X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用

自然界中的材料,比如无机材料,有机材料,生物材料等等,均有其独特的物理和化学性质。而材料的性能又与材料的结构息息相关,只有充分了解了材料的结构,才能更加深入的研究材料性质。因此,材料结构的确定在化学、物理、生物等学科中的显得尤为重要。X射线晶体学作为传统的结构解析技术仍然是目前最重要的结构解析手段,但是对于复杂结构,X射线衍射晶体学解析结构也存在一些不足,往往需要其他技术手段相补充才能完成复杂结构的结构解析。电子晶体学虽然起步比X射线晶体学晚,但是,经过近几十年的发展,已经是结构解析领域一个非常重要的手段。本文将主要介绍X射线晶体学结合电子晶体学在复杂无机晶体结构解析中的应用。     

Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein–ligand complex structure analysis

Room-temperature (RT) protein crystallography provides significant information to elucidate protein function under physiological conditions. In particular, contrary to typical binding assays, X-ray crystal structure analysis of a protein–ligand complex can determine the three-dimensional (3D) configuration of its binding site. This allows the development of effective drugs by structure-based and fragment-based (FBDD) drug design. However, RT crystallography and RT crystallography-based protein–ligand complex analyses require the preparation and measurement of numerous crystals to avoid the X-ray radiation damage. Thus, for the application of RT crystallography to protein–ligand complex analysis, the simultaneous preparation of protein–ligand complex crystals and sequential X-ray diffraction measurement remain challenging. Here, we report an RT crystallography technique using a microfluidic protein crystal array device for protein–ligand complex structure analysis. We demonstrate the microfluidic sorting of protein crystals into microwells without any complicated procedures and apparatus, whereby the sorted protein crystals are fixed into microwells and sequentially measured to collect X-ray diffraction data. This is followed by automatic data processing to calculate the 3D protein structure. The microfluidic device allows the high-throughput preparation of the protein–ligand complex solely by the replacement of the microchannel content with the required ligand solution. We determined eight trypsin–ligand complex structures for the proof of concept experiment and found differences in the ligand coordination of the corresponding RT and conventional cryogenic structures. This methodology can be applied to easily obtain more natural structures. Moreover, drug development by FBDD could be more effective using the proposed methodology.

Room temperature protein crystallography and its application to protein–ligand complex structure analysis was demonstrated using a microfluidic protein crystal array device.     

基于透射电子显微镜的沸石分子筛结构研究进展

透射电子显微镜是解析沸石分子筛新结构、 分析结构缺陷和研究活性位点等的有力工具. 应用于分子筛研究的透射电子显微术总体上可以分为图像法和衍射法, 包括透射电子显微镜和扫描透射电子显微图像、 选区电子衍射和三维电子衍射, 通常结合其中的几种方法进行分析. 近年来, 随着电子显微镜硬件性能的不断提升, 特别是球差矫正器的广泛应用及各种适用于分子筛等电子束敏感材料的探测器和图像处理技术的不断革新, 在原子尺度观察分子筛的结构已成为可能. 此外, 利用原位电子显微镜技术研究分子筛的生长和催化反应机理也在逐步展开. 本文按电子显微镜方法分类, 综述了近些年基于电子显微镜的分子筛研究, 包括新结构解析、 手性确认和金属负载等的最新进展.     

Electron Diffraction with the Transmission Electron Microscope as a Phase-Determining Diffractometer—From Spatial Frequency Filtering to the Three-Dimensional Structure Analysis of Ribosomes

Chemists recognize X-ray crystal structure analysis and electron microscopy as powerful methods of analysis. In the last 20 years the basic ideas of X-ray diffraction analysis have been extended to the field of electron microscopy, whereby an image-forming apparatus is converted into an electron diffractometer, and through which an old dream of crystallographers can be realized—the measurement of the phase shift of scattered waves, a prerequisite for the direct calculation of structures. Its most important area of application, like that of the X-ray diffractometer, is in three-dimensional structure analysis—in all fields of science. However, beyond crystallography, aperiodic structures (comparable to crystals with a single unit cell) can also be analyzed three-dimensionally. In this progress report, the development of the first idea (spatial frequency filtering) to the analysis of ribosomal particles is outlined. Attention will be focused primarily on quantitative methods for the measurement of scattered rays, which are also usable beyond the conventional limit of resolution, down to atomic resolution. In the course of this work in 1968, the principle of the three-dimensional analysis of native biological crystal structures using the electron microscope, as worked with today in many laboratories, was developed. In Munich, however, further research focused on the three-dimensional analysis of aperiodic and individual (especially biological) objects. The analysis of 50S-subunits of the procaryotic ribosome of E. coli showed surprisingly good reproducibility of the results (although only within the same orientation), allowing the deduction of almost ideal average model structures from a limited number of particles.     

