Computational Studies of Membrane Proteins Based on NMR Observables

膜蛋白在许多重要的细胞过程中起着重要的作用，如跨膜信号传导、离子和小分子的运输、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射线晶体学在确定具有多个TM螺旋的膜蛋白结构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。这些膜蛋白含量丰富，通常通过异质/同源寡聚物的形成参与重要的tm诱导信号传导和调控。尽管通过测量这些膜蛋白的远程noe来获得螺旋间距离信息存在困难，但它们的结构可以通过测量各种定向核磁共振观测来确定，例如固态核磁共振（ssNMR）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，目前膜蛋白的核磁共振结构测定方法不能提取重要的动力学和相互作用信息，这些信息可能嵌入在时间和集合平均核磁共振观测值中。该项目将通过利用定向核磁共振约束电位来利用现有的实验观察结果，并从膜系统的实际分子动力学模拟中获得额外的好处，从而填补知识空白。该研究小组最近开发的ssNMR集成动力学技术将使提取不同域的内在动力学和/或不同构型成为可能。将沿关键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精化和系综动力学结果进行比较，将从不同的角度对膜蛋白、结构和动力学进行交叉验证。本研究选择的复杂膜蛋白模型将增强我们对具有一个或几个TM螺旋及其低聚物的膜蛋白的结构，动力学和功能的理解。该项目还寻求通过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，从而促进协同的科学研究和教育。该网站由研究者的研究小组开发。除了研究生训练外，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，该项目将通过发表研究成果和参与研讨会来提高公众的科学素养。最后，这个项目将通过支持对高中学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“高中生分子建模和模拟暑期研究项目”。

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.