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架构，以使PH可以与生物分子的分子动力学模拟研究中的温度和压力相同的水平。这些工具和方法需要强大而直接地采用。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。其他人已经实施了类似的方法，关键应用证明了将pH效应直接纳入分子模拟的实用性。我们的具体目的是针对建立可靠溶剂恒定pH模拟的可靠方法，并由对核酸的应用和特定的蛋白质系统驱动，我们将探索条件无序蛋白质的伴侣活性中的pH感应元素。目的1是开发用于核酸的新型和鲁棒的显式溶剂CPHMD方法。核酸对隐式溶剂模型提出了特殊的挑战，因为来自核酸聚会的强静电场以及其其显着影响。 离子气氛。具有显式离子的显式溶剂为隐式溶剂模型提供了替代方案。 CPHMD中的新发展将扩展使用明确的溶剂表示的方法，并将提高方法论的精度，准确性和鲁棒性。我们的发展将针对RNA和DNA测量关键基础的PKA值进行基准测试，主要是基础A和C，并通过与实验同事的明确合作。 AIM 2将应用CPHMD来探索pH在介导DNA/RNA构象和碱基相互作用中的作用。我们将检查许多特定病例，即SARS-COV冠状病毒中的pH介导的构象转换，在U6偶有的旋转茎环中的pH介导，pH值的pH构象转换以及pH的作用在发夹核酶的催化机理中的作用。这些应用解决了有关pH驱动的质子化平衡在结构，动力学和核酸功能中的作用的基本问题。与密歇根州的Al-Hashimi和Walter集团以及哈佛大学的Victoria D'Souza合作提供了我们计算的实验基准，并允许从计算中获取其他实验和分析。 AIM 3的目的是应用CPHMD来描述并重新设计细菌pH应激反应蛋白伴侣HDEA中的pH感应机制。使用Bardwell组，我们重新设计了HDEA中的pH响应元素，以在pH 7处产生组成型活性和本质上无序的蛋白质。这提供了一个基础 用于探索在很大程度上无序中的相互作用，但伴侣的活性，蛋白质和 它与基材进行的交互。与Bardwell和Al-Hashimi组的合作将与CPHMD和NMR合并，以探索活动无序集合的性质以及其成员如何与底物分子相互作用。