激光拉曼光谱在蛋白质构象研究中的应用和进展

激光拉曼光谱法被公认为是研究生物大分子的结构、动力学和功能的有效方法。近年来拉曼光谱在蛋白质构象研究中的最新进展,涉及到拉曼光谱在非折叠蛋白质、蛋白质装配的特征描述,拉曼晶体学在实时监控蛋白质单晶中化学变化等方面的应用。另外,介绍了蛋白质拉曼光谱分析在生物技术中的应用现状。并对拉曼光谱技术在蛋白质等生物大分子领域中的研究前景做了进一步的展望。     

振动光谱与蛋白质二级结构

红外光谱和拉曼光谱(统称分子振动光谱)应用于蛋白质构象研究经历了定性阶段和半定量阶段.近5年来,去卷积和二阶导教等提高分辨率方法以及曲线拟合方法的应用,使得振动光谱在定量计算蛋白质二级结构和监测蛋白质构象变化等方面取得突破性的进展,进入了定量化的阶段.     

多炔彩虹探针在生物学研究中的应用与展望

多炔彩虹探针(Carbow)是一种基于聚炔支架的超多路复用拉曼探针,通过受激拉曼散射(stimulated Raman scattering, SRS)显微技术可以对振动频率不同的20余种彩虹探针分子进行区分。利用探针分子的特异性修饰, Carbow可以对活细胞内的多种细胞器,以及蛋白质和脂质等大分子进行同时成像。多炔分子的高光稳定性与低细胞毒性结合SRS的多通道光学检测将使Carbow在生物学领域具有巨大的应用潜力。该文综述了基于SRS平台的拉曼标记技术和Carbow的设计合成原理与优势,并对Carbow在活细胞中不同细胞器的特异性标记成像以及在细胞与组织免疫染色、细胞分选与高通量分析中的生物学应用进行总结。最后,对拉曼标记技术的提升改进及其在植物学领域中的应用进行了展望。     

SERS标记方法在生化分析中的应用

表面增强拉曼散射(SERS)标记方法结合现代生物标记方法与SERS光谱技术,使吸附到金或银等贵金属表面的标记分子的拉曼信号显著增强,并将其作为标记示踪信号,具有生物兼容性好、灵敏度高、分子特征性强和快速简便等优点,已成为新颖的标记示踪技术的研究热点之一。本文综述近年来SERS标记技术应用于基因分析、蛋白质检测、微生物检测、肿瘤靶向和小分子物质的最新进展,着重介绍蛋白质和小分子物质的检测,并展望了今后的发展方向。     

非标记表面增强拉曼光谱在DNA检测中的应用

表面增强拉曼光谱(SERS)是一种超灵敏的生化分析技术,已经被广泛运用于细胞、核酸、蛋白质等生物分子的检测,在生物医学领域表现出了巨大的应用潜力。近年来,将表面增强拉曼光谱技术应用于遗传物质DNA的精准检测,引起了人们广泛的关注。本文简要叙述了表面增强拉曼光谱技术的基本原理及其在DNA检测中的优势,主要介绍了非标记的DNA-SERS检测应用进展,其中包括本项目组的相关工作。研究表明,非标记DNA-SERS技术有望成为一种快速、准确的临床诊断方式。     

多孔β—TCP生物陶瓷植入兔股骨后的拉曼光谱

以５１４．５ｎｍ和６３２．８ｎｍ激光激发,采用显微拉曼光谱和近红外傅里叶变换拉曼光谱分别研究了磷酸三钙（β－ＴＣＰ）生物陶瓷植入兔股骨后陶瓷、界面和兔股骨的拉曼光谱。对其拉曼光谱特征频率进行了初步的归属,叙述了可见光和近红外光谱的优缺点。在植入区和界面的拉曼光谱中,磷酸钙、胶原、蛋白质和脂类的拉曼特征频率同时出现,说明除磷酸钙外,还含有胶原、蛋白质和脂类,他们是有机骨基质主要组成。实验结果表明,生     

