Exploring RNA Folding and Dynamics Using a Polarizable Force Field

描述（申请人提供）：所提出的研究的目标是（1）在Drude极化力场的背景下导出一组用于连续介质Poisson-Boltzmann（PB）和溶剂可及性（SA）隐式溶剂计算的合适的原子半径，以及（2）应用这种扩展的PB-可极化力场处理增加了RNA分子的复杂性，以量化RNA折叠，稳定性和动力学的驱动力。首要目标是通过量化构象状态之间的自由能差异来研究RNA折叠，从而以定量的方式描述RNA的折叠途径。PB/SA方法也可用于蛋白质模拟。RNA折叠的模拟将使用增强的采样方法进行，以研究具有各种特征（发夹，假结等）的RNA分子的折叠，未折叠和中间状态。从MM/PBSA计算的自由能将与从量子力学（QM）计算的碱基堆积能量学的信息相结合，以获得RNA折叠过程中发生的事件的定量分子理解。这一信息不仅从理解RNA折叠的基本观点来看很重要，而且还因为导致错误折叠的RNA突变通常会导致疾病。此外，SAM-II核糖开关，结合S-腺苷甲硫氨酸（SAM）在细菌中的研究，将被用来定量描述载脂蛋白和SAM结合配置的差异。由于许多细菌物种使用核糖开关来控制基因表达，因此拟议的研究将提供可用于开发新型抗生素的信息。可极化力场在这些研究中特别相关，因为强电荷RNA分子的构象是高度动态的并且依赖于金属结合。在这个项目中描述的三个目标是：1。扩展现有的Drude极化力场，以包括MM/PBSA计算的参数。MM/PBSA计算的使用允许大分子构型的自由能的准确估计。MM/PBSA计算的原子半径将根据FEP和实验的溶剂化自由能进行调整。2.定量极化对小RNA分子折叠和稳定的影响。RNA折叠途径是复杂的，驱动力尚未完全了解。使用增强的采样方法结合MM/PBSA和QM计算，我们将定量极化和金属结合对小RNA分子折叠途径的作用。3.研究SAM-II核糖开关构象状态之间的动力学和自由能。核糖开关功能依赖于代谢物结合引起的构象变化。在这个目标中，我们将研究这些结合事件背后的驱动力和由此产生的构象变化。

DESCRIPTION (provided by applicant): The goals of the proposed research are to (1) to derive a set of suitable atomic radii for use in continuum dielectric Poisson-Boltzmann (PB) and solvent accessibility (SA) implicit solvent calculations within the context of a Drude polarizable force field and (2) apply this extended PB-polarizable force field treatment to RNA molecules of increasing complexity to quantify the driving forces for RNA folding, stability, and dynamics. The overarching objective is to study RNA folding by quantifying the free energy differences between conformational states and thus describe folding pathways for RNA in a quantitative manner. The PB/SA methodology could also be used in protein simulations. Simulations of RNA folding will be conducted using enhanced sampling methods to investigate folded, unfolded, and intermediate states of RNA molecules with various features (hairpins, pseudoknots, etc). Free energies from the MM/PBSA calculations will be coupled with information on base stacking energetics from quantum mechanics (QM) calculations to obtain a quantitative molecular understanding of events occurring during RNA folding. This information is important not only from a fundamental standpoint of understanding RNA folding, but also due to the fact that mutations in RNA that cause misfolding often lead to disease. In addition, studies on the SAM-II riboswitch, which binds S-adenosylmethionine (SAM) in bacteria, will be used to quantitatively describe the differences in apo- and SAM-bound configurations. Since many bacterial species use riboswitches to control gene expression, the proposed studies will provide information that can be used in the development of novel antibiotics. Polarizable force fields are especially relevant in these studies since the conformations of the strongly charged RNA molecules are highly dynamic and dependent upon metal binding. The three Aims described in this project are: 1. Extend the existing Drude polarizable force field to include parameters for MM/PBSA calculations. The use of MM/PBSA calculations allows for accurate estimates of free energies of macromolecular configurations. Atomic radii for MM/PBSA calculations will be tuned based on free energies of solvation from FEP and experiments. 2. Quantitate the effect of polarization on the folding and stabilization of small RNA molecules. RNA folding pathways are complex, and driving forces are not completely understood. Using enhanced sampling methods in conjunction with MM/PBSA and QM calculations, we will quantitate the role of polarization and metal binding on the folding pathway(s) of small RNA molecules. 3. Investigate the dynamics and free energy between conformational states of the SAM-II riboswitch. Riboswitch function depends on conformational changes induced by metabolite binding. In this Aim, we will investigate the driving forces behind these binding events and the resulting conformational changes.