Internet resources in GPCR modelling1

G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology models of human histamine H1 receptor (HRH1) and thrombin receptor (PAR-1) have been generated which explain the binding mode of the standard antagonists of these receptors and may be useful in designing their novel antagonists.     

Surfaces and interfaces in short-period GaAs/AlAs superlattices

Photoelectron spectroscopy, in particular the angular resolved photoemission excited by ultraviolet radiation (ARUPS), provides the most direct experimental information about the electron structure of crystals, both of the bulk and of the low-index surfaces. The sensitivity of the method, as well as its difficulties, when applied to GaAs/AlAs superlattices are described. The new periodicity of these man-made crystals in the direction of their growth (e.g., in the layer-by-layer growth in molecular beam epitaxy), is responsible for opening of the new energy gaps (so-called minigaps) in the electron energy bands of crystals forming the superlattice. In addition to the well-known confinement of electrons at the valence and conduction band edges in long-period superlattices, the electron confinement to the interfaces has also been found in the vicinity of minigaps in short-period superlattices. The role of this confinement in the intensities of electrons photoemitted from superlattice surfaces is discussed. Superlattices with different thicknesses in the topmost layers represent systems with a simple change of the surface atomic structure. The predictions of one-dimensional models about a change of the surface-state energy within the band gap with a change of crystal potential termination are tested for the ideally terminated (1 0 0) surface of a very thin superlattice (GaAs)₂(AlAs)₂. The results of the energy distributions of photoemitted electrons, calculated in the one-step model of photoemission, show that the ARUPS experimental observation of surface-state shifts should be possible, at least in larger minigaps. The results indicate the possibility of a straightforward tuning of the electronic structure of the superlattice surface by geometrical means.     

Internet resources in GPCR modelling

G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology models of human histamine H1 receptor (HRH1) and thrombin receptor (PAR-1) have been generated which explain the binding mode of the standard antagonists of these receptors and may be useful in designing their novel antagonists.     

Electron microscopic study of dehydration transformations. I. Twin formation and mosaic structure in hematite derived from goethite

A study by means of electron microscopy at high resolution has enabled the analysis of the microstructure of hematite as produced by dehydration from goethite. The apparently “polycrystalline” structure is found to consist of aggregates of well-oriented twin-related hematite crystals, separated by regularly spaced H(001) walls of voids resulting from the loss of water. The material is thus broken up into blocks with sizes smaller than 50 Å. The crystallography of the twinned structure can be analyzed by electron diffraction data and dark-field imaging. These aggregates of hematite crystals provide an ideal mosaic structure. In particular the effect of this mosaic structure on the individual reflections of the diffraction patterns has been analyzed and discussed.     

Light-Induced Structural Changes in the Primary Processes of Photosynthesis: Watching an Enzyme in Action

Continuous illumination and subsequent freezing of the crystal enabled the structure of the light-induced charge-separated state in the reaction center of a photosynthetic bacterium to be obtained by X-ray crystallography. A comparison of the position of the secondary ubiquinone cofactor Q_B in this structure (shown in gray on the right) with that in the “dark” structure (shown in black) reveals substantial motions, which are required for the subsequent electron and proton transfer processes.     

Image processing and lattice determination for three-dimensional nanocrystals

Three-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.     

包埋Ru(bpy)3Cl2非线性光催化薄膜在图像处理中的应用

用sol-gel法以正硅酸乙酯、乙醇和蒸馏水为原料,以盐酸为催化剂,包埋三联吡啶钌[Ru(bpy)₃Cl₂]制备催化 Belousov-Zhabotinsky (BZ)反应的非线性光催化薄膜,并利用紫外分光光度法测定了在薄膜中Ru(bpy)₃Cl₂的包埋量.通过投影图像的方法光激发BZ反应,在包埋Ru(bpy)₃Cl₂的薄膜上产生化学波图像.在薄膜中演化形成的图像具有相当高的图像清晰度.在图像的演化过程中,具有图像反转、边界增强、图像分割等图像处理能力,并可以通过改变BZ反应条件来调控增强某些图像处理能力.     