正常和癌变胃粘膜组织的共焦拉曼光谱初探

目的:分析研究胃正常和癌变粘膜组织的拉曼光谱特征,为拉曼光谱应用于胃癌的临床检测诊断奠定基础。方法:收集胃镜检查中活检的19例正常和12例癌变胃粘膜组织标本,采用785 nm激发光拉曼光谱仪进行拉曼光谱采集。比较分析胃正常和癌变粘膜组织的拉曼光谱特征差异并研究其区分正常和癌变组织的价值。结果:1)特征峰1 098 cm-1、1 444 cm-1、1 555 cm-1、1 660 cm-1等在胃癌组织中发生了移位,平均位移(2.57±1.28)cm-1,以红移为主;2)癌变组织中相对峰强比I1087 cm-1/I1207 cm-1≥1.87,其区别胃癌和正常胃粘膜组织的准确率、灵敏度和特异度分别为87.1%、83.3%、89.5%;3)癌组织中增加了表征蛋白质的特征峰1 262 cm-1、1 586 cm-1,但同时减少了表征蛋白质和脂质特征峰1 172 cm-1。结论:拉曼光谱不仅可以准确区分正常和癌变,而且可以探索癌变相关的分子生化改变。拉曼光谱在胃癌的跟踪发现和检测诊断中具有良好前景。     

苯并(a)芘诱导的肺细胞癌变过程中时间异质性的拉曼光谱分析

目的 肺癌在生物学特性、基因组变异、增殖速度及化疗响应方面的时间异质性,构成了对有效治疗的显著阻碍。肺癌时间异质性的复杂性,结合其空间异质性,为研究带来了极大挑战。本文将为肺癌研究开辟新的方向,有助于更深入地理解肺癌的时间异质性,从而提升对肺癌的治疗成功率。方法 应用拉曼光谱显微技术作为监测肺癌细胞生物分子组成实时变化的有力工具,揭示了疾病的时间异质性。通过拉曼光谱与多元统计分析的结合,对苯并(a)芘处理后人类肺上皮细胞的生物分子变化进行了细致观察。结果 随时间推移,核酸、脂质、蛋白质及类胡萝卜素含量呈现下降趋势,而葡萄糖浓度上升。这些变化模式暗示,苯并(a)芘可导致遗传物质结构损伤、促进脂质过氧化、干扰蛋白质代谢、降低类胡萝卜素生成,并改变葡萄糖代谢路径。运用拉曼光谱技术,以实时、无侵入性、非破坏性的方式监控肺癌细胞内的生物分子动态,进而阐明其关键分子特性。结论 本项研究深化了对肺癌演进的认识,并为发展个性化治疗策略提供支持,助力提升患者的临床治疗效果。     

基于密度泛函理论方法的核酸碱基拉曼光谱研究

核酸碱基是核酸的重要组成部分,而拉曼光谱是研究分子结构的一种重要技术,利用拉曼光谱对核酸碱基分子进行研究对于研究核酸大分子的结构变化,以及核酸分子与小分子之间的作用具有重要的意义.本研究以表征核酸碱基的拉曼光谱为目的,利用密度泛函理论(density functional theory,DFT)的方法优化腺嘌呤、鸟嘌呤、胞嘧啶、胸腺嘧啶和尿嘧啶的分子结构,对这5种核酸碱基的分子内化学键振动进行了量化计算并获得了理论拉曼光谱结果.利用计算结果对实验获得的碱基的固体拉曼光谱进行了表征,并且结合前人的研究结果对每种碱基的一些重要特征拉曼谱峰进行了细致的阐释,为进一步利用拉曼光谱研究核酸分子的结构信息奠定了理论基础.     

