Computational Studies of Membrane Proteins Based on NMR Observables

基于 NMR 可观测值的膜蛋白计算研究

• 批准号: 1157677
• 负责人: Wonpil Im
• 金额: $ 56.28万
• 依托单位: University of Kansas Center for Research Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1157677&HistoricalAwards=false
• 关键词: Computational; Studies; Membrane; Proteins; Based

Membrane proteins play important roles in many vital cellular processes, such as transmembrane (TM) signaling, transport of ions and small molecules, energy transduction, and cell-cell recognition. This project seeks to acquire novel insights into membrane proteins, dynamics and interactions with lipids, which are important determinants of their functions. Despite impressive successes of X-ray crystallography in structure determination of membrane proteins with multiple TM helices, it is still challenging to obtain the structural information of membrane proteins with one or a few TM helices. These membrane proteins are abundant and often involved in important TM-induced signaling and regulation through formation of hetero-/homo-oligomers. Although difficulties exist in obtaining inter-helix distance information by measuring long-range NOEs for these membrane proteins, their structures are determinable by measuring various orientational NMR observables, such as chemical shift anisotropy (CSA) and dipolar coupling (DC) in solid-state NMR (ssNMR), and residual dipolar coupling (RDC) in solution NMR experiments. However, the present NMR structure determination methods for membrane proteins are not able to extract important dynamics and interaction information that possibly are embedded in time- and ensemble-averaged NMR observables. This project will fill the knowledge gap by utilizing the orientational NMR restraint potentials to use the available experimental observables with additional benefits from the realistic molecular dynamics simulation of membrane systems. The ssNMR ensemble dynamics technique recently developed in the investigator's research group will make it possible to extract the intrinsic dynamics and/or distinct configurations of different domains. Comparisons of the free energy calculation results along key TM helix motions with NMR observable-based structure refinement and ensemble dynamics results will offer cross-validation of membrane proteins, structures and dynamics from different approaches. This research with selected complex membrane protein models will enhance our understanding of structure, dynamics, and function of membrane proteins with one or a few TM helices and their oligomers.This project also seeks to foster synergistic scientific research and education by providing reliable and general computational methods to students and researchers in the membrane protein NMR field and other disciplines through the CHARMM-GUI website (www.charmm-gui.org), which has been developed in the investigator's research group. In addition to graduate student training, undergraduate students will be involved in the proposed research to promote their interests in computational biophysics. In addition, this project will raise the scientific literacy of the public through the publication of research results and workshop participation. Finally, this project will help further development of our summer program called "Summer Research Program for HIgh School Students (SURPHISS) in Molecular Modeling and Simulations" by supporting graduate and undergraduate students interested in the education of high school students.

膜蛋白在许多重要的细胞过程中发挥重要作用，如跨膜（TM）信号传导、离子和小分子的转运、能量转导和细胞-细胞识别。该项目旨在获得膜蛋白，动力学和与脂质的相互作用的新见解，这是其功能的重要决定因素。尽管X射线晶体学在多个TM螺旋的膜蛋白的结构测定方面取得了令人印象深刻的成功，但获得具有一个或几个TM螺旋的膜蛋白的结构信息仍然具有挑战性。这些膜蛋白是丰富的，通常参与重要的TM诱导的信号和调节，通过形成异源/同源寡聚体。虽然在获得螺旋间距离的信息，通过测量这些膜蛋白的长程NOE存在困难，它们的结构是可确定的，通过测量各种取向NMR观测，如化学位移各向异性（CSA）和偶极耦合（DC）在固态NMR（ssNMR），和残余偶极耦合（RDC）在溶液NMR实验。然而，目前的膜蛋白的NMR结构测定方法不能提取重要的动力学和相互作用的信息，可能是嵌入在时间和整体平均NMR观测。该项目将通过利用取向NMR约束势来使用现有的实验观测值，并从膜系统的现实分子动力学模拟中获得额外的好处，从而填补知识空白。ssNMR系综动力学技术最近开发的研究人员的研究小组将有可能提取的内在动力学和/或不同的配置不同的域。比较自由能计算结果沿着关键TM螺旋运动与NMR可观测的结构细化和系综动力学结果将提供交叉验证膜蛋白，结构和动力学从不同的方法。本研究通过选定的复杂膜蛋白模型，加深对具有一个或几个TM螺旋的膜蛋白及其寡聚体的结构、动力学和功能的理解，并通过研究者课题组开发的CHARMM-GUI网站（www.charmm-gui.org），为膜蛋白NMR领域和其他学科的学生和研究人员提供可靠的通用计算方法，促进协同科学研究和教育。除了研究生培训，本科生将参与拟议的研究，以促进他们在计算生物物理学的兴趣。此外，该项目将通过出版研究成果和参加讲习班来提高公众的科学素养。最后，该项目将通过支持对高中生教育感兴趣的研究生和本科生，帮助进一步发展我们的暑期项目，称为“高中生暑期研究计划（SURPHISS）分子建模和模拟”。