Parameters for crystal growth of ribosomal subunits

A systematic analysis of the parameters that control the crystal growth of the large subunit of ribosomes from B stearothermophilus has been carried out. Several parameters have been identified and classified according to their significance. It was found that only biologically active particles can crystallize and that the critical period for the crystallization process is the first few days, during which changes in the volume and content of the crystallization drop are of importance for both nucleation and crystal growth. Consequently, an experimental procedure for fine control of these variables has been developed. As a result of these studies, the reproducibility of crystal formation was increased, and larger and more stable crystals have been obtained.     

Virus crystallography

Virus crystallography can provide atomic resolution structures for intact isometric virus particles and components thereof. The methodology is illustrated by reference to a particularly complex example, the core of the bluetongue virus (700 Å).     

Charting the surfaces of the purple membrane

The preponderance of structural data of the purple membrane from X-ray diffraction (XRD), electron crystallography (EC), and atomic force microscopy (AFM) allows us to ask questions about the structure of bacteriorhodopsin itself, as well as about the information derived from the different techniques. The transmembrane helices of bacteriorhodopsin are quite similar in both EC and XRD models. In contrast, the loops at the surfaces of the purple membrane show the highest variability between the atomic models, comparable to the height variance measured by AFM. The excellent agreement of the AFM topographs with the atomic models from XRD builds confidence in the results. Small technical difficulties in EC lead to poorer resolution of the loop structures, although the combination of atomic models with AFM surfaces allows clear interpretation of the extent and flexibility of the loop structures. While XRD remains the premier technique to determine very-high-resolution structures, EC offers a method to determine loop structures unhindered by three-dimensional crystal contacts, and AFM provides information about surface structures and their flexibility under physiological conditions.     

Elongated oligomers assemble into mammalian PrP amyloid fibrils

In prion diseases, the mammalian prion protein PrP is converted from a monomeric, mainly alpha-helical state into beta-rich amyloid fibrils. To examine the structure of the misfolded state, amyloid fibrils were grown from a beta form of recombinant mouse PrP (residues 91-231). The beta-PrP precursors assembled slowly into amyloid fibrils with an overall helical twist. The fibrils exhibit immunological reactivity similar to that of ex vivo PrP Sc. Using electron microscopy and image processing, we obtained three-dimensional density maps of two forms of PrP fibrils with slightly different twists. They reveal two intertwined protofilaments with a subunit repeat of approximately 60 A. The repeating unit along each protofilament can be accounted for by elongated oligomers of PrP, suggesting a hierarchical assembly mechanism for the fibrils. The structure reveals flexible crossbridges between the two protofilaments, and subunit contacts along the protofilaments that are likely to reflect specific features of the PrP sequence, in addition to the generic, cross-beta amyloid fold.     

Collagen fibril morphology in developing chick metatarsal tendon: 2. Electron microscope studies

Transverse section of embryonic chick metatarsal tendons ranging in age from 11 days to 18 days fetal were examined by electron microscopy to determine both the diameters and the lateral arrangements of the cylindrical collagen fibrils. In early developmental stages, from 11 days to 14 days fetal, sharp unimodal distributions of diameters centred near 32 or 40 nm were observed, but increasingly heterogeneous diameters were seen with increasing age. The heterogeneous diameter distributions were not uniform, but showed discrete populations of preferred diameters. The centre-to-centre distance separating the fibrils in the early developmental stages was about twice the fibril diameter and constant with age. Comparison of X-ray diffraction results with these observations indicated that the saptial relationships of the structures are preserved during the preparative procedures for electron microscopy, but that a transverse shrinkage of 25–30% had occurred relative to the wet dimension.     

β-Glucanases in Malt That Form Insoluble Materials

When brewing barley malt extracts were incubated with malt β-glucans, insoluble materials were formed in the reaction mixture. To investigate the cause of this, we studied various factors that may participate in the formation of these materials. The isolated malt β-glucans were similar to barley β-glucans with the β-(l→3) and (1→4)-linkages in a molar ratio of 1:2.38, and the molecular weight was 950,000. Three enzymes were detected and purified from malt by ammonium sulfate precipitation, ion exchange chromatography, gel filtration, and isoelectric focusing. One of these enzymes was β-(1→4)-d-glucanase (I) with a molecular weight of 40,000 and an optimum pH of 5.0. The other enzyme was β-(l→3), (l→4)-d-glucan 4-glucanohydrolase, with a molecular weight of 33,000 and an optimum pH 5.0. The third enzyme was β-(1→4)-d-glucanase (II), with a molecular weight of 49,000 and an optimum pH of 4.5. Among these three β-glucanases, β(1→4)-d-glucanases (I) and (II) had not been identified before in malt, and β-(l→4)-d-glucanase (II) was most stable on heat treatment and formed most of the precipitates in the reaction mixture.     

