用研究中获得的见解预计将改变以本地为中心的 蛋白质稳定性和功能的范例，并转变基于静态结构的蛋白质观点 静电学。他们还将帮助建立计算蛋白质设计的一般原则。