蛋白質(zhì)的二維紫外光譜模擬
發(fā)布時(shí)間：2018-09-19 16:58
【摘要】：結(jié)構(gòu)生物學(xué)的基礎(chǔ)之一是蛋白質(zhì)序列與其結(jié)構(gòu)和功能之間的相互關(guān)聯(lián)。有幾種技術(shù)能夠在不同的空間和時(shí)間分辨率下對蛋白質(zhì)結(jié)構(gòu)和動力學(xué)行為進(jìn)行監(jiān)測。X-射線晶體學(xué)能夠在原子分辨下探測蛋白質(zhì)的靜態(tài)結(jié)構(gòu),但是這種技術(shù)要求研究體系是可結(jié)晶的,對于像蛋白質(zhì)聚集這類感興趣但不能結(jié)晶的體系,X-射線技術(shù)則無能為力(同時(shí),X-射線也不能監(jiān)測蛋白質(zhì)的動力學(xué)行為)。NMR能夠在原子分辨的基礎(chǔ)上提供三維結(jié)構(gòu)信息,但是這種技術(shù)相當(dāng)復(fù)雜和耗時(shí),程序執(zhí)行設(shè)計(jì)數(shù)據(jù)收集、共振歸屬、抑制產(chǎn)生和最終的結(jié)構(gòu)計(jì)算和優(yōu)化,一個(gè)完整的結(jié)構(gòu)檢測通常需要耗費(fèi)幾天的時(shí)間進(jìn)行實(shí)驗(yàn)操作,同時(shí)需要幾周的時(shí)間對實(shí)驗(yàn)數(shù)據(jù)進(jìn)行分析,這對于需要快速篩選點(diǎn)突變或者溶液條件的特殊蛋白質(zhì)是不合適的。多種光譜技術(shù)能夠被用來研究蛋白質(zhì)的二級結(jié)構(gòu),同時(shí)能夠區(qū)分不同的結(jié)構(gòu)單元。它們包括紫外(UV)和紅外(IR)吸收,紫外(UV)和紅外(IR)圓二色光譜(CD)以及紫外(UV)共振拉曼散射。這些方法的優(yōu)點(diǎn)是耗費(fèi)時(shí)間短,但是只能提供局部光譜信息,不能夠提供關(guān)于二級結(jié)構(gòu)的更多精細(xì)信息。最近一系列的理論研究表明2DUV光譜在提供蛋白質(zhì)二級結(jié)構(gòu)信息、研究激子動力學(xué)過程以及蛋白質(zhì)取向和二級結(jié)構(gòu)的定量測量方面有著非常廣泛的應(yīng)用前景。2DUV可以看做是UV吸收和CD光譜的延伸與擴(kuò)展,在2DUV光譜中,包含了兩個(gè)頻率坐標(biāo)軸,能夠顯著增強(qiáng)光譜信息的內(nèi)容和結(jié)構(gòu)敏感性。2DUV的一個(gè)優(yōu)點(diǎn)是能夠避免同位素標(biāo)記,通過探測蛋白質(zhì)骨架的nπ*/ππ*電子躍遷(以及兩種躍遷之間的耦合),或者使用三種相對稀少的芳香殘基(色氨酸(Trp)、酪氨酸(Tyr)和苯丙氨酸(Phe))進(jìn)行局域結(jié)構(gòu)測量。本論文的一個(gè)目標(biāo)是將2DUV光譜打造成為一種診斷多肽和蛋白質(zhì)結(jié)構(gòu)和動力學(xué)研究的工具。我們希望這種方法在技術(shù)上具有直接、高效的特點(diǎn),同時(shí)能夠獲得更多的有用信息,為蛋白質(zhì)去折疊的粗糙評估和完整的結(jié)構(gòu)信息之間搭建橋梁,從而能夠快速的測定蛋白質(zhì)的變化或者準(zhǔn)備更多涉及結(jié)構(gòu)和動力學(xué)研究的樣品準(zhǔn)備。發(fā)色團(tuán)的電子激發(fā)取決于它們周圍的電子相互作用,這對于探測局部結(jié)構(gòu)有利。肽鍵的骨架nπ*/ππ*電子躍遷頻率在遠(yuǎn)紫外(190～250nm)區(qū)域,通常被用來探測蛋白質(zhì)局部二級結(jié)構(gòu)。而具有芳香側(cè)鏈的氨基酸則在近紫外區(qū)域(250-300nm)有著明顯的吸收。