Computational Studies of Membrane Proteins Based on NMR Observables

膜蛋白在许多重要的细胞过程中发挥着重要的作用，如跨膜信号、离子和小分子的运输、能量转导和细胞-细胞识别。这个项目寻求对膜蛋白、动力学以及与脂类的相互作用获得新的见解，这些都是它们功能的重要决定因素。尽管X射线结晶学在确定具有多个TM螺旋的膜蛋白的结构方面取得了令人印象深刻的成功，但获得具有一个或多个TM螺旋的膜蛋白的结构信息仍然是具有挑战性的。这些膜蛋白含量丰富，经常通过形成异源/同源寡聚体参与TM诱导的重要信号和调控。虽然通过测量这些膜蛋白的长程NOE来获得螺旋间距信息存在困难，但它们的结构可以通过测量各种取向的核磁共振观测数据来确定，例如固体核磁共振中的化学位移各向异性(CSA)和偶极耦合(DC)，以及溶液核磁共振实验中的残余偶极耦合(RDC)。然而，目前膜蛋白质的核磁共振结构测定方法不能提取可能包含在时间平均和系综平均的核磁共振观测数据中的重要的动力学和相互作用信息。这个项目将通过利用取向核磁共振约束势来利用现有的实验观测数据来填补知识空白，并从膜系统的真实分子动力学模拟中获得额外的好处。研究者研究小组最近开发的单核磁共振系综动力学技术将使提取不同结构域的本征动力学和/或不同构型成为可能。将关键TM螺旋运动的自由能计算结果与基于核磁共振观测的结构改进和系综动力学结果进行比较，将从不同的方法提供膜蛋白质、结构和动力学的交叉验证。这项精选的复合膜蛋白模型的研究将加深我们对含有一个或几个TM螺旋及其低聚物的膜蛋白的结构、动力学和功能的理解。本项目还试图通过研究小组开发的CHARMM-GUI网站(www.charmm-gui.org)为膜蛋白核磁共振领域和其他学科的学生和研究人员提供可靠和通用的计算方法，从而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，以促进他们对计算生物物理学的兴趣。此外，该项目还将通过发表研究成果和参加讲习班来提高公众的科学素养。最后，这个项目将通过支持对高中生教育感兴趣的研究生和本科生，进一步发展我们的暑期项目，名为“高中生暑期研究项目(SURPHISS)分子建模和模拟”。

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.