Acid-mediated processes in nucleic acids and proteins

核酸和蛋白质中酸介导的过程

• 批准号: 8691310
• 负责人: CHARLES L BROOKS
• 金额: $ 28.63万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2018-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8691310
• 关键词: Acids; Address; Affect; Area; Bacterial Proteins; Benchmarking; Biochemical; Biological; Biological Process; Catalysis; Cereals; Collaborations; Coronavirus; DNA; Development; Disease; Electrostatics; Enteral; Equilibrium; Event; Funding; Goals; Indium; Institution; Investigation; Ions; Measures; Mediating; Methodology; Methods; Michigan; Modeling; Molecular; Molecular Chaperones; Nature; Nucleic Acids; Play; Process; Proteins; RNA; RNA Conformation; Response Elements; Role; SARS coronavirus; Sodium Chloride; Solvents; Structure; System; Temperature; Viral; Work; base; biological adaptation to stress; computer framework; computer infrastructure; design; hairpin ribozyme; human disease; improved; interest; member; molecular dynamics; novel; peptide structure; planetary Atmosphere; polyanion; pressure; protein folding; protein misfolding; protein structure function; protonation; public health relevance; research study; simulation; stem; tool; usability

DESCRIPTION (provided by applicant): Our overall goal is to develop the computational infrastructure to enable pH to be treated the same level as temperature and pressure in molecular dynamics simulation studies of biological molecules. These tools and methods need to be robust and straightforward to employ. Our work to date in this area has had a significant impact on the field; others have implemented similar methods, and key applications demonstrate the utility of direct incorporation of pH effects into molecular simulations. Our specific aims are directed toward the establishment of a robust methodology for explicit solvent constant pH simulations and are driven by applications to nucleic acids and to a specific protein system where we will explore pH sensing elements in the chaperon activity of a conditionally disordered protein. Aim 1 is to develop novel and robust explicit solvent CpHMD methods for nucleic acids. Nucleic acids present special challenges to implicit solvent models because of strong electrostatic fields from the nucleic acid polyanion and the significant influences of their ion atmosphere. Explicit solvent, with explicit ions, provides an alternative to the implicit solvet models. New developments in CpHMD will extend the approach to use an explicit solvent representation and will improve the precision, accuracy and robustness of the methodology. Our developments will be benchmarked against RNA and DNA measured pKa values for key bases, predominately the bases A and C, and through explicit collaborations with experimental colleagues. Aim 2 will apply CpHMD to explore the role of pH in mediating DNA/RNA conformation and base-base interactions. We will examine a number of specific cases, pH-mediated conformational switching in the SARS-CoV coronavirus, in the U6 intra-molecular stem loop of the splicosome, and the role of pH in the catalytic mechanism of the hairpin ribozyme. These applications address fundamental questions regarding the role of pH-driven protonation equilibrium in structure, dynamics and function in nucleic acids. Collaborations with the Al-Hashimi and Walter groups at Michigan and with Victoria D'Souza from Harvard provide both experimental benchmarks for our calculations and enable additional experiment and analysis to be informed from the calculations. Aim 3 aims to apply CpHMD to delineate and redesign the pH sensing mechanism in the Bacterial pH stress response protein chaperon HdeA. With the Bardwell group, we have redesigned the pH response elements in HdeA to produce a constitutively active and intrinsically disordered protein at pH 7. This provides a basis for exploration of the interactions within the largely disordered, but chaperon active, protein and the interactions it makes with its substrates. Collaboration with the Bardwell and Al-Hashimi groups will combine, coarse-grained simulations with CpHMD and NMR to explore the nature of the active disordered ensemble and how its members interact with substrate molecules.

描述（由申请人提供）：我们的总体目标是开发计算基础设施，使生物分子的分子动力学模拟研究中的 pH 值能够被视为与温度和压力相同的水平。这些工具和方法必须稳健且易于使用。迄今为止，我们在这一领域的工作对该领域产生了重大影响；其他人也实施了类似的方法，并且关键应用证明了将 pH 效应直接纳入分子模拟的效用。我们的具体目标是建立一种用于显式溶剂常数 pH 模拟的稳健方法，并由核酸和特定蛋白质系统的应用驱动，我们将在条件无序蛋白质的伴侣活性中探索 pH 传感元件。目标 1 是开发新颖且稳健的核酸显式溶剂 CpHMD 方法。由于核酸聚阴离子的强静电场及其对隐式溶剂模型的显着影响，核酸对隐式溶剂模型提出了特殊的挑战。 离子气氛。具有显式离子的显式溶剂提供了隐式溶剂模型的替代方案。 CpHMD 的新发展将扩展该方法以使用显式溶剂表示，并将提高该方法的精度、准确性和稳健性。我们的开发将以 RNA 和 DNA 测量的关键碱基（主要是碱基 A 和 C）的 pKa 值为基准，并通过与实验同事的明确合作。目标 2 将应用 CpHMD 探索 pH 在介导 DNA/RNA 构象和碱基相互作用中的作用。我们将研究一些具体案例，SARS-CoV 冠状病毒中、剪接体 U6 分子内干环中 pH 介导的构象转换，以及 pH 在发夹核酶催化机制中的作用。这些应用解决了有关 pH 驱动的质子化平衡在核酸结构、动力学和功能中的作用的基本问题。与密歇根州的 Al-Hashimi 和 Walter 小组以及哈佛大学的 Victoria D'Souza 的合作为我们的计算提供了实验基准，并使得能够从计算中了解更多的实验和分析。目标 3 旨在应用 CpHMD 描绘和重新设计细菌 pH 应激反应蛋白伴侣 HdeA 中的 pH 传感机制。我们与 Bardwell 团队合作，重新设计了 HdeA 中的 pH 响应元件，以在 pH 7 时产生组成型活性且本质上无序的蛋白质。这提供了基础 探索基本无序但具有活性的伴侣蛋白和蛋白质之间的相互作用 它与其底物发生的相互作用。与 Bardwell 和 Al-Hashimi 小组的合作将把粗粒度模拟与 CpHMD 和 NMR 结合起来，探索活性无序系综的性质及其成员如何与底物分子相互作用。