蛋白质的二维紫外光谱模拟
发布时间：2018-09-19 16:58
【摘要】：结构生物学的基础之一是蛋白质序列与其结构和功能之间的相互关联。有几种技术能够在不同的空间和时间分辨率下对蛋白质结构和动力学行为进行监测。X-射线晶体学能够在原子分辨下探测蛋白质的静态结构,但是这种技术要求研究体系是可结晶的,对于像蛋白质聚集这类感兴趣但不能结晶的体系,X-射线技术则无能为力(同时,X-射线也不能监测蛋白质的动力学行为)。NMR能够在原子分辨的基础上提供三维结构信息,但是这种技术相当复杂和耗时,程序执行设计数据收集、共振归属、抑制产生和最终的结构计算和优化,一个完整的结构检测通常需要耗费几天的时间进行实验操作,同时需要几周的时间对实验数据进行分析,这对于需要快速筛选点突变或者溶液条件的特殊蛋白质是不合适的。多种光谱技术能够被用来研究蛋白质的二级结构,同时能够区分不同的结构单元。它们包括紫外(UV)和红外(IR)吸收,紫外(UV)和红外(IR)圆二色光谱(CD)以及紫外(UV)共振拉曼散射。这些方法的优点是耗费时间短,但是只能提供局部光谱信息,不能够提供关于二级结构的更多精细信息。最近一系列的理论研究表明2DUV光谱在提供蛋白质二级结构信息、研究激子动力学过程以及蛋白质取向和二级结构的定量测量方面有着非常广泛的应用前景。2DUV可以看做是UV吸收和CD光谱的延伸与扩展,在2DUV光谱中,包含了两个频率坐标轴,能够显著增强光谱信息的内容和结构敏感性。2DUV的一个优点是能够避免同位素标记,通过探测蛋白质骨架的nπ*/ππ*电子跃迁(以及两种跃迁之间的耦合),或者使用三种相对稀少的芳香残基(色氨酸(Trp)、酪氨酸(Tyr)和苯丙氨酸(Phe))进行局域结构测量。本论文的一个目标是将2DUV光谱打造成为一种诊断多肽和蛋白质结构和动力学研究的工具。我们希望这种方法在技术上具有直接、高效的特点,同时能够获得更多的有用信息,为蛋白质去折叠的粗糙评估和完整的结构信息之间搭建桥梁,从而能够快速的测定蛋白质的变化或者准备更多涉及结构和动力学研究的样品准备。发色团的电子激发取决于它们周围的电子相互作用,这对于探测局部结构有利。肽键的骨架nπ*/ππ*电子跃迁频率在远紫外(190～250nm)区域,通常被用来探测蛋白质局部二级结构。而具有芳香侧链的氨基酸则在近紫外区域(250-300nm)有着明显的吸收。在蛋白质中,只有三种氨基酸:色氨酸、酪氨酸和苯丙氨酸具有芳香侧链,同时由于芳香氨基酸在蛋白质结构中相当稀有(大致比例为:色氨酸-4%,酪氨酸-3%和苯丙氨酸-1.5%),所以它们可以被用内嵌进局部结构探测而不需要进行同位素标记。理解生物体系的激子动力学行为对于操作其功能具有十分重要的意义。我们将量子力学(QM)和分子动力学(MD)相结合,并使用Trp-cage这一迷你蛋白作为研究对象,研究相干2DNUV光谱在探测激子动力学过程中的应用。由芳香跃迁而来的2DNUV信号受到残基间耦合作用的影响,这决定了激子的传输和能量的弛豫路径。时间演化的2DNUV光谱能够捕获蛋白质重要的结构信息,包括几何结构细节信息和肽键的取向信息。我们使用时间演化2DNUV光谱研究了模型蛋白中结构依赖的激子动力学过程,我们发现激子的传输和能量的弛豫速率取决于蛋白质中几何结构细节和肽键取向等结构参数。这对于研究蛋白质结构以及揭示蛋白质结构-功能之间的关系具有十分重要的意义。同时,我们可以期待2DNUV在蛋白质各向异性和各向同性研究中的应用,这将有助于理解和操作诸如配体结合等生物化学相关相互作用,这对于促进相关的药物设计将提供重要的帮助。定量测量蛋白质取向和二级结构组成对于蛋白质的生物技术应用和疾病治疗都十分重要,同时,这对于光谱研究也是一个巨大的挑战。基于QM/MM理论,我们发现2DLD光谱能够探测蛋白质二级结构单元的取向。此外,通过计算2D光谱中横向ππ*信号与纵向ππ*信号的比率,我们能够获取a-螺旋在蛋白质的含量。二级结构的定量测量则是蛋白质结构分析的重要内容。我们的研究表明2DUV zzzz和2DLD信号能够监测螺旋、折叠以及淀粉样纤维蛋白的取向变化。我们同时建立了不同的取向依赖与不同的结构图案之间的对应关系。与一维光谱相比,2D光谱能够提供更多与取向有关的结构信息,同时具有更高的分辨率。通过分析2DUVzzzz信号并进行方程拟合,我们计算了螺旋结构在蛋白质中所占的比例。定量信息对于描述精确的蛋白质结构图像很有帮助。我们的研究工作可能为淀粉样纤维结构测量和动力学演化过程以及相关的光物理和光化学过程的研究打开了新的研究之门,这是理解和操控它们的功能的基础。
[Abstract]:One of the foundations of structural biology is the correlation between protein sequences and their structures and functions. Several techniques can be used to monitor protein structures and dynamics at different spatial and temporal resolutions. X-ray crystallography can detect the static structure of proteins at atomic resolution, but this technique requires investigation. The system is crystalline, and X-ray technology is powerless for systems that are interested in but unable to crystallize, such as protein aggregation (and X-ray does not monitor the kinetic behavior of proteins). NMR can provide three-dimensional structural information on the basis of atomic resolution, but this technology is complex and time-consuming, and program execution design is time-consuming. Data collection, resonance attribution, suppression generation and final structural calculations and optimization, a complete structural detection usually takes days to carry out the experimental operation, and takes weeks to analyze the experimental data, which is not suitable for the need to quickly screen point mutations or solution conditions for specific proteins. They include ultraviolet (UV) and infrared (IR) absorption, ultraviolet (UV) and infrared (IR) circular dichroism (CD) spectroscopy, and ultraviolet (UV) resonance Raman scattering. These methods are time-consuming, but only provide local spectral information. Recently, a series of theoretical studies have shown that 2D UV spectroscopy has a very wide application prospect in providing information on secondary structure of proteins, studying exciton dynamics and quantitative measurement of protein orientation and