Quantitative Determination of Hydrate Content of Theophylline Powder by Chemometric X-ray Powder Diffraction Analysis

The purpose of this study was to establish a calibration model to predict the hydrate content in powder materials consisting of anhydrate (theophylline anhydrate (THA)) and theophylline monohydrate (THM) by using various kinds of X-ray powder diffraction (XRPD) analytical methods. XRPD profiles were measured five times each for 11 standard samples containing of THA and THM. THM content in the standard samples was evaluated based on XRPD profiles by the diffraction peak height and area methods, and the Wakelin’s and principal component regression (PCR) methods, respectively. Since THA and THM were cube- and rod-shaped particles, the standard samples consisted of THA and THM showed crystal orientation due to THM crystal shape. THA showed reproducible XRPD profiles, but THM showed fluctuating intensities in some specific peaks in the profiles. The linear calibration models were evaluated based on calibration XRPD datasets of the standard materials by various methods. In the result based on validation XRPD datasets, the order of the mean bias and the mean accuracy were peak height > peak area > Wakelin’s > PCR, indicating that PCR was the best method to correct sample crystal orientation. The effectiveness of the PCR method in construction of calibration models was discussed by a scientific approach based on regression vectors.     

Heat-Moisture Treatment of Cereal Starch Observed by X-ray Diffraction

Chitinases I and II were purified from the culture supernatant of Aeromonas sp. 10S-24 by ammonium sulfate precipitation, SP-Sephadex C-50 chromatography, Sephacryl S-200 gel filtration, and chromatofocusing. Both enzymes were most active at pH 4.0 and the optimum temperature for I and II were 50°C and 60°C. Chitinase I was stable at pHs between 4 and 9 and at temperatures below 50°C and chitinase II was stable at pHs between 5 and 7 and at temperatures below 45°C. The molecular weights were estimated by 8D8 polyacrylamide gel electrophoresis to be 112,000 and 115,000 for I and II respectively, while gel filtration showed the molecular weight to be 114,000 for both types of the enzyme. The pIs for I and II were 7.9 and 8.1, respectively. The activities of both enzymes were inhibited by Ag⁺ and iodoacetic acid.     

X射线衍射晶体法解析脱卤酶DehDIV-R结构的研究

R-2-卤代酸脱卤酶能立体选择性水解R-2-卤代酸。解析酶的单晶结构对提高酶的选择性和活性提供了直接的结构指导,是目前酶结构领域研究的前沿。以实验室前期得到的来自假单胞菌ZJU26的R-2-氯丙酸脱卤酶(Deh DIV-R)为研究对象,采用X射线衍射晶体法进行结构解析。采用pp SUMO载体融合表达Deh DIV-R蛋白,依次通过Ni-NTA亲和层析、透析酶切、二次NiNTA亲和层析以及凝胶过滤层析纯化得到单一条带,且均一性好的蛋白。接着对结晶条件进行初筛与优化,得到的最佳结晶条件为0.1mol/L HEPES p H 7,12%PEG 6 000,0.2mol/L Mg Cl2,8mmol/L CHAPS。晶体在上海同步辐射光源BL18U1线站上收集衍射数据,采用分子置换法成功解析获得了分辨率为2.35的Deh DIV-R的晶体结构。Ramachandran图表明98.02%的氨基酸位于最适区,证明了该结构的合理性。Deh DIV-R的纯化、结晶以及结构解析为进一步深入了解其结构和功能奠定了基础。     

Cation-selective Pathway of OmpF Porin Revealed by Anomalous X-ray Diffraction

The OmpF porin from the Escherichia coli outer membrane folds into a trimer of β-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the β-barrel pore to form a narrow “constriction zone”. A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the β-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6₃ space group and two different data sets were obtained at 2.6 Å and 3.0 Å resolution with K⁺ and Rb⁺, respectively. The Rb⁺-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 Å and cation positions were determined. A PEG molecule was observed in the pore region for both the K⁺ and Rb⁺-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.     

