Electrostatic modulation of protein stability and folding

描述（由申请人提供）：静电现象在蛋白质折叠、结合和催化等生物过程中普遍存在。我们目前对静电对蛋白质稳定性的影响的认识主要来自蛋白质工程实验和基于静态结构的泊松-玻尔兹曼计算的理论研究。然而，虽然宏观测量通常不能将静电效应与其他效应隔离开来，但由于缺乏对蛋白质介电响应、构象动力学和未折叠状态下剩余结构的影响的明确处理，理论预测的准确性受到限制。因此，尽管进行了二十年的研究，但诸如静电相互作用如何以及在多大程度上调节蛋白质稳定性等重要问题尚未得到充分回答。缺乏准确预测静电贡献的方法不仅阻碍了对蛋白质稳定性的基本理解，而且对推进计算蛋白质设计构成了障碍。本应用的具体目标是：1)通过进一步发展连续恒定pH分子动力学和相关方法，推进pH依赖现象的原子水平研究；2)通过研究核糖体L9蛋白n端结构域、绒毛蛋白头亚结构域、亮氨酸拉链和中介孔等模型系统，提高对蛋白质稳定性静电调节的定量预测和详细理解。外周亚基结合域的嗜热和超嗜热变异体。该方法的发展将为研究生物学中广泛的静电现象提供强有力的工具。在应用研究中获得的见解有望改变以天然为中心的蛋白质稳定性和功能范式，并改变基于静态结构的蛋白质静电观。它们还将有助于建立计算蛋白质设计的一般原则。

DESCRIPTION (provided by applicant): 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.