结构基因组学中的衍射相位问题

简要介绍了结构基因组学研究中,用于测定蛋白质结构的X射线分析在解决衍射相位问题方面的最新进展。     

X射线辐射引起的apo-GAPDH酶晶体衍射谱的反常变化

apo-GAPDH晶体X射线衍射实验发现,有些衍射谱的强度随着X射线照射时间增加而出现反常变化.联系蛋白质构象的可变性做了初步探讨.     

蛋白质分子的构象运动及其功能意义

 <正> 自从五十年代末成功地运用X射线衍射分析技术测定肌红蛋白分子的晶体结构以来,我们关于蛋白质在三维水平的结构及其与功能关系的认识,已经历了两个阶段。第一个阶段包括60年代初至70年代中期。在这一期间,解决了蛋白质晶体结构测定方法的一般化问题,使以同晶置换法为主的一套X射线衍射分析技术成为研究生物大分子三维结构的成熟手段,给     

固氮酶晶体学研究进展

生物大分子的功能取决于它的空间结构.X射线衍射分析是获得生物大分子结构信息的常用方法.本文对固氮酶晶体的生长及其X射线衍射分析的主要进展简要地进行了介绍和评论.最后展望了今后的发展及问题.     

黄原胶与丙烯酰胺接枝共聚反应的研究

以过硫酸铵为引发剂,在N2气保护下,研究了黄原胶(XG)与丙烯酰胺(AM)的接枝共聚反应.考察了单体浓度、引发剂浓度、反应温度和反应时间等因素对接枝率及接枝效率的影响,探讨了过硫酸铵引发黄原胶接枝丙烯酰胺共聚反应的基本规律.采用红外光谱(FT-IR)、X射线粉末衍射(XRD)对接枝共聚物的结构进行研究,用热重分析(TGA)法表征了产物的热性能,并初步探讨了接枝机理.     

应用于生物科学研究的一门新技术——中子散射分析技术

近十年来,中子散射分析技术已经发展成为研究物质结构的重要方法,最近又把这个方法应用到生物科学研究中去。研究生物的细微结构,一般采用电子显微镜和X射线衍射技术。应用电子显微镜,来检查细胞、细胞的组成部分。用X射线衍射技术来研究蛋白质等生物大分子内的原子空间排列。可是在这两个范畴之间,尚有一个空隙:细胞的某些部分,用电子显微镜检测嫌小,用X射线衍射研究原子细节嫌大。而这个中间水平的结构资料,却又往往非常重要。象核糖体就是一个例子。核糖体是一切细胞里都有的、非常重要的细胞器,它由55个蛋白质分子和三个RNA分子所组成。如果不首先了解这些蛋白质、RNA分子是如何进行装配的,我们几乎无法了解核糖体在蛋白质合成中如何执行其任务。可是核糖体在电子显微镜图象中,只能是一个轮廓,从这些图象中获取的结构资料是     

铜(II)-酪氨酸螯合物合成与分析

研究了铜(II)-酪氨酸螯合物的合成方法,探讨了影响合成工艺的主要因素,确定了原料配比、pH值、温度、反应时间等最佳合成条件.采用X射线衍射光谱对螯合物进行了表征,结果表明铜(II)能与酪氨酸形成螯合物.     

蛋白质二级结构的真空紫外圆二色性研究

利用同步辐射真空紫外圆二色谱仪和特制的样品池,测定溶液中蛋白质的真空紫外圆二色谱,测定波长低至175nm,并应用一种新的计算法分析计算了蛋白质5种二级结构的含量,所得结果与用X射线衍射法测定的结果一致.讨论了获得好的真空紫外圆二色谱的几个重要因素.结果表明,真空紫外圆二色法是目前测定溶液中蛋白质二级结构的较好方法之一.     

