Acid-mediated processes in nucleic acids and proteins

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值在生物分子的分子动力学模拟研究中与温度和压力相同。这些工具和方法需要健壮且易于使用。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；其他人已经实现了类似的方法，关键的应用证明了将pH效应直接纳入分子模拟的实用性。我们的具体目标是针对建立一种强大的方法，用于显式溶剂恒定pH模拟，并由核酸和特定蛋白质系统的应用驱动，在该系统中，我们将探索条件无序蛋白质的伴侣子活性中的pH传感元件。目的1是开发新的和稳健的显式溶剂CpHMD方法核酸。由于核酸聚阴离子产生的强静电场以及它们的显著影响，核酸对隐式溶剂模型提出了特殊的挑战

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.