针对膜蛋白结构解析的核磁共振方法发展和应用
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摘要
细胞膜为细胞构筑一道物质自由出入的屏障,保证胞内各种生化反应能在一个相对稳定的环境中有序运行。膜蛋白在胞内生命活动与周围环境发生信息、物质与能量交换过程中起着重要作用,但因样品稳定性及研究方法的限制,其结构和功能的研究进展缓慢。本论文主要目的就是发展优化膜蛋白样品制备和基于核磁共振的膜蛋白结构研究的方法。
本文用两章分别对膜蛋白及核磁共振做简要描述。第一章中简要介绍膜蛋白的种类、功能以及结构研究现状。第二章介绍了核磁基本理论以及液体和固体核磁中常用于蛋白质结构和功能研究的一些方法,包括一些特殊的同位素标记技术。
第三章中我们应用传统液体核磁共振和电子顺磁共振相结合的方法解析了一个结核分枝杆菌的“外膜蛋白”Rv0899的结构。之前的相关功能研究表明,Rv0899是一个外膜通道蛋白,从外界摄取诸如丝氨酸和葡萄糖一类的小分子水溶性营养物质,同时还对菌体适应外界酸性环境具有重要作用。但我们通过对其去垢剂和水溶液中的三维结构研究显示Rv0899只是以一个跨膜螺旋锚定在外膜上的单体蛋白,不太可能是一个分子通道。通过核磁滴定和等温量热滴定方法发现Rv0899可与Zn2+有较强的结合,所以我们推测Rv0899可能对Zn2+摄入有一定辅助作用。
第四章中发展基于交叉极化原理的高效CA-CO重耦方法并应用到全标记的蛋白样品中。膜蛋白质在样品中与去垢剂或磷脂结合后总体分子量增大,在溶液中的运动速度减慢,弛豫速率增大,液体核磁方法很难检测到信号。固体核磁一般直接研究固态样品,不存在此类问题。但固体核磁发展起步较晚,还需发展更好的硬件和更多适用于蛋白质研究的脉冲程序。基于交叉极化原理的高效CA-CO重耦方法传递效率在CO和CA原子感受到的有效磁场之和等于两倍样品转速时达到最大。经过优化,此方法使得CO和CA之间的传递效率超过30%,比之前常用的自旋扩散方法高出70%左右。我们将其应用到具体的实验中,发展出一套完整的用于蛋白质主链归属的二维和三维固体核磁谱。
在第五章中我们发展了一种基于气相色谱的去垢剂定量分析方法。大多数蛋白质结构研究过程中都需要对其进行纯化,去垢剂可模拟磷脂双分子层的双亲性环境,对膜蛋白维持功能和稳定结构具有重要作用。此前一直没有快速有效的方法来对膜蛋白样品中的去垢剂进行定量分析。我们用气相色谱对去垢剂进行定量分析,并用此方法监测了膜蛋白浓缩过程中去垢剂的浓度,发现其损失的规律,找到一种简易的移除膜蛋白样品中多余去垢剂的方法。
第六章中对膜蛋白结构研究的现状和核磁研究膜蛋白结构和功能的方向进行简单分析。截止到目前,被解析的膜蛋白结构仅占所有解析的蛋白质结构的1.5%左右,未来发展空间很大。因去垢剂导致的弛豫速率加快的问题,使得液体核磁共振不太适于膜蛋白结构的研究,而魔角旋转的固体核磁共振才是以后发展的方向。同时,很多膜蛋白正常功能的行使需要磷脂分子的协助,所以如何在磷脂双分子层或原位细胞膜环境中研究膜蛋白结构和功能也将是未来发展的一个很重要的方向。
All cells and organelles are contained within a hydrophobic lipid bilayer membrane to get a stable environment for vital function. A wide variety of biological processes for communications between cells and surrounding environment are controlled by the integral membrane proteins. However, due to partially hydrophobic surfaces and lack of stability, membrane proteins continue to be among the most challenging targets in structural biology. Here, we will apply some new methods for membrane protein purification and NMR based structure biology study.
A brief review of function and current structure studies of membrane proteins is introduced in Chapter1. Then a brief review of the basic theory and protein study methods of Nuclear Magnetic Resonance (NMR) are introduced in Chapter2.