FS36作为新型人源Hsp90抑制剂的发现（英文）

热休克蛋白90(Hsp90)通过对几百种蛋白质底物(客户蛋白质)进行合理的折叠、成熟其构象并且激活,在肿瘤细胞的生长和繁殖中发挥重要作用.因此,Hsp90成为非常有吸引力、有前途的抗肿瘤药物靶点,并且超过20种抑制剂已经进入临床实验阶段.我们在这里设计并合成了一个小分子抑制剂:FS36.收集了Hsp90~N-FS36复合物晶体结构的X射线衍射实验数据.高分辨率X射线晶体结构表明,FS36在ATP结合位点上与Hsp90~N相互作用,并且FS36可能替代核苷酸与Hsp90~N结合.FS36和Hsp90~N的复合物晶体结构和相互作用为后期设计和优化新型抗肿瘤药物奠定基础.     

生物学研究中利用强X射线源的衍射技术

X射线衍射技术应用于生物学研究,六十年代主要是采用固定靶或旋转靶X射线源,研究蛋白质和核酸等的静态晶体结构,以从分子解剖学的角度认识有关的生命现象。但是,这种技术方法对于较复杂的生物体系和生命现象中发生在分予水平的瞬时动态过程,诸如酶促反应巾酶分子结构变化与功能的关系,肌肉收缩过程巾肌动蛋白和肌球蛋白的变化规律等分了生理学变化,却无从观祭。因此,近年来开始利用电子同步加速器的强X射线作为衍射光源,来研究肌肉运动和酶反应等复杂体系的动态过程。目前,国际上已建立了若干可供生物学研究应用的电子同步加速器强X射线源。     

The mechanism of beta-hematin formation in acetate solution. Parallels between hemozoin formation and biomineralization processes

Formation of beta-hematin in acidic acetate solution has been investigated using quantitative infrared spectroscopy, X-ray diffraction, and scanning and transmission electron microscopy. The process occurs via rapid precipitation of amorphous (or possibly nanocrystalline) hematin, followed by slow conversion to crystalline beta-hematin. Definitive evidence that the reaction occurs during incubation in acetate medium, rather than during the drying stage, is provided by X-ray diffraction and infrared spectroscopy of the wet material. The reaction follows a sigmoidal function indicative of a process of nucleation and growth and was modeled using the Avrami equation. Reaction rates and the dimensionality of growth (as indicated by the value of the Avrami constant) are strongly influenced by stirring rate. The reaction follows Arrhenius behavior, and there is a strong dependence of both the rate constant and the Avrami constant on acetate concentration. Acetate may act as a phase transfer catalyst, solubilizing hematin and facilitating its redeposition as beta-hematin. The pH dependence of the process indicates that only the monoprotonated species of hematin is active in forming beta-hematin. The formation of beta-hematin closely parallels many mineralization processes, and this suggests that hemozoin formation may be a unique biomineralization process. Inferences are drawn with respect to the formation of hemozoin in vivo.     

Mechanistic studies on the binding of Acid Yellow 99 on coir pith

The interaction of Acid Yellow 99 (AY 99) with coir pith has been investigated in aqueous medium to understand the mechanism of adsorption and explore the potentiality of this biomass towards controlling pollution resulting from textile dyes. The obtained results establish that one gram of coir pith can adsorb 442.13 mg of AY 99. The adsorption process is found to be a function of pH of the solution, the optimum pH value being 2.0. The process follows Langmuir-Freundlich dual isotherm model. Scanning electron microscopic analysis demonstrates that on dye adsorption the biomass develops uneven and irregular surface. X-ray diffraction study indicates incorporation of the dye into the micropores and macropores of the adsorbent and thereby enhancing its degree of crystallinity. The results of Fourier transform infrared (FTIR) spectroscopy and chemical modification of the functional groups establish that binding of AY 99 on coir pith occurs through electrostatic and complexation reaction.     

Protein titration in the crystal state.

Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model system. By altering only one physico-chemical parameter in a controlled manner, we are able to quantify the structural changes induced in the protein. Atomic resolution X-ray diffraction data were collected for crystals at six pH* values ranging from 5.2 to 8.8, and the six independently refined structures reveal subtle, albeit well-defined variations directly related to the pH titration of the protein. The deprotonation of the catalytic His12 residue is clearly evident in the electron density maps, confirming the reaction mechanism proposed by earlier enzymatic and structural studies. The concerted structural changes observed in the regions remote from the active-site point to an adaptation of the protein structure to the changes in the physico-chemical environment. Analysis of the stereochemistry of the six structures provided accurate estimates of p Kavalues of most of the histidine residues. This study gives further evidence for the advantage of atomic resolution X-ray crystallographic analyses for revealing small but significant structural changes which provide clues to the function of a biological macromolecule.     