Quick Shear-Flow Alignment of Biological Filaments for X-ray Fiber Diffraction Facilitated by Methylcellulose

X-ray fiber diffraction is one of the most useful methods for examining the structural details of live biological filaments under physiological conditions. To investigate biologically active or labile materials, it is crucial to finish fiber alignment within seconds before diffraction analysis. However, the conventional methods, e.g., magnetic field alignment and low-speed centrifugations, are time-consuming and not very useful for such purposes. Here, we introduce a new alignment method using a rheometer with two parallel disks, which was applied to observe fiber diffractions of axonemes, tobacco mosaic tobamovirus, and microtubules. We found that fibers were aligned within 5 s by giving high shear flow (1000-5000 s⁻¹) to the medium and that methylcellulose contained in the medium (∼1%) was essential to the accomplishment of uniform orientation with a small angular deviation (<5°). The new alignment method enabled us to execute structure analyses of axonemes by small-angle x-ray diffraction. Since this method was also useful for the quick alignment of purified microtubules, as well as tobacco mosaic tobamovirus, we expect that we can apply it to the structural analysis of many other biological filaments.     

The X-ray Diffraction Pattern of Spores of Bacillus subtilis

ORD and CD of d(+) pantothenic acid, d(+) pantothenyl alcohol and d(?) pantolactone were studied. The acid and the alcohol gave positive Cotton effects with a peak at 227 and 225 mμ, respectively, and the lactone gave a negative Cotton effect with trough at 233 mμ. They gave CD maxima at 214, 213 and 219 mµ corresponding to the inflection points of their ORD curves.

The concentrations were found to be linear to the rotation angles and the possibility of the application to quantitative analysis of the ORD was cited. The ORD showed the quantitative formation of the lactone by acid treatment of the vitamins without any racemization and hence the determination via lactone was suggested.     

Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering

Small-angle scattering of X-rays (SAXS) is an established method to study the overall structure and structural transitions of biological macromolecules in solution. For folded proteins, the technique provides three-dimensional low resolution structures ab initio or it can be used to drive rigid-body modeling. SAXS is also a powerful tool for the quantitative analysis of flexible systems, including intrinsically disordered proteins (IDPs), and is highly complementary to the high resolution methods of X-ray crystallography and NMR. Here we present the basic principles of SAXS and review the main approaches to the characterization of IDPs and flexible multidomain proteins using SAXS. Together with the standard approaches based on the analysis of overall parameters, a recently developed Ensemble Optimization Method (EOM) is now available. The latter method allows for the co-existence of multiple protein conformations in solution compatible with the scattering data. Analysis of the selected ensembles provides quantitative information about flexibility and also offers insights into structural features. Examples of the use of SAXS and combined approaches with NMR, X-ray crystallography, and computational methods to characterize completely or partially disordered proteins are presented.     

High Stearic Acid Soybean Mutant Induced by X-ray Irradiation

Seeds of soybean [Glycine max (L.) Merr. var. Bay] were subjected to X-ray irradiation (21.4 kR), and the M2 generation was evaluated for the stearic acid content in the seed oil. Treatment with X-ray irradiation significantly increased genetic variability in the stearic acid content of the oil from Bay variety in comparison with the control plants. Among the 2513 M₂ plants tested, one mutant named M25 was selected for its stearic acid content of 20.8%, about seven-fold higher than that of the original variety. An inverse relationship of stearic acid with oleic and linoleic acids was observed. Mutant M25 always had higher stearic acid content under different environmental conditions in the M₃ generation.     

Recent X-ray Diffraction and Electron Microscope Studies of Striated Muscle

The sliding filament model for muscular contraction supposes that an appropriately directed force is developed between the actin and myosin filaments by some process in which the cross-bridges are involved. The cross-bridges between the filaments are believed to represent the parts of the myosin molecules which possess the active sites for ATPase activity and actin-binding ability, and project out sidewise from the backbone of the thick filaments. The arrangement of the cross-bridges is now being studied by improved low-angle X-ray diffraction techniques, which show that in a resting muscle, they are arranged approximately but not exactly in a helical pattern, and that there are other structural features of the thick filaments which give rise to additional long periodicities shown up by the X-ray diagram. The actin filaments also contain helically arranged subunits, and both the subunit repeat and the helical repeat are different from those in the myosin filaments. Diffraction diagrams can be obtained from muscles in rigor (when permanent attachment of the cross-bridges to the actin subunits takes place) and now, taking advantage of the great increase in the speed of recording, from actively contracting muscles. These show that changes in the arrangement of the cross-bridges are produced under both these conditions and are no doubt associated in contraction with the development of force. Thus configurational changes of the myosin component in muscle have been demonstrated: these take place without any significant over-all change in the length of the filaments.     

