X-ray diffraction from magnetically oriented solutions of macromolecular assemblies

A simple system was developed for obtaining x-ray diffraction patterns from magnetically oriented solutions of macromolecular assemblies. A small permanent magnet was designed that produces a magnetic field of 16 kilogauss in a volume of 1 cubic millimeter and is mountable on most x-ray cameras. Many subcellular structures have sufficient diamagnetic anisotropy that they exhibit orientation in dilute solution when placed between the poles of the magnet. Diffraction from solutions oriented in this magnet can provide substantially more structural information than small-angle scattering from isotropic solutions. In favorable cases, such as dilute solutions of filamentous bacteriophages, it is possible to produce oriented fiber diffraction patterns from which intensities along layer lines can be measured to 7-angstrom resolution. The magnetically induced birefringence observed in solutions of other macromolecular assemblies suggests that this technique may have broad applicability to subcellular structures.     

Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit

Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates.     

Imaging of humic substance macromolecular structures in water and soils

Humic substances (HSs) are the natural organic polyelectrolytes formed from the biochemical weathering of plant and animal remains. Their macromolecular structure and chemistry determine their role in biogeochemical processes. In situ spectromicroscopic evidence showed that the HS macromolecular structures (size and shape) vary as a function of HS origin (soil versus fluvial), solution chemistry, and the associated mineralogy. The HSs do not simply form coils in acidic or strong electrolyte solutions and elongated structures in dilute alkaline solutions. The macromolecular structural changes of HSs are likely to modify contaminant solubility, biotransformation, and the carbon cycle in soils and sediments.     

Linking crystallographic model and data quality

In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.     

稻瘟病菌群体的分子遗传学研究——广东省稻瘟病菌群体遗传及致病型结构的时空变化分析

 为了全面、系统地了解最近几年来广东省稻瘟病菌群体遗传及致病型结构的时空变化特征，通过基于SRAP（sequence-related amplified polymorphism）标记的分子指纹方法对由广东省2000 2002年度各83个菌株构成的试验群体进行了遗传结构分析。结果表明，当相似性系数为0.92时，3个年度的供试菌株分别被分为33、25和13个遗传宗谱，其宗谱频率分别为39.8%、30.1%和15.7%。由此推测，广东省稻瘟病菌群体在这3年间其遗传多样性呈减少趋势，而且2001 2002年度的减少幅度要比2000 2001年度的大。另一方面，对上述3个群体进行了基于中国鉴别品种的致病型结构分析。结果表明，上述3个群体分别被划分为20、17和15个致病型，其致病型频率分别为24.4%、20.5% 和18.1%。由此说明，3个稻瘟病菌群体的致病型多样性大体上也呈减少趋势。本文对稻瘟病菌群体遗传结构与致病型结构的互动关系，以及稻瘟病菌群体致病性遗传结构与寄主群体抗性遗传结构的互动关系进行了分析。据此推测，广东省水稻品种抗性遗传结构的稳定化和简单化是造成其稻瘟病菌群体的遗传和致病型多样性减少的主要因素。     

Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor

A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.     

Progress in modeling of protein structures and interactions

The prediction of the structures and interactions of biological macromolecules at the atomic level and the design of new structures and interactions are critical tests of our understanding of the interatomic interactions that underlie molecular biology. Equally important, the capability to accurately predict and design macromolecular structures and interactions would streamline the interpretation of genome sequence information and allow the creation of macromolecules with new and useful functions. This review summarizes recent progress in modeling that suggests that we are entering an era in which high-resolution prediction and design will make increasingly important contributions to biology and medicine.     

The spatial dimension in population fluctuations

Theoretical research into the dynamics of coupled populations has suggested a rich ensemble of spatial structures that are created and maintained either by external disturbances or self-reinforcing interactions among the populations. Long-term data of the Canadian lynx from eight Canadian provinces display large-scale spatial synchrony in population fluctuations. The synchronous dynamics are not time-invariant, however, as pairs of populations that are initially in step may drift out of phase and back into phase. These observations are in agreement with predictions of a spatially-linked population model and support contemporary population ecology theory.     

DNA: a model compound for solution studies of macromolecules

Well-defined, monodisperse, homologous series of oligonucleotides and DNA restriction fragments may now be produced and used as models of rigid and semirigid rodlike molecules in solution. Information from optical experiments on these model systems aids in the formulation and testing of theories of macromolecular dynamics in both dilute and concentrated solution.     

斜拉三层网架结构动力反应分析

为解决斜拉网架结构减震装置造价高,位置和数量难以确定的问题,提出了斜拉局部三层网架的结构形式,利用ANSYS分析了这种结构的动力特性,并和斜拉双层网架对比,结果表明这种结构形式的抗震性能明显提高。     

Three-dimensional model of Salmonella's needle complex at subnanometer resolution

Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.     

Molecular dynamics of a cytochrome c-cytochrome b5 electron transfer complex

Cytochrome c and cytochrome b5 form an electrostatically associated electron transfer complex. Computer models of this and related complexes that were generated by docking the x-ray structures of the individual proteins have provided insight into the specificity and mechanism of electron transfer reactions. Previous static modeling studies were extended by molecular dynamics simulations of a cytochrome c-cytochrome b5 intermolecular complex. The simulations indicate that electrostatic interactions at the molecular interface results in a flexible association complex that samples alternative interheme geometries and molecular conformations. Many of these transient geometries appear to be more favorable for electron transfer than those formed in the initial model complex. Of particular interest is a conformational change that occurred in phenylalanine 82 of cytochrome c that allowed the phenyl side chain to bridge the two cytochrome heme groups.     

