Electrostatic modulation of protein stability and folding

描述(申请人提供)：静电现象普遍存在于蛋白质折叠、结合和催化等生物过程中。我们目前关于静电对蛋白质稳定性影响的知识主要来自蛋白质工程实验和基于静态结构的Poisson-Boltzmann计算的理论研究。然而，虽然宏观测量往往不能将静电效应与其他效应分开，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残留结构的影响的显式处理，理论预测的准确性受到限制。因此，尽管进行了20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还没有得到充分的回答。缺乏准确的方法来预测静电贡献不仅阻碍了对蛋白质稳定性的基本理解，也给推进蛋白质计算设计造成了障碍。这项应用的具体目标是：1)通过进一步发展连续恒定pH分子动力学和相关方法，促进对pH依赖现象的原子水平的研究；2)通过研究几个模型系统，包括核糖体L9蛋白的N-末端结构域、Villin头饰亚结构域、亮氨酸拉链和外周亚基结合域的中温、高温和超嗜热变体，改进对蛋白质稳定性的静电调节的定量预测和详细了解。所提出的方法开发将为社区提供强大的工具来研究生物学中广泛的静电现象。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，并改变蛋白质静电学基于静态结构的观点。他们还将帮助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.