Structural studies of adenovirus type 2 by neutron and X-ray scattering

Small-angle neutron and X-ray scattering have been used to investigate various aspects of the structural organization of adenovirus type 2. Neutron scattering allows the determination of the radial distribution of DNA and protein, which because of the highly icosahedral form of the virus allows it to be described in terms of three icosahedral shells. X-ray scattering shows that the distance between the major coat proteins (hexons) in the capsid is 100 +/- A. Evidence was also observed for an organization in the nucleoprotein core that gives rise to a maximum in the X-ray scattering at 1/29 A-1.     

Structural basis of cellulosome efficiency explored by small angle X-ray scattering

Cellulose, the main structural component of plant cell walls, is the most abundant carbohydrate polymer in nature. To break down plant cell walls, anaerobic microorganisms have evolved a large extracellular enzyme complex termed cellulosome. This megadalton catalytic machinery organizes an enzymatic assembly, tenaciously bound to a scaffolding protein via specialized intermodular "cohesin-dockerin" interactions that serve to enhance synergistic activity among the different catalytic subunits. Here, we report the solution structure properties of cellulosome-like assemblies analyzed by small angle x-ray scattering and molecular dynamics. The atomic models, generated by our strategy for the free chimeric scaffoldin and for binary and ternary complexes, reveal the existence of various conformations due to intrinsic structural flexibility with no, or only coincidental, inter-cohesin interactions. These results provide primary evidence concerning the mechanisms by which these protein assemblies attain their remarkable synergy. The data suggest that the motional freedom of the scaffoldin allows precise positioning of the complexed enzymes according to the topography of the substrate, whereas short-scale motions permitted by residual flexibility of the enzyme linkers allow "fine-tuning" of individual catalytic domains.     

Structural studies of the neural-cell-adhesion molecule by X-ray and neutron reflectivity

The structures of adhesion proteins play an important role in the formation of intercellular junctions and the control of intermembrane spacing. This paper describes the combination of neutron and X-ray specular reflectivity measurements to investigate the structure of the ectodomain of the neural-cell-adhesion molecule (NCAM). The measurements with unmodified NCAM suggest the presence of a bend in the extracellular region. Measurements with the polysialic-acid-modified form of NCAM reveal that, at physiological ionic strength, the carbohydrate chains extend beyond the range of the unmodified protein. The excluded volume of the polymer is also ionic-strength-dependent, as expected for a polyelectrolyte. The structural characteristics obtained from these independent analyses of X-ray and neutron reflectivity data agree with each other, with prior reflectivity studies, and with molecular dimensions obtained from direct-force measurements. These results provide structural insights into the configuration of the NCAM ectodomain and the regulation of NCAM adhesion by post-translational modification.     

Microbeam X-ray Diffraction Study of Granular Crystals Formed in Water-in-Oil Emulsion

Margarine and fat spread contain typical water-in-oil emulsions, including semi-solid fats, as continuous oil phases. The application of palm oil, one of the most promising trans-fat alternatives, for semi-solid fats is increasing. However, granular crystals often occur in palm-oil-based solid fats and cause deterioration. In this study, we carried out differential scanning calorimetry (DSC), optical microscopy, and X-ray diffraction (XRD) experiments on granular crystals in margarine. A conventional laboratory-scale technique was applied to examine thermal properties of high-melting fat fractions in granular crystals. In addition, microstructures of the granular crystal were precisely observed with a synchrotron radiation small-angle XRD (SR-μ-SAXD) technique by using a microbeam having a cross section of 5 × 5 μm². The following results were obtained. (1) DSC indicated that granular crystals are composed of high-melting fractions having a melting temperature of 23 °C. (2) Conventional XRD of granular crystals indicated that β-fat crystals of a triple chain length structure (β-3) melted below the melting of β′-fat of a double chain length structure (β′-2). (3) SR-μ-SAXD indicated that the fat crystals in normal margarine were β′-2. However, the fat crystals of the double and triple chain length structures were simultaneously observed at the center region of a granular crystal, whereas only the fat crystals of β-3 were observed at the outer region of a granular crystal. We analyzed the microstructures and formation processes of granular crystals in relation to the fractional crystallization of the β form of 1,3-dipalmitoyl-2-oleoyl-sn-glycerol promoted by crystallization and transformation of tripalmitin and tristearin fractions.     