In Chapter3, we apply the combined use of solution NMR and EPR (Electron Paramagnetic Resonance) methods for the structural analysis of a Mycobacterium tuberculosis "outer membrane protein". Rv0899functions as a pore-forming protein and the deletion of this gene impairs the uptake of some water-soluble substances, such as serine, glucose, and glycerol. It has also been shown to play a part in low-pH environment adaption, which may play a part in pathogenic mycobacteria overcoming the host's defense mechanisms. Here, biochemical and structural data indicated that Rv0899is a monomeric membrane-anchoring protein with two separate domains, rather than an oligomeric pore. Using NMR chemical shift perturbation and isothermal calorimetric titration assays, we show that Rv0899was able to interact with Zn2+ions, which may indicate a role in the process of Zn2+acquisition.
In Chapter4, an efficient dipolar-based band-selective homonuclear CO-CA cross-polarization transfer method was applied in solid state NMR spectrum of protonated proteins. Due to increased relaxation rate, NMR signal is more broad and undetectable for detergent bound membrane protein in solution buffer. So we turned our attention to Solid state NMR which used for the immobilized sample study. The most efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate. More than30%of the CO magnetization can be transferred to CA using BSH-CP, and the transfer efficiency is increased by up to70%compared to the most frequently applied spin diffusion (PDSD) procedure. This BSH recoupling method has been adapted for a complete set of sensitivity-enhanced protein sequential resonance assignment experiment.
In Chapter5, A novel and reliable gas chromatography method was developed to separate and quantify detergents frequently used in membrane protein samples. In membrane protein biochemical and structural studies, detergents are always used to mimic membrane environment and maintain functional, stable conformation of membrane proteins in the absence of lipid bilayers. However, detergent concentration, esp. molar ratio of membrane protein to detergent is usually unknown. To remove excessive detergents, a filtered centrifugation using Centricon tubes was applied. Detergent concentrations in the upper and lower fraction of the Centricon tube were measured after each round of centrifugation. Coupling of GC-MS-SIM and detergent removal by Centricon tubes, detergents concentration, esp. molar ratio of membrane protein to detergent could be controlled, which will expedite membrane protein structural and biochemical studies.
In Chapter6, a brief review of the current and the future structure investigation of membrane protein is introduce. As of Sep.2013less than1.5%of protein structures determined were membrane proteins despite being20-30%of the total proteome and significant functional importance. Detergents used in protein purification procedures leads to slower molecular tumbling, impeding the application of solution-state NMR. Solid-state magic-angle spinning NMR spectroscopy could be an emerging method for membrane-protein structural biology that can overcome these technical problems. Meanwhile, the functional diversity of membrane proteins is determined not only by themselves, but also by their interactions with membranes. People should pay more attention on how to analysis membrane protein structure and function in lipids or its native membrane in the future.
本文用两章分别对膜蛋白及核磁共振做简要描述。第一章中简要介绍膜蛋白的种类、功能以及结构研究现状。第二章介绍了核磁基本理论以及液体和固体核磁中常用于蛋白质结构和功能研究的一些方法,包括一些特殊的同位素标记技术。
第三章中我们应用传统液体核磁共振和电子顺磁共振相结合的方法解析了一个结核分枝杆菌的“外膜蛋白”Rv0899的结构。之前的相关功能研究表明,Rv0899是一个外膜通道蛋白,从外界摄取诸如丝氨酸和葡萄糖一类的小分子水溶性营养物质,同时还对菌体适应外界酸性环境具有重要作用。但我们通过对其去垢剂和水溶液中的三维结构研究显示Rv0899只是以一个跨膜螺旋锚定在外膜上的单体蛋白,不太可能是一个分子通道。通过核磁滴定和等温量热滴定方法发现Rv0899可与Zn2+有较强的结合,所以我们推测Rv0899可能对Zn2+摄入有一定辅助作用。
第四章中发展基于交叉极化原理的高效CA-CO重耦方法并应用到全标记的蛋白样品中。膜蛋白质在样品中与去垢剂或磷脂结合后总体分子量增大,在溶液中的运动速度减慢,弛豫速率增大,液体核磁方法很难检测到信号。固体核磁一般直接研究固态样品,不存在此类问题。但固体核磁发展起步较晚,还需发展更好的硬件和更多适用于蛋白质研究的脉冲程序。基于交叉极化原理的高效CA-CO重耦方法传递效率在CO和CA原子感受到的有效磁场之和等于两倍样品转速时达到最大。经过优化,此方法使得CO和CA之间的传递效率超过30%,比之前常用的自旋扩散方法高出70%左右。我们将其应用到具体的实验中,发展出一套完整的用于蛋白质主链归属的二维和三维固体核磁谱。
在第五章中我们发展了一种基于气相色谱的去垢剂定量分析方法。大多数蛋白质结构研究过程中都需要对其进行纯化,去垢剂可模拟磷脂双分子层的双亲性环境,对膜蛋白维持功能和稳定结构具有重要作用。此前一直没有快速有效的方法来对膜蛋白样品中的去垢剂进行定量分析。我们用气相色谱对去垢剂进行定量分析,并用此方法监测了膜蛋白浓缩过程中去垢剂的浓度,发现其损失的规律,找到一种简易的移除膜蛋白样品中多余去垢剂的方法。