secondary structure. One advantage of 2DUV is its ability to avoid isotope labeling by detecting NPI * / pi * electron transitions (and coupling between the two transitions) in the protein skeleton, or by using three relatively rare aromas. Local structure measurements of residues (trp, tyrosine and phenylalanine) have been carried out. One of the objectives of this paper is to develop 2DUV spectroscopy as a tool for diagnosing the structure and kinetics of peptides and proteins. We hope that this method will be technically straightforward and efficient, and that more useful information can be obtained. The excitation of chromophores depends on the interaction of electrons around them, which is beneficial for detecting local structures. In the far ultraviolet (190-250 nm) region, the electron transition frequencies of n * / N * * skeleton are usually used to detect the local secondary structure of proteins, while the amino acids with aromatic side chains have obvious absorption in the near ultraviolet region (250-300 nm). In proteins, only three amino acids: tryptophan, tyrosine and phenylalanine have aromatic side chains. Because aromatic amino acids are very rare in protein structures (roughly tryptophan-4%, tyrosine-3% and phenylalanine-1.5%), they can be detected by embedded local structures without isotope labeling. Understanding the exciton dynamics of biological systems is important for manipulating their functions. We combine quantum mechanics (QM) with molecular dynamics (MD) and study the application of coherent 2DNUV spectroscopy in the detection of exciton dynamics using Trp-cage as a mini-protein. The time-evolution 2DNUV spectroscopy can capture important structural information of proteins, including geometric details and orientation of peptide bonds. We studied the structure-dependent exciton dynamics in model proteins using time-evolution 2DNUV spectroscopy. We found that exciton transport and energy relaxation rates depend on the number of proteins. It is very important to study protein structure and reveal the relationship between protein structure and function. At the same time, we can look forward to the application of 2DNUV in the study of protein anisotropy and isotropy, which will help us understand and manipulate organisms such as ligand binding. Quantitative measurements of protein orientation and secondary structure composition are important for the application of protein biotechnology and disease treatment. At the same time, it is also a great challenge for spectroscopic research. Based on QM/MM theory, we found that 2DLD spectroscopy In addition, by calculating the ratio of transverse and longitudinal pion * signals in 2D spectra, we can obtain the content of a-helix in protein. Quantitative measurement of secondary structure is an important part of protein structure analysis. Our study shows that 2DUV ZZZZZZ and 2DLD signals can be monitored. Helix, folding and orientation change of amyloid fibrin. We also established the corresponding relationship between different orientation dependencies and different structural patterns. Compared with one-dimensional spectra, 2D spectra can provide more orientation-related structural information and have higher resolution. We calculated the proportion of helical structures in proteins. Quantitative information is helpful for describing precise structural images of proteins. Our research work may open the door to new research on amyloid fiber structure measurement, dynamic evolution and related photophysical and photochemical processes. The basis for solving and manipulating their functions.