Structural Basis for Silicic Acid Uptake by Higher Plants

Many of the world's most important food crops such as rice, barley and maize accumulate silicon (Si) to high levels, resulting in better plant growth and crop yields. The first step in Si accumulation is the uptake of silicic acid by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins, also named metalloid porins. Here, we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). The OsNIP2;1 channel is closed in the crystal structure by the cytoplasmic loop D, which is known to regulate channel opening in classical plant aquaporins. The structure further reveals a novel, five-residue extracellular selectivity filter with a large diameter. Unbiased molecular dynamics simulations show a rapid opening of the channel and visualise how silicic acid interacts with the selectivity filter prior to transmembrane diffusion. Our results will enable detailed structure–function studies of metalloid porins, including the basis of their substrate selectivity.     

X-ray Diffraction Studies of Cell Walls and Peptidoglycans from Gram-positive Bacteria

THE cell walls of Gram-positive bacteria consist principally of a water-insoluble polymer and peptidoglycan (synonyms, murein, mucopeptide, glycosaminopeptide), which in some cases accounts for as much as 90% of the cell wall. After other components (teichoic acid, teichuronic acid, polysaccharide or protein) have been gently removed from the cell walls, peptidoglycan remains as a cell-shaped structure at least 100 Å thick. We report here results of X-ray diffraction observations on whole cell walls and peptidoglycans of Staphylococcus aureus, Bacillus licheniformis and Micrococcus lysodeikticus. Chemical data shows that all the muramic acid residues in the glycan chains of the peptidoglycan of S. aureus are substituted with the peptide L Ala-D GluNH₂-L Lys-D Ala and that there is extensive cross linking by pentaglycine bridges between peptides on adjacent glycan chains^1,3. Such a peptidoglycan might be expected to have an ordered crystalline structure. On the contrary, peptidoglycans of the bacilli, in which the cross linking between peptides is direct and considerably less^4,5 might be expected to have a less ordered structure. The mode of packing of the glycan and peptide moieties has been considered by Kelemen and Rogers⁶. When the glycan chains are stacked in pairs, as in the analogous polysaccharide chitin⁷, the muramic acid residues are orientated in such a way as to allow a three-dimensional structure to be built. If the bulk of the peptides are then arranged in a pseudo β configuration, calculations show that the expected dimensions of the cell wall calculated from the model are of the right order and also such a model allows for the existence of extensive stabilizing hydrogen bonds between adjacent peptide chains.     

Structural memory of natively unfolded tau protein detected by small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) is a universal low-resolution method to study size and shape of globular proteins in solution but recent developments facilitate the quantitative characterization of the structure and structural transitions of metastable systems like partially or completely unfolded proteins. We present here a study of temperature induced transitions in tau, a natively unfolded protein involved in Alzheimer's disease. Previous studies on full length tau and several disease-related mutants provided information about the residual structure in different domains revealing a specific role and extended conformations of the so-called repeat domains, which are considered to be responsible for the formation of amyloid-like fibrils ("paired helical filaments"). Here, we employ SAXS to investigate the temperature dependent properties of tau. Slow heating/cooling of the full length protein from 10°C to 50°C did not lead to detectable changes in the overall size. Surprisingly, quick heating/cooling caused tau to adopt a significantly more compact conformation, which was stable over up to 3 h and represents a structural "memory" effect. This compaction is not observed for the shorter tau constructs containing largely the repeat domains. The structural and functional implications of the observed unusual behavior of tau under nonequilibrium conditions are discussed.     

X-ray Diffraction Study of a New Crystal Form of Yeast Phenylalanine tRNA

IN our continuing studies on the crystallography of tRNA¹ we have obtained a new crystal form of phenylalanine tRNA from baker's yeast. The crystals show particularly good stability to X-ray irradiation, lasting generally for about 100 h in the X-ray beam. Most importantly they produce reflexions which extend out to a resolution of about 3.0 Å. The crystals belong to the monoclinic system, space group P2i with two molecules of tRNA per unit cell (Table 1). Thus, there is only one molecule per asymmetric unit of structure. The unit cell dimensions (a=56.0, b=33.4, c=63.0 and β=90.9°) are the smallest yet reported for tRNA and place stringent constraints on the possible dimensions of the tRNA molecule.