Interpretation of the electron microscopical appearance of collagen fibrils from corneal stroma

The appearance in the electron microscope of mechanically-dispersed corneal collagen has been observed after positive staining with phosphotungstic acid and/or uranyl acetate and after negative staining with phosphotungstate ions. The distributions of positive stains (both cationic and anionic) were similar to those observed in other type I collagens (e.g. skin, tendon). A high correlation was found between charge density in the fibril and the distribution of charged amino acids predicted from the sequence of calf skin collagen. This correlation could be improved by including type III sequence data, suggesting the presence of 20% type III collagen within each fibril. Negative staining showed the usual collagen D-periodicity but without a clear gap/overlap structure. Detailed analysis revealed at least six sites where stain penetration was inhibited. Specific staining of glycosides using N,N,N′,N′-tetramethylethylenediamine(TEMED)-osmate suggested that these sites identify the covalent attachment of disaccharides to the collagen. Using synchroton X-ray diffraction from TEMED-osmate stained corneas we have determined the locations of the stain ions (and hence the glycosides) in the moist tissue. The results demonstrate that even though the detailed charge distribution and axial molecular packing in corneal collagen are similar to other type I collalgens, carbohydrate material, probably disaccharide, is attached at fairly regular intervals. This does not occur in other type I collagens. In particular, the presence of glycoside in the overlap region may play a role in producing the narrow uniform fibrils which are essential for the transparency of the cornea.     

Carboxymethylation of cellulose using reactive extrusion

Carboxymethyl cellulose was prepared using a continuous, reduced solvent, reactive extrusion process with a short reaction time. The effects of the amounts of NaOH (30 g, 40 g and 50 g), water:ethanol ratio (100%, 70%, 50%, 30% and 10% H₂O) and their interactions on the physical, chemical and morphological properties of carboxymethyl cellulose were studied. Experiments were conducted using to a 5 × 3 blocked factorial design. X-ray diffraction analyses revealed higher degrees of crystallinity and fractions of cellulose-II crystalline structure when 100% H₂O was used as compared to that for 70%, 50%, 30% and 10% H₂O and a commercially available brand of carboxymethyl cellulose, AQUASORB A500. Statistical analysis revealed a significant interaction between the effects of NaOH and H₂O on the degrees of substitutions. The degrees of substitutions decreased with increasing amounts of NaOH and tended to increase with increasing alcohol concentrations. Liquid uptake measurements revealed that the extent of saline uptake, measured at intervals of 1 min, 5 min and 10 min, by carboxymethyl cellulose prepared with 100% H₂O, especially when 40 g and 50 g NaOH was used, was higher than that for 70%, 50%, 30% and 10% H₂O and AQUASORB A500. This may have been because of the higher crystallinity in carboxymethyl cellulose prepared with 100% H₂O. Carboxymethyl cellulose prepared with 70% H₂O and 30 g and 50 g NaOH had the highest saline absorption, using the soak method, before and after centrifugation, respectively. Scanning electron microscopy for carboxymethyl cellulose prepared with 100% and 10% H₂O, through images at 120X magnification, revealed fibers 100 μ to >800 μ in length and 0.8-3.3 μ in breadth. Some non fibrous particles, 0.8-6.7 μ in dimensions, also were observed for 100% H₂O. Images at 900× magnification revealed partially damaged fiber surfaces.     

Influence of phorbol esters on ionophore-mediated calcium exchange-diffusion in liposomes

The interference of phorbol esters upon the process of A23187-mediated calcium exchange diffusion was examined in multilamellar liposomes formed of different types of lipids and incubated at variable temperatures. Phorbol esters facilitated the process of calcium ionophoresis in liposomes formed of dipalmitoylphosphatidylcholine (DPPC) or dimyristoylphosphatidyl-choline (DMPC) and incubated below transition temperature. The magnitude of this facilitating action was negatively correlated with the tumor-promoting capacity of the phorbol esters. The phorbol esters also facilitated calcium ionophoresis in liposomes formed of a mixture of DPPC and cholesterol, provided that the temperature exceeded 34 degrees