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、结合和生物降解。 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自于蛋白质 工程实验和理论研究使用静态结构基于泊松-玻尔兹曼计算。 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， 理论预测的准确性受到缺乏蛋白质介电响应的明确处理的限制， 构象动力学和由于未折叠状态下的残留结构的影响。因此，在本发明中， 尽管有二十年的研究，重要的问题，如如何和在多大程度上静电相互作用， 调节蛋白质稳定性尚未得到充分的回答。缺乏准确的方法 预测静电的贡献不仅阻碍了对蛋白质稳定性的基本理解， 也为推进计算蛋白质设计设置了障碍。本申请的具体目的是 是1）通过进一步开发连续的 恒定pH分子动力学和相关方法学，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-末端结构域、绒毛蛋白头片段亚结构域、亮氨酸拉链， 以及外周亚基结合结构域的中嗜热、嗜热和超嗜热变体。拟议 方法的发展将为社会提供强大的工具，研究广泛的静电 生物学中的现象在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，并将基于静态结构的 蛋白质静电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.