Electrostatic modulation of protein stability and folding

描述（由申请人提供）：静电现象在生物过程中普遍存在，如蛋白质折叠、结合和催化。我们目前的知识静电对蛋白质稳定性的影响主要来自蛋白质工程实验和理论研究，使用静态结构的泊松-玻尔兹曼计算。然而，虽然宏观测量往往不能从别人隔离静电效应，理论预测的准确性是有限的，缺乏明确的治疗蛋白质介电响应，构象动力学和影响，由于在未折叠状态下的残留结构。因此，尽管二十年的研究，重要的问题，如如何以及在何种程度上静电相互作用调节蛋白质的稳定性还没有得到充分的回答。缺乏准确的手段来预测静电的贡献，不仅阻碍了蛋白质稳定性的基本理解，但也提出了一个路障，推进计算蛋白质的设计。本申请的具体目的是1）通过进一步发展连续恒定pH分子动力学和相关方法来推进pH依赖性现象的原子水平研究，以及2）通过研究包括核糖体L9蛋白的N-末端结构域、绒毛蛋白头片段亚结构域、亮氨酸拉链和meso-的几个模型系统来改进蛋白质稳定性的静电调节的定量预测和详细理解，外周亚单位结合域的嗜热和超嗜热变体。所提出的方法的发展将为研究生物学中广泛的静电现象提供强大的工具。在应用研究中获得的见解有望改变蛋白质稳定性和功能的天然中心范式，并转变基于静态结构的蛋白质静电学观点。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.