Electrostatic modulation of protein stability and folding

静电现象在生物过程中普遍存在，例如蛋白质折叠、结合和 催化作用。我们目前关于静电对蛋白质稳定性影响的知识主要来源于蛋白质 使用基于静态结构的泊松玻尔兹曼计算进行工程实验和理论研究。 然而，虽然宏观测量通常无法将静电效应与其他效应隔离开来， 由于缺乏对蛋白质介电响应的明确处理，理论预测的准确性受到限制， 构象动力学和未折叠状态下残余结构的影响。结果， 尽管进行了二十年的研究，诸如静电相互作用如何以及程度如何等重要问题 调节蛋白质稳定性尚未得到充分解答。缺乏准确手段 预测静电贡献不仅妨碍对蛋白质稳定性的基本理解，而且 也为推进计算蛋白质设计带来了障碍。此应用程序的具体目标 1) 通过进一步发展连续性来推进 pH 依赖性现象的原子水平研究 恒定 pH 分子动力学和相关方法，以及 2) 改进定量预测 通过研究几个模型系统，详细了解蛋白质稳定性的静电调节 包括核糖体L9蛋白的N端结构域、绒毛头亚结构域、亮氨酸拉链、 以及外周亚基结合域的中观、嗜热和超嗜热变体。拟议的 方法的开发将为社会提供强大的工具来研究各种静电 生物学中的现象。应用研究中获得的见解预计将改变 蛋白质稳定性和功能的以天然为中心的范式，并转变基于静态结构的观点 蛋白质静电学。他们还将帮助建立计算蛋白质设计的一般原则。

Electrostatic phenomena are ubiquitous in biological processes such as protein folding, binding, and catalysis. Our current knowledge of electrostatic effects on protein stability is mainly derived from protein engineering experiments and theoretical studies using static-structure based Poisson-Boltzmann calculations. However, while macroscopic measurements often can not isolate electrostatic effects from others, the accuracy of theoretical predictions is limited by the lack of explicit treatment of protein dielectric response, conformational dynamics and effects due to residual structures in the unfolded state. As a result, despite two decades of research, important questions such as how and to what extent electrostatic interactions modulate protein stability have not been adequately answered. The lack of accurate means to predict electrostatic contributions not only hampers fundamental understanding of protein stability but also poses a roadblock for advancing computational protein design. The specific aims of this application are 1) to advance atomic-level studies of pH-dependent phenomena by further developing continuous constant pH molecular dynamics and related methodologies, and 2) to improve quantitative prediction and detailed understanding of electrostatic modulation of protein stability by studying several model systems including the N-terminal domain of ribosomal L9 protein, villin headpiece subdomain, leucine zipper, and meso-, thermo- and hyperthermophilic variants of peripheral subunit binding domain. The proposed method development will provide the community with powerful tools for studying a wide range of electrostatic phenomena in biology. The insights gained in the application studies are expected to shift the native-centric paradigm of protein stability and function and transform the static-structure based view of protein electrostatics. They will also help establish general principles for computational protein design.