Electrostatic modulation of protein stability and folding

静电现象在生物过程中普遍存在，如蛋白质的折叠、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自蛋白质 工程实验和理论研究采用基于静态结构的泊松-玻尔兹曼计算。 然而，尽管宏观测量往往不能将静电效应与其他因素隔离开来， 由于缺乏对蛋白质介电响应的显式处理，理论预测的准确性受到限制， 展开状态下的构象动力学和残余结构的影响。结果, 尽管经过了20年的研究，但一些重要的问题，如静电相互作用的方式和程度 调节蛋白质稳定性的问题还没有得到充分的回答。缺乏准确的手段 预测静电贡献不仅阻碍了对蛋白质稳定性的基本理解，而且 这也为推进蛋白质计算设计设置了障碍。本申请的具体目的 1)通过进一步发展连续发展，促进对pH依赖现象的原子水平的研究 恒定pH分子动力学和相关方法，以及2)改进定量预测 并通过对几个模型系统的研究，详细了解了静电对蛋白质稳定性的调节作用 包括核糖体L9蛋白的N-末端结构域、绒毛蛋白头饰亚区、亮氨酸拉链、 以及外周亚基结合域的中温、高温和超高温变体。建议数 方法的发展将为社区提供强大的工具来研究广泛的静电 生物学中的现象。从应用研究中获得的见解预计将改变 以天然为中心的蛋白质稳定性和功能范式，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.