Acid-mediated processes in nucleic acids and proteins

核酸和蛋白质中酸介导的过程

• 批准号: 8854117
• 负责人: CHARLES L BROOKS
• 金额: $ 28.52万
• 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/8854117
• 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; Health; 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; 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pH值能够在生物分子的分子动力学模拟研究中与温度和压力相同的水平进行处理。这些工具和方法必须是可靠和直接的。迄今为止，我们在这一领域的工作已经对该领域产生了重大影响;其他人已经实施了类似的方法，关键应用程序证明了将pH效应直接纳入分子模拟的实用性。我们的具体目标是建立一种用于显式溶剂恒定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，我们将在其中探索条件无序蛋白质的伴侣活性中的pH传感元件。目的1是发展新的和强大的明确的溶剂CpHMD方法的核酸。由于核酸聚阴离子产生的强静电场及其对溶剂的影响，核酸对隐式溶剂模型提出了特殊的挑战。 离子气氛显式溶剂，与明确的离子，提供了一种替代隐式溶剂模型。CpHMD的新发展将扩展该方法以使用明确的溶剂表示，并将提高该方法的精密度、准确度和耐用性。我们的发展将以RNA和DNA测量的关键碱基的pKa值为基准，主要是碱基A和C，并通过与实验同事的明确合作。目的二是利用CpHMD研究pH对DNA/RNA构象和碱基间相互作用的影响。我们将研究一些特定的情况下，pH值介导的构象转换在SARS冠状病毒，在U6分子内茎环的剪接体，和pH值的作用，在催化机制的发夹核酶。这些应用程序解决了关于pH驱动的质子化平衡在核酸的结构，动力学和功能中的作用的基本问题。与密歇根大学的哈希米和沃尔特小组以及哈佛大学的维多利亚·德索萨的合作为我们的计算提供了实验基准，并使更多的实验和分析能够从计算中得到信息。目的3利用CpHMD对细菌pH应激反应伴侣蛋白HdeA的pH敏感机制进行研究。与Bardwell小组一起，我们重新设计了HdeA中的pH响应元件，以在pH 7下产生组成型活性和内在无序的蛋白质。这提供了一个基础 为了探索在很大程度上无序的，但伴侣活性，蛋白质和 与基质的相互作用。与Bardwell和Al-Hashimi小组的合作将联合收割机、粗粒度模拟与CpHMD和NMR相结合，以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。