拉曼光谱分析技术在细胞生物学研究中的应用进展

细胞是生物体结构和功能的基本单位,自被发现以来新的研究方法不断涌现。单细胞拉曼光谱能提供细胞内核酸、蛋白质、脂质含量等大量信息,可在不损伤细胞的条件下实时动态地监测细胞分子结构变化,亦可获得细胞的“分子指纹”,具有敏感性高、实时检测、活样品不需固定或染色、不损伤细胞等众多特点。近年来国内外研究者将拉曼光谱应用于细胞药物处理、细胞水平疾病诊断、单细胞生命活动监测、亚细胞结构等研究,取得了不同程度的进展。随着研究的深入,拉曼光谱分析技术必将在干细胞,癌症研究、细胞分选、药物筛选等领域大有作为。     

The importance of silica type for reverse-phase protein separations

Various large-pore-diameter silicas have been coated with n-alkylchlorosilanes and tested for efficacy in protein separation. The optimal silica has been characterized for loading and column-length effects by means of resolution, load capacity, and desorption tests. The mechanism of interaction between protein and stationary phase is discussed. Theoretical plate values determined for small, unretained molecules are found to be noncorrelative to protein resolution. A test mixture is proposed for comparing the ability of commercial columns to resolve proteins.     

On the influence of pigment-protein interactions on energy transfer processes in photosynthetic membrane structures. 3. The FMO complex of Chlorobium tepidum at high pressure

The low-temperature absorption spectra of the Chlorobium tepidum FMO bacteriochlorophyll-protein complex at various pressures have been calculated within the framework of mini-exciton theory. The dependences of the Qy transition energies of the monomeric pigments on pressure have been found by means of functional minimization. This functional includes the parameters of both theoretical and experimental absorption spectra at low temperatures and various pressures. The dependences obtained are compared with those derived for the exciton transition energies, which have been obtained by deconvoluting absorption spectra with seven Gaussian components at each pressure. The pressure increase has been shown to result in the increased coupling energy between both the pigment molecules themselves and pigments and amino acid residues. The pigment molecules capable of binding histidines and water molecules have been shown to have the greatest and smallest responses to increased pressure, respectively. The couplings of Bchl molecules with the surrounding amino acid residues have been shown to change both the exciton delocalization index and the exciton distribution between the pigment molecules within the protein subunit; the increased pressure does not change these parameters significantly.     

Discovery and synthesis of novel benzofurazan derivatives as inhibitors of influenza A virus

The identification of a novel hit compound inhibitor of the protein–protein interaction between the influenza RNA-polymerase PA and PB1 subunits has been accomplished by means of high-throughput screening. A small family of structurally related molecules has been synthesized and biologically evaluated with most of the compounds showing micromolar potency of inhibition against viral replication.     

Chemical methods of protein synthesis and modification.

Chemical and recombinant methods have continued to complement one another in the synthesis of protein analogues. Chemical methods remain particularly valuable when non-coded modifications are to be introduced, although it has been accepted since the commercialization of semisynthetic human insulin that they can also be used effectively for coded changes, in certain cases. The main objective of all such operations is not methodological, but is the production of molecules for practical use and further study. This goal has been reached frequently by chemical means during the past year.     

Modeling Intercellular Transfer of Biomolecules Through Tunneling Nanotubes

Tunneling nanotubes (TNTs) have previosly been observed as long and thin transient structures forming between cells and intercellular protein transfer through them has been experimentally verified. It is hypothesized that this may be a physiologically important means of cell–cell communication. This paper attempts to give a simple model for the rates of transfer of molecules across these TNTs at different distances. We describe the transfer of both cytosolic and membrane bound molecules between neighboring populations of cells and argue how the lifetime of the TNT, the diffusion rate, distance between cells, and the size of the molecules may affect their transfer. The model described makes certain predictions and opens a number of questions to be explored experimentally.     