木材裂纹尖端应力、应变场的数值分析

借助Ansys有限元软件,采用二维正交各项异性有限元模型,对带有裂纹的正交各向异性白桦试件进行3点弯曲的裂纹尖端应力、应变场的研究。为了较真实的反映裂纹尖端力学情况,分别采用在裂纹尖端进行有限元网格细化法和布置奇异单元法来模拟裂纹尖端奇异场,并将计算结果用Matlab平台下编写的后处理程序进行分析和比较。结果表明:2种方法均可满足工程实际的要求,但在裂纹尖端布置奇异单元法优于有限元网格细化法。     

LIII-Edge Anomalous X-ray Scattering by Cesium Measured with Synchrotron Radiation

Diffraction of monochromatized synchrotron radiation by crystals of cesium hydrogen tartrate has been used to measure the magnitude and phase of x-ray scattering for cesium near the LIII absorption edge. In this wavelength region the scattering amplitude of cesium is reduced by as much as 25 electrons per atom, compared to scattering of copper Kalpha x-rays. This change, which varies as a function of wavelength, affects the diffraction intensities in a manner similar to isomorphous substitution, and it is large enough to have promise for phase determination in the study of macromolecular structures. This experiment also demonstrates that accurate diffractometer measurements are possible with synchrotron radiation produced by an electron storage ring.     

Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC

TBP (TATA-binding protein)-associated factors (TAF(II)s) are components of large multiprotein complexes such as TFIID, TFTC, STAGA, PCAF/GCN5, and SAGA, which play a key role in the regulation of gene expression by RNA polymerase II. The structures of TFIID and TFTC have been determined at 3.5-nanometer resolution by electron microscopy and digital image analysis of single particles. Human TFIID resembles a macromolecular clamp that contains four globular domains organized around a solvent-accessible groove of a size suitable to bind DNA. TFTC is larger and contains five domains, four of which are similar to TFIID.     

Polymers, fractals, and ceramic materials

Concepts borrowed from polymer science have been applied to tailor the properties of inorganic materials, especially those derived from amorphous precursors. Fractal geometry can be used to characterize macromolecular precursors and to relate their structures to kinetic growth processes. Within the silica system, for example, it is possible to manipulate the conditions of solution polymerization to yield a variety of macromolecules from branched chains to smooth colloidal particles.     

戊二醛对壳聚糖交联聚乙烯吡咯烷酮水凝胶结构和性能的影响

[目的]把聚乙烯吡咯烷酮与壳聚糖的大分子链进行交联,破坏壳聚糖大分子链的规整结构,增强壳聚糖的亲水性,改善对脂肪的吸附能力。[方法]以戊二醛为交联剂,通过壳聚糖大分子链的羟基和氨基,在壳聚糖大分子链之间形成化学交联点,同时网络聚乙烯吡咯烷酮,形成半互穿网络结构,合成聚乙烯吡咯烷酮(PVP)/壳聚糖(CS)交联水凝胶。最后,考察交联剂的用量对凝胶溶胀度和脂肪吸附能力的影响。[结果]红外光谱分析证明发生了交联反应,形成半互穿网络结构。SEM照片观察到PVP/CS交联凝胶表面呈微相分离。性能的测定结果表明,该凝胶在水中有很好的溶胀性,当交联剂的用量为2.5 ml时,凝胶的溶胀度最大。[结论]壳聚糖交联聚维酮凝胶对脂肪的吸附能力比起单纯的壳聚糖有很大的提高。     

Formation and subdivision of deformation structures during plastic deformation

During plastic deformation of metals and alloys, dislocations arrange in ordered patterns. How and when these self-organization processes take place have remained elusive, because in situ observations have not been feasible. We present an x-ray diffraction method that provided data on the dynamics of individual, deeply embedded dislocation structures. During tensile deformation of pure copper, dislocation-free regions were identified. They showed an unexpected intermittent dynamics, for example, appearing and disappearing with proceeding deformation and even displaying transient splitting behavior. Insight into these processes is relevant for an understanding of the strength and work-hardening of deformed materials.     

Long-range ordered carbon clusters: a crystalline material with amorphous building blocks

Solid-state materials can be categorized by their structures into crystalline (having periodic translation symmetry), amorphous (no periodic and orientational symmetry), and quasi-crystalline (having orientational but not periodic translation symmetry) phases. Hybridization of crystalline and amorphous structures at the atomic level has not been experimentally observed. We report the discovery of a long-range ordered material constructed from units of amorphous carbon clusters that was synthesized by compressing solvated fullerenes. Using x-ray diffraction, Raman spectroscopy, and quantum molecular dynamics simulation, we observed that, although carbon-60 cages were crushed and became amorphous, the solvent molecules remained intact, playing a crucial role in maintaining the long-range periodicity. Once formed, the high-pressure phase is quenchable back to ambient conditions and is ultra-incompressible, with the ability to indent diamond.     

Discovery of a Frank-Kasper sigma phase in sphere-forming block copolymer melts

Sphere-forming block copolymers are known to self-assemble into body-centered cubic crystals near the order-disorder transition temperature. Small-angle x-ray scattering and transmission electron microscopy experiments on diblock and tetrablock copolymer melts have revealed an equilibrium phase characterized by a large tetragonal unit cell containing 30 microphase-separated spheres. This structure, referred to as the sigma (σ) phase by Frank and Kasper more than 50 years ago, nucleates and grows from the body-centered cubic phase similar to its occurrence in metal alloys and is a crystal approximant to dodecagonal quasicrystals. Formation of the σ phase in undiluted linear block copolymers (and certain branched dendrimers) appears to be mediated by macromolecular packing frustration, an entropic contribution to the interparticle interactions that control the sphere-packing geometry.