Maturation dynamics of a viral capsid: visualization of transitional intermediate states

Typical of DNA bacteriophages and herpesviruses, HK97 assembles in two stages: polymerization and maturation. First, capsid protein polymerizes into closed shells; then, these precursors mature into larger, stabler particles. Maturation is initiated by proteolysis, producing a metastable particle primed for expansion-the major structural transition. We induced expansion in vitro by acidic pH and monitored the resulting changes by time-resolved X-ray diffraction and cryo-electron microscopy. The transition, which is not synchronized over the population, proceeds in a series of stochastically triggered subtransitions. Three distinct intermediates were identified, which are comparable to transitional states in protein folding. The intermediates' structures reveal the molecular events occurring during expansion. Integrated into a movie (see Dynamic Visualization below), they show capsid maturation as a dynamic process.     

Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy

The atomic resolution structure of Pf1 coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution is compared to the structures previously determined by X-ray fiber and neutron diffraction, the structure of its membrane-bound form, and the structure of fd coat protein. These structural comparisons provide insights into several biological properties, differences between class I and class II filamentous bacteriophages, and the assembly process. The six N-terminal amino acid residues adopt an unusual "double hook" conformation on the outside of the bacteriophage particle. The solid-state NMR results indicate that at 30 degrees C, some of the coat protein subunits assume a single, fully structured conformation, and some have a few mobile residues that provide a break between two helical segments, in agreement with structural models from X-ray fiber and neutron diffraction, respectively. The atomic resolution structure determined by solid-state NMR for residues 7-14 and 18-46, which excludes the N-terminal double hook and the break between the helical segments, but encompasses more than 80% of the backbone including the distinct kink at residue 29, agrees with that determined by X-ray fiber diffraction with an RMSD value of 2.0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers.     

Eucaryotic DNA Replication Complex: Study of Structure and Function Using the Affinity Modification Technique

Eucaryotic DNA replication complex is now one of the most intensively studied subjects of molecular biology and biochemistry. In addition to detailed studies on the structures and functions of individual DNA polymerases involved in this process, other enzymes and protein factors are also given much attention. The structures and functions of proteins in the replication complexes are studied by various approaches, including X-ray diffraction analysis. At present, this approach provides sufficient information about the structures and functions of individual biopolymers and their complexes with ligands. However, this approach is unsuitable for studies on proteins, which cannot be cloned and isolated in amounts sufficient for X-ray diffraction analysis. Moreover, this approach is inapplicable for studies on multicomponent systems, such as DNA replication and repair complexes. Furthermore, data of X-ray diffraction analysis virtually never characterize the variety of dynamic interactions in enzymatic systems. Affinity modification is an alternative and rather successful approach for studies on structure-functional organization of supramolecular structures. This approach can be used for studies on individual enzymes and their complexes with substrates and also on systems consisting of numerous interacting proteins and nucleic acids. The purpose of this review is to analyze the available data obtained by affinity modification studies on the eucaryotic replication complex.     

Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X-ray structure analysis

Glutaraldehyde has been used for several decades as an effective crosslinking agent for many applications including sample fixation for microscopy, enzyme and cell immobilization, and stabilization of protein crystals. Despite of its common use as a crosslinking agent, the mechanism and chemistry involved in glutaraldehyde crosslinking reaction is not yet fully understood. Here we describe feasibility study and results obtained from a new approach to investigate the process of protein crystals stabilization by glutaraldehyde crosslinking. It involves exposure of a model protein crystal (Lysozyme) to glutaraldehyde in alkaline or acidic pH for different incubation periods and reaction arrest by medium exchange with crystallization medium to remove unbound glutaraldehyde. The crystals were subsequently incubated in diluted buffer affecting dissolution of un-crosslinked crystals. Samples from the resulting solution were subjected to protein composition analysis by gel electrophoresis and mass spectroscopy while crosslinked, dissolution resistant crystals were subjected to high resolution X-ray structural analysis. Data from gel electrophoresis indicated that the crosslinking process starts at specific preferable crosslinking site by lysozyme dimer formation, for both acidic and alkaline pH values. These dimer formations were followed by trimer and tetramer formations leading eventually to dissolution resistant crystals. The crosslinking initiation site and the end products obtained from glutaraldehyde crosslinking in both pH ranges resulted from reactions between lysine residues of neighboring protein molecules and the polymeric form of glutaraldehyde. Reaction rate was much faster at alkaline pH. Different reaction end products, indicating different reaction mechanisms, were identified for crosslinking taking place under alkaline or acidic conditions.     

