Electrostatic modulation of protein stability and folding

蛋白质稳定性和折叠的静电调节

基本信息

批准号：
8549265
负责人：
Jana Shen
金额：
$ 28.14万
依托单位：
UNIVERSITY OF MARYLAND BALTIMORE
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-09-01 至 2016-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8549265
关键词：
Address Benchmarking Binding Biological Models Biological Process Biology Catalysis Charge Communities Computer software Computing Methodologies Coupled Data Development Disease Electrostatics Environment Goals Homologous Gene Hybrids Ions Knowledge Leucine Zippers Measurement Methodology Methods N-terminal Nature Peptide Fragments Peripheral Postdoctoral Fellow Protein Engineering Proteins Protocols documentation Protons Psychological Techniques Qualifying Research Residual state Role Scheme Sodium Chloride Solvents Structure Study models Surface Techniques Testing Theoretical Studies Titrations Validation Variant Work base computer cluster computing resources design driving force graduate student improved insight method development molecular dynamics novel novel strategies post-doctoral training protein folding research study response ribosomal protein L9 simulation theories tool villin

项目摘要

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.

静电现象在生物学过程中无处不在，例如蛋白质折叠，结合和催化。我们目前对静电对蛋白质稳定性影响的了解主要来自蛋白质使用基于静态结构的Poisson-Boltzmann计算的工程实验和理论研究。但是，尽管宏观测量通常无法与其他人分离静电效应，但理论预测的准确性受到蛋白质介电反应的明确处理的限制，构象动力和效应是由于未折叠状态的残留结构引起的。因此，尽管进行了二十年的研究，但重要的问题，例如如何以及在何种程度上静电相互作用调节蛋白质稳定性尚未得到充分回答。缺乏准确的手段为了预测静电贡献，不仅会阻碍对蛋白质稳定性的基本理解，而且还可以还为推进计算蛋白设计的障碍构成了障碍。此应用程序的具体目的是1）通过进一步发展连续的pH依赖性现象的原子水平研究恒定的pH分子动力学和相关方法，以及2）改善定量预测通过研究多种模型系统，对蛋白质稳定性的静电调节的详细理解包括核糖体L9蛋白的N末端结构域，villin头饰子域，亮氨酸拉链，以及外周亚基结合结构域的中，热疗和热疗变体。提议方法开发将为社区提供强大的工具，用于研究广泛的静电生物学现象。申请研究中获得的见解将改变蛋白质稳定性和功能的天然为中心的范式，并改变了基于静态结构的视图蛋白质静电。它们还将帮助建立计算蛋白设计的一般原则。