第六章中对膜蛋白结构研究的现状和核磁研究膜蛋白结构和功能的方向进行简单分析。截止到目前,被解析的膜蛋白结构仅占所有解析的蛋白质结构的1.5%左右,未来发展空间很大。因去垢剂导致的弛豫速率加快的问题,使得液体核磁共振不太适于膜蛋白结构的研究,而魔角旋转的固体核磁共振才是以后发展的方向。同时,很多膜蛋白正常功能的行使需要磷脂分子的协助,所以如何在磷脂双分子层或原位细胞膜环境中研究膜蛋白结构和功能也将是未来发展的一个很重要的方向。
All cells and organelles are contained within a hydrophobic lipid bilayer membrane to get a stable environment for vital function. A wide variety of biological processes for communications between cells and surrounding environment are controlled by the integral membrane proteins. However, due to partially hydrophobic surfaces and lack of stability, membrane proteins continue to be among the most challenging targets in structural biology. Here, we will apply some new methods for membrane protein purification and NMR based structure biology study.
A brief review of function and current structure studies of membrane proteins is introduced in Chapter1. Then a brief review of the basic theory and protein study methods of Nuclear Magnetic Resonance (NMR) are introduced in Chapter2.
In Chapter3, we apply the combined use of solution NMR and EPR (Electron Paramagnetic Resonance) methods for the structural analysis of a Mycobacterium tuberculosis "outer membrane protein". Rv0899functions as a pore-forming protein and the deletion of this gene impairs the uptake of some water-soluble substances, such as serine, glucose, and glycerol. It has also been shown to play a part in low-pH environment adaption, which may play a part in pathogenic mycobacteria overcoming the host's defense mechanisms. Here, biochemical and structural data indicated that Rv0899is a monomeric membrane-anchoring protein with two separate domains, rather than an oligomeric pore. Using NMR chemical shift perturbation and isothermal calorimetric titration assays, we show that Rv0899was able to interact with Zn2+ions, which may indicate a role in the process of Zn2+acquisition.
In Chapter4, an efficient dipolar-based band-selective homonuclear CO-CA cross-polarization transfer method was applied in solid state NMR spectrum of protonated proteins. Due to increased relaxation rate, NMR signal is more broad and undetectable for detergent bound membrane protein in solution buffer. So we turned our attention to Solid state NMR which used for the immobilized sample study. The most efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate. More than30%of the CO magnetization can be transferred to CA using BSH-CP, and the transfer efficiency is increased by up to70%compared to the most frequently applied spin diffusion (PDSD) procedure. This BSH recoupling method has been adapted for a complete set of sensitivity-enhanced protein sequential resonance assignment experiment.
In Chapter5, A novel and reliable gas chromatography method was developed to separate and quantify detergents frequently used in membrane protein samples. In membrane protein biochemical and structural studies, detergents are always used to mimic membrane environment and maintain functional, stable conformation of membrane proteins in the absence of lipid bilayers. However, detergent concentration, esp. molar ratio of membrane protein to detergent is usually unknown. To remove excessive detergents, a filtered centrifugation using Centricon tubes was applied. Detergent concentrations in the upper and lower fraction of the Centricon tube were measured after each round of centrifugation. Coupling of GC-MS-SIM and detergent removal by Centricon tubes, detergents concentration, esp. molar ratio of membrane protein to detergent could be controlled, which will expedite membrane protein structural and biochemical studies.
In Chapter6, a brief review of the current and the future structure investigation of membrane protein is introduce. As of Sep.2013less than1.5%of protein structures determined were membrane proteins despite being20-30%of the total proteome and significant functional importance. Detergents used in protein purification procedures leads to slower molecular tumbling, impeding the application of solution-state NMR. Solid-state magic-angle spinning NMR spectroscopy could be an emerging method for membrane-protein structural biology that can overcome these technical problems. Meanwhile, the functional diversity of membrane proteins is determined not only by themselves, but also by their interactions with membranes. People should pay more attention on how to analysis membrane protein structure and function in lipids or its native membrane in the future.
引文
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