在蛋白質(zhì)中,只有三種氨基酸:色氨酸、酪氨酸和苯丙氨酸具有芳香側(cè)鏈,同時(shí)由于芳香氨基酸在蛋白質(zhì)結(jié)構(gòu)中相當(dāng)稀有(大致比例為:色氨酸-4%,酪氨酸-3%和苯丙氨酸-1.5%),所以它們可以被用內(nèi)嵌進(jìn)局部結(jié)構(gòu)探測而不需要進(jìn)行同位素標(biāo)記。理解生物體系的激子動力學(xué)行為對于操作其功能具有十分重要的意義。我們將量子力學(xué)(QM)和分子動力學(xué)(MD)相結(jié)合,并使用Trp-cage這一迷你蛋白作為研究對象,研究相干2DNUV光譜在探測激子動力學(xué)過程中的應(yīng)用。由芳香躍遷而來的2DNUV信號受到殘基間耦合作用的影響,這決定了激子的傳輸和能量的弛豫路徑。時(shí)間演化的2DNUV光譜能夠捕獲蛋白質(zhì)重要的結(jié)構(gòu)信息,包括幾何結(jié)構(gòu)細(xì)節(jié)信息和肽鍵的取向信息。我們使用時(shí)間演化2DNUV光譜研究了模型蛋白中結(jié)構(gòu)依賴的激子動力學(xué)過程,我們發(fā)現(xiàn)激子的傳輸和能量的弛豫速率取決于蛋白質(zhì)中幾何結(jié)構(gòu)細(xì)節(jié)和肽鍵取向等結(jié)構(gòu)參數(shù)。這對于研究蛋白質(zhì)結(jié)構(gòu)以及揭示蛋白質(zhì)結(jié)構(gòu)-功能之間的關(guān)系具有十分重要的意義。同時(shí),我們可以期待2DNUV在蛋白質(zhì)各向異性和各向同性研究中的應(yīng)用,這將有助于理解和操作諸如配體結(jié)合等生物化學(xué)相關(guān)相互作用,這對于促進(jìn)相關(guān)的藥物設(shè)計(jì)將提供重要的幫助。定量測量蛋白質(zhì)取向和二級結(jié)構(gòu)組成對于蛋白質(zhì)的生物技術(shù)應(yīng)用和疾病治療都十分重要,同時(shí),這對于光譜研究也是一個(gè)巨大的挑戰(zhàn)�；赒M/MM理論,我們發(fā)現(xiàn)2DLD光譜能夠探測蛋白質(zhì)二級結(jié)構(gòu)單元的取向。此外,通過計(jì)算2D光譜中橫向ππ*信號與縱向ππ*信號的比率,我們能夠獲取a-螺旋在蛋白質(zhì)的含量。二級結(jié)構(gòu)的定量測量則是蛋白質(zhì)結(jié)構(gòu)分析的重要內(nèi)容。我們的研究表明2DUV zzzz和2DLD信號能夠監(jiān)測螺旋、折疊以及淀粉樣纖維蛋白的取向變化。我們同時(shí)建立了不同的取向依賴與不同的結(jié)構(gòu)圖案之間的對應(yīng)關(guān)系。與一維光譜相比,2D光譜能夠提供更多與取向有關(guān)的結(jié)構(gòu)信息,同時(shí)具有更高的分辨率。通過分析2DUVzzzz信號并進(jìn)行方程擬合,我們計(jì)算了螺旋結(jié)構(gòu)在蛋白質(zhì)中所占的比例。定量信息對于描述精確的蛋白質(zhì)結(jié)構(gòu)圖像很有幫助。我們的研究工作可能為淀粉樣纖維結(jié)構(gòu)測量和動力學(xué)演化過程以及相關(guān)的光物理和光化學(xué)過程的研究打開了新的研究之門,這是理解和操控它們的功能的基礎(chǔ)。
[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.
【學(xué)位授予單位】：中國科學(xué)技術(shù)大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2017
【分類號】：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.
【學(xué)位授予單位】：中國科學(xué)技術(shù)大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2017
【分類號】：O657.3;O629.73
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