Mechanisms of Membrane Proteins Through in situ Modeling

通过原位建模研究膜蛋白的机制

• 批准号: 8509706
• 负责人: Klaus Schulten
• 金额: $ 27.91万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-05-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8509706
• 关键词: Achievement; Address; Affect; Atomic Force Microscopy; Automobile Driving; Binding; Cell physiology; Complement; Complex; Computer Simulation; Computing Methodologies; Coupled; Cryoelectron Microscopy; Data; Development; Drug Targeting; Electron Microscopy; Equilibrium; Goals; Human Genome; In Situ; Individual; Knowledge; Lipids; Measurement; Measures; Membrane; Membrane Proteins; Methodology; Modeling; Molecular; Molecular Machines; Pathway interactions; Pharmacotherapy; Process; Protein Biosynthesis; Proteins; Resolution; Ribosomes; Source; Staging; Structure; Therapeutic Intervention; Time; X-Ray Crystallography; data integration; design; disease-causing mutation; knowledge base; models and simulation; molecular dynamics; next generation; novel; polypeptide; protein folding; protein structure; research study; simulation; tool

DESCRIPTION (provided by applicant): Membrane proteins comprise nearly a third of the human genome and over half of all drug targets, yet re- main relatively poorly characterized with less than 1% of all resolved protein structures representing them. Furthermore, the mechanisms of membrane protein development are not well understood, particularly with respect to their folding and membrane insertion. This lack of understanding is especially critical given that the majority of known disease-causing mutations in membrane proteins affect not their function but rather how they develop. To remedy the dearth of structural and developmental information on membrane proteins, the PIs aim to determine new structures and detailed models covering processes relevant to membrane protein folding, insertion, and assembly. By employing advanced computational modeling tools and molecular dynamics simulations, three key deficiencies will be targeted. Through newly resolved structural data and very long (microsecond) simulations, the means by which a nascent membrane protein is oriented and directed from the ribosome, a large molecular machine that synthesizes all proteins, to the translocon, a membrane-bound channel that catalyzes membrane insertion, will be determined. Additionally, the energetics governing insertion of a membrane protein into the membrane as well as its complement, extraction from the membrane, will be quantified and compared with experiments addressing the same insertion and extraction processes. In particular, a close connection to atomic force microscopy experiments will permit the identification and verification of the individual molecular interactions that stabilize a given protein's structure. Finally, the folding propensity of membrane proteins at stages early in their development will be measured, an aspect which is suspected to determine the efficiency of their targeting to the membrane insertion pathway. These measurements will utilize new structures of developmental intermediates solved through the integration of data from multiple experimental sources, including X-ray crystallography and electron microscopy. The unique structures and quantitative models generated through successful achievement of the stated aims will provide the unprecedented atomic-scale detail required both for a complete understanding of membrane protein development and for the design of novel pharmacotherapies.

描述（由申请人提供）：膜蛋白占人类基因组的近三分之一和所有药物靶点的一半以上，但其特征仍然相对较差，代表它们的所有解析蛋白质结构中不到 1%。此外，膜蛋白发育的机制尚不清楚，特别是在它们的折叠和膜插入方面。鉴于大多数已知的膜蛋白致病突变不影响其功能，而是影响其发育方式，因此缺乏了解尤其重要。为了弥补膜蛋白结构和发育信息的缺乏，PI 旨在确定涵盖与膜蛋白折叠、插入和组装相关过程的新结构和详细模型。通过采用先进的计算建模工具和分子动力学模拟，将解决三个关键缺陷。通过新解析的结构数据和非常长（微秒）的模拟，新生膜蛋白从核糖体（合成所有蛋白质的大型分子机器）定向和引导到易位子（催化膜的膜结合通道）插入，将被确定。此外，控制膜蛋白插入膜及其补体、从膜中提取的能量学将被量化，并与涉及相同插入和提取过程的实验进行比较。特别是，与原子力显微镜实验的密切联系将允许识别和验证稳定给定蛋白质结构的单个分子相互作用。最后，将测量膜蛋白在其发育早期阶段的折叠倾向，这一方面被怀疑确定其靶向膜插入途径的效率。这些测量将利用通过整合来自多个实验来源（包括 X 射线晶体学和电子显微镜）的数据来解决的开发中间体的新结构。通过成功实现既定目标而产生的独特结构和定量模型将为全面了解膜蛋白的发展和设计新型药物疗法提供所需的前所未有的原子尺度细节。