A low-dose electron diffraction assay for protection of protein structure against damage from drying.

A new assay using low-dose electron diffraction to measure the protection of protein structure against damage from drying is described. When thin single crystals of catalase are dried within water alone, low-dose electron diffraction yields no Bragg spots. Drying within an experimental aqueous solution that permits detection of diffraction spots thereby indicates a positive result, and the extent of these Bragg reflections into the high angle range gives a quantitative measure of the degree of protection. Bragg spots out to 3.73.9 are recorded for drying within 100 mM solutions of the known structure-preserving sugars, sucrose, tannin, and trehalose. The ability of trehalose to maintain native protein structure during drying starts between 10 and 25 mM, and changes only slightly at concentrations above this threshold; with drying in 150-mM trehalose, catalase crystals yield diffraction spots out to 3.7. Drying within the organic nonsugar polymer polyvinylpyrrolidone gives Bragg spots to 4.0. This new assay should be useful to measure the unexamined structure-preserving capabilities of modified sugars, other nonsugars, and mixtures to identify which protective matrix maintains native protein structure to the greatest extent during drying; electron crystallography using that optimal matrix should yield protein structure at improved levels of high resolution.     

Nucleic Acid–Promoted Electron Transfer to Cytochrome c

Gold electrodes were modified with short oligonucleotides in order to facilitate the electron transfer to the small redox protein cytochrome c. DNA immobilization was followed by impedance spectroscopy. The electron exchange was found to be quasi-reversible for both the protein in solution or adsorbed at the electrode surface. Variations of base sequence or structure (DNA-PNA hybrids) of the nucleic acid promoter layer did not significantly change the electron transfer rate constant which was in the range of 0.2–1×10⁻² cm/s. Cytochrome c adsorbed at low ionic strength was coupled to molecules in solution such as superoxide or laccase. Aspects of the DNA conductivity and possibilities for DNA detection are also discussed.     

On the experimental use of light metal salts for negative staining.

All common negative stains are salts of heavy metals. To remedy several technical defects inherent in the use of heavy metal compounds, this study investigates whether salts of the light metals sodium, magnesium, and aluminum can function as negative stains. Screening criteria require aqueous solubility at pH 7.0, formation of a smooth amorphous layer upon drying, and transmission electron microscope imaging of the 87-A (8.7-nm) lattice periodicity in thin catalase crystals. Six of 23 salts evaluated pass all three screens; detection of the protein shell in ferritin macromolecules indicates that light metal salts also provide negative staining of single particle specimens. Appositional contrast is less than that given by heavy metal negative stains; image density can be raised by increasing electron phase contrast and by selecting salts with phosphate or sulfate anions, thereby adding strong scattering from P or S atoms. Low-dose electron diffraction of catalase crystals negatively stained with 200 mM magnesium sulfate shows Bragg spots extending out to 4.4 A. Future experimental use of sodium phosphate buffer and magnesium sulfate for negative staining is anticipated, particularly in designing new cocktail (multicomponent) negative stains able to support and protect protein structure to higher resolution levels than are currently achieved.     