Absorption of x-radiation by single crystals of proteins containing labile metal components: the determination of the number of iron atoms within the central core of ferritin

The number of metal atoms contained within a displaceable inorganic component of a metalloprotein was determined by considering X-ray absorption by single crystal samples of holo- and apo-proteins. Since this method is non-destructive, it can be used to determine the number of metal atoms associated with the molecules forming the crystal actually used for X-ray diffraction data collection and subsequent structure solution. The method has been applied to the iron storage protein ferritin, isolated from horse spleen, to give a reliable estimate of the average iron content of the ferritin molecules within the crystal. This value, of around 2000 iron atoms per molecule is consistent with that found for a typical ferritin preparation in solution and suggests non-selectivity of the crystallisation process for ferritin in terms of molecular iron content.     

X-ray diffraction studies on chromatophore membrane from photosynthetic bacteria. I. Diffraction pattern of the photoreaction unit isolated from Rhodospirillum rubrum chromatophore and some characteristics of the structure

The X-ray diffraction pattern from chromatophore membranes of a photosynthetic bacterium, Rhodospirillum rubrum, indicates that a highly organized protein assembly exists in the membrane. The X-ray scatterer was solubilized from chromatophores by a mixture of cholate and deoxycholate. The basic component was identified as the photoreaction unit, which consists of light-harvesting bacteriochlorophyll proteins and a reaction center. The radial autocorrelation function, calculated directly from the X-ray intensity dats, made it possible to deduce certain structural features of the X-ray scatterer. 1. The maximum dimension of the X-ray scatterer is estimated to be 110-130 A. 2. The arrangement of the units in the chromatophore membrane is random. 3. Protein molecules in the unit form a rigid structure, being arranged mutually in fixed positions to give a distinct X-ray diffraction pattern. 4. The most probable structure is one which has rotational symmetry.     

Sedimentation equilibrium measurements of the intermediate-size tobacco mosaic virus protein polymers

Short-column sedimentation equilibrium methods have been applied for the first time to tobacco mosaic virus (TMV) protein (0.1 M ionic strength orthophosphate) at pH 6.5 and at pH 7.0 to estimate molecular weights. Previous sedimentation velocity experiments at pH 6.5, 20 degrees C have led to the conclusion that the major boundary with an S0(20),w value of 24.4 +/- 0.1 S consists of a distribution of polymers which are mainly three-turn, 48-51-subunit helical rod aggregates. The directly measured z-average molecular weights together with sedimentation velocity data are entirely consistent with this assignment of a three-turn aggregate. Molecular weights have also been determined under two conditions where a large mass fraction of the protein sediments with an S0(20),w value of 20.3 +/- 0.2 S. At pH 6.5, 6-8 degrees C, the aggregates in this boundary are metastable and correspond to 50-60% of the preparation. At pH 7.0, 20 degrees C at equilibrium, 65-75% of the protein sediments at 20.3 S. The 20.3S boundary is very similar under both conditions and is interpreted as being composed of a distribution of protein aggregates centered about 39 +/- 2 subunits. This result is important in the interpretation of previous kinetic measurements of TMV self-assembly. The current view is that the 34-subunit structure of TMV protein, in the form of a cylindrical disk which is made up of two 17-subunit layers and has been characterized in single-crystal X-ray diffraction studies, plays a central role in the initial binding steps with RNA. The present results are not consistent with the view that there is a significant concentration of the TMV protein disk structure in solution under the usual conditions of TMV self-assembly.