Characterization of wild-type and mutant M13 gene V proteins by means of 1H-NMR

Recording of good quality NMR spectra of the single-stranded DNA binding protein gene V of the bacteriophage M13 is hindered by a specific protein aggregation effect. Conditions are described for which NMR spectra of the protein can best be recorded. The aromatic part of the spectrum has been reinvestigated by means of two-dimensional total correlation spectroscopy. Sequence-specific assignments were obtained for all of the aromatic amino acid residues with the help of a series of single-site mutant proteins. The solution properties of the mutants of the aromatic amino acid residues have been fully investigated. It has been shown that, for these proteins, either none or only local changes occur compared to the wild-type molecule. Spin-labeled oligonucleotide-binding studies of wild-type and mutant gene V proteins indicate that tyrosine 26 and phenylalanine 73 are the only aromatic residues involved in binding to short stretches of single-stranded DNA. The degree of aggregation of wild-type gene V protein is dependent on both the total protein and salt concentration. The data obtained suggest the occurrence of specific protein-protein interactions between dimeric gene V protein molecules in which the tyrosine residue at position 41 is involved. This hypothesis is further strengthened by the observation that the solubility of tyrosine 41 mutants of gene V protein is significantly higher than that of the wild-type protein. The discovery of the so-called 'solubility' mutants of M13 gene V protein has finally made it possible to study the solution structure of gene V protein and its interaction with single-stranded DNA by means of two-dimensional NMR.     

Environment of tryptophan side chains in proteins

Although relatively rare, the tryptophan residue (Trp), with its large hydrophobic surface, has a unique role in the folded structure and the binding site of many proteins, and its fluorescence properties make it very useful in studying the structures and dynamics of protein molecules in solution. An analysis has been made of its environment and the geometry of its interaction with neighbors using 719 Trp residues in 180 different protein structures. The distribution of the number of partners interacting with the Trp aromatic ring shows a peak at 6 (considering protein residues only) and 8 (including water and substrate molecules also). The means of the solvent-accessible surface areas of the ring show an exponential decrease with the increase in the number of partners; this relationship can be used to assess the efficiency of packing of residues around Trp. Various residues exhibit different propensities of binding the Trp side chain. The aromatic residues, Met and Pro have high values, whereas the smaller and polar-chain residues have weaker propensities. Most of the interactions are with residues far away in sequence, indicating the importance of Trp in stabilizing the tertiary structure. Of all the ring atoms NE1 shows the highest number of interactions, both along the edge (hydrogen bonding) as well as along the face. Various weak but specific interactions, engendering stability to the protein structure, have been identified.     

Optical investigation of the electron transfer protein azurin-gold nanoparticle system

The hybrid system obtained by conjugating the protein azurin, which is a very stable and well-described protein showing a unique interplay among its electron transfer and optical properties, with 20-nm sized gold nanoparticles has been investigated. Binding of azurin molecules to gold nanoparticle surface results in the red shift of the nanoparticle resonance plasmon band and in the quenching of the azurin single tryptophan fluorescence signal. These findings together with the estimate of the hydrodynamic radius of the composite, obtained by means of Dynamic Light Scattering, are consistent with the formation of a monolayer of protein molecules, with preserved natural folding, on nanoparticle surface. The fluorescence quenching of azurin bound molecules is explained by an energy transfer from protein to metal surface and it is discussed in terms of the involvement of the Az electron transfer route in the interaction of the protein with the nanoparticle.     

Myelin basic protein interaction with zinc and phosphate: fluorescence studies on the water-soluble form of the protein.

The interaction of myelin basic protein (MBP) with zinc and phosphate ions has been studied by using the emission properties of the single tryptophan residue of the protein (Trp-115). The studies have been carried out by means of both static and time-resolved fluorescence techniques. The addition of either zinc to MBP in the presence of phosphate or phosphate to MBP in the presence of zinc resulted in an increase of fluorescence intensity and a blue shift of the emission maximum wavelength. Furthermore, a concomitant increase in the scattering was also detected. Anisotropy decay experiments demonstrated that these effects are due to the formation of MBP molecules into large aggregates. A possible physiological role for such interaction is discussed.