Structural Studies of Transition Metal Compounds

A historical overview will be given on the structural studies on transition metal compounds and their interaction with other fields of coordination chemistry. About three decades have passed away since the structure and absolute configuration of tris(ethylenediamine)cobalt(III) complex ion were determined. At present accumulation of the structural data for isomers has enabled us to understand structural principles of chelate complexes in considerable detail. The energy minimization calculations can predict the detailed geometries of the complexes. Differences in thermodynamic properties between different conformers are well reproduced. Aspherical distribution of 3d electrons in transition metal complexes was detected for the first time in crystals of [Co(NH3)₆][Co(CN)₆] in 1973. Such an accurate electron density study provides important information on the d electrons placed in a ligand field. The high-spin and low-spin states can be distinguished unequivocally. In spite of a very small valence/total electron ratio, the asphericity of 4d and 5d electrons in a ligand field can be detected. The crystal structures of a series of dimeric copper(II) carboxylate adducts of the general formula [Cu(RCOO)₂L]₂ have been determined or redetermined as accurately as possible. The temperature dependent magnetic susceptibility of these crystals indicated that the isolated pairs of Cu(II) ions interact strongly through exchange forces. Molecular orbital calculations revealed that the electron population in the carbon atom of the bridging OCO group plays an important role in determining the strength of the spin superexchange interaction. In the crystals of some cobaloxime complexes, racemization of chiral groups bonded to Co proceeds on X-ray exposure without degradation of crystallinity. Several intermediate stages could be determined by X-ray analysis. Various reaction pathways were recognized and the reaction rate could be correlated with the atomic arrangement in the crystal.     

电子探针图像的实用处理软件

基于Ｗｉｎｄｏｗｓ９５操作平台,用ＶｉｓｕａｌＣ＾＋＋５．０语言开发了电子探针图像实用处理软件,可对数字电子探针图像进行颜色转换、图像合成、内插放大、三维视图、直方图、灰度级切片、灰度级反转、灰度级平移、灰度级映射、平滑和锐化等自理灵活地运用这些处理技术,能够有效地突出数字电子探针图像中任何感兴趣信息、改善图像质量、增强视觉效果,其中,合成图像是一种表达矿物组分信息的新方法。     

A Structural Basis of Light Energy and Electron Transfer in Biology (Nobel Lecture)

Aspects of intramolecular light energy and electron transfer are discussed for three protein cofactor complexes whose three-dimensional structures have been elucidated by X-ray crystallography: the light harvesting phycobilisomes of cyanobacteria, the reaction center of purple bacteria, and the blue multi-copper oxidases. A wealth of functional data is available for these systems which allows specific correlations to be made between structure and function and general conclusions to be drawn about light energy and electron transfer in biological materials.     

On the mechanism of the P2-Na0.70CoO2→O2-LiCoO2 exchange reaction—Part I: proposition of a model to describe the P2-O2 transition

A model was proposed to describe the exchange reaction of sodium by lithium in P2 crystals. The exchange consists on the formation of nucleation centers and then on the growth of O2 domains in P2 crystals from these nucleation centers. Octahedral environments for lithium ions are obtained when one slab over two glides by (2/3,1/3,0) or by (1/3,2/3,0) in P2 structure. The existence of two different gliding vectors should lead to stacking faulted structures that can be simulated using DIFFaX software. The comparison of simulated and experimental XRD patterns for O2-LiCoO₂ (ex-Na_0.7CoO₂) has shown that in that case the growth of the O2 domains in the P2 crystals is faster than the formation of nucleation centers.     

基于影像处理的干涉测量相位重构研究

随着计算机技术和光电成像元件的发展,影像信息处理技术已经在无损检测、医学检测以及干涉测量等领域得到广泛应用。本文主要研究了影像信息在干涉测量领域的波前相位提取方法。干涉条纹图是干涉测量领域中影像信息的载体,在干涉条纹处理方面,针对空域卡雷算法的特点,提出一种基于影像处理的单幅闭合干涉条纹图相位重构新算法。在空域卡雷算法处理方法的基础上,利用迭代修正算法对干涉图相位进行二次逼近,实现了对单幅干涉条纹图的高精度相位重构。Matlab仿真结果表明,迭代修正后的相位残差降低了25.8%,表明该算法在空域卡雷算法的基础上能够有效提高相位重构精度,实现干涉测量领域中影像信息的高精度处理。     

Growth of protein crystals in hydrogels prevents osmotic shock

High-throughput protein X-ray crystallography offers a significant opportunity to facilitate drug discovery. The most reliable approach is to determine the three-dimensional structure of the protein-ligand complex by soaking the ligand in apo crystals. However, protein apo crystals produced by conventional crystallization in a solution are fatally damaged by osmotic shock during soaking. To overcome this difficulty, we present a novel technique for growing protein crystals in a high-concentration hydrogel that is completely gellified and exhibits high strength. This technique allowed us essentially to increase the mechanical stability of the crystals, preventing serious damage to the crystals caused by osmotic shock. Thus, this method may accelerate structure-based drug discoveries.