【学位授予单位】：中国科学技术大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：O657.3;O629.73
[Abstract]:One of the foundations of structural biology is the correlation between protein sequences and their structures and functions. Several techniques can be used to monitor protein structures and dynamics at different spatial and temporal resolutions. X-ray crystallography can detect the static structure of proteins at atomic resolution, but this technique requires investigation. The system is crystalline, and X-ray technology is powerless for systems that are interested in but unable to crystallize, such as protein aggregation (and X-ray does not monitor the kinetic behavior of proteins). NMR can provide three-dimensional structural information on the basis of atomic resolution, but this technology is complex and time-consuming, and program execution design is time-consuming. Data collection, resonance attribution, suppression generation and final structural calculations and optimization, a complete structural detection usually takes days to carry out the experimental operation, and takes weeks to analyze the experimental data, which is not suitable for the need to quickly screen point mutations or solution conditions for specific proteins. They include ultraviolet (UV) and infrared (IR) absorption, ultraviolet (UV) and infrared (IR) circular dichroism (CD) spectroscopy, and ultraviolet (UV) resonance Raman scattering. These methods are time-consuming, but only provide local spectral information. Recently, a series of theoretical studies have shown that 2D UV spectroscopy has a very wide application prospect in providing information on secondary structure of proteins, studying exciton dynamics and quantitative measurement of protein orientation and secondary structure. One advantage of 2DUV is its ability to avoid isotope labeling by detecting NPI * / pi * electron transitions (and coupling between the two transitions) in the protein skeleton, or by using three relatively rare aromas. Local structure measurements of residues (trp, tyrosine and phenylalanine) have been carried out. One of the objectives of this paper is to develop 2DUV spectroscopy as a tool for diagnosing the structure and kinetics of peptides and proteins. We hope that this method will be technically straightforward and efficient, and that more useful information can be obtained. The excitation of chromophores depends on the interaction of electrons around them, which is beneficial for detecting local structures. In the far ultraviolet (190-250 nm) region, the electron transition frequencies of n * / N * * skeleton are usually used to detect the local secondary structure of proteins, while the amino acids with aromatic side chains have obvious absorption in the near ultraviolet region (250-300 nm). In proteins, only three amino acids: tryptophan, tyrosine and phenylalanine have aromatic side chains. Because aromatic amino acids are very rare in protein structures (roughly tryptophan-4%, tyrosine-3% and phenylalanine-1.5%), they can be detected by embedded local structures without isotope labeling. Understanding the exciton dynamics of biological systems is important for manipulating their functions. We combine quantum mechanics (QM) with molecular dynamics (MD) and study the application of coherent 2DNUV spectroscopy in the detection of exciton dynamics using Trp-cage as a mini-protein. The time-evolution 2DNUV spectroscopy can capture important structural information of proteins, including geometric details and orientation of peptide bonds. We studied the structure-dependent exciton dynamics in model proteins using time-evolution 2DNUV spectroscopy. We found that exciton transport and energy relaxation rates depend on the number of proteins. It is very important to study protein structure and reveal the relationship between protein structure and function. At the same time, we can look forward to the application of 2DNUV in the study of protein anisotropy and isotropy, which will help us understand and manipulate organisms such as ligand binding. Quantitative measurements of protein orientation and secondary structure composition are important for the application of protein biotechnology and disease treatment. At the same time, it is also a great challenge for spectroscopic research. Based on QM/MM theory, we found that 2DLD spectroscopy In addition, by calculating the ratio of transverse and longitudinal pion * signals in 2D spectra, we can obtain the content of a-helix in protein. Quantitative measurement of secondary structure is an important part of protein structure analysis. Our study shows that 2DUV ZZZZZZ and 2DLD signals can be monitored. Helix, folding and orientation change of amyloid fibrin. We also established the corresponding relationship between different orientation dependencies and different structural patterns. Compared with one-dimensional spectra, 2D spectra can provide more orientation-related structural information and have higher resolution. We calculated the proportion of helical structures in proteins. Quantitative information is helpful for describing precise structural images of proteins. Our research work may open the door to new research on amyloid fiber structure measurement, dynamic evolution and related photophysical and photochemical processes. The basis for solving and manipulating their functions.
【学位授予单位】：中国科学技术大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：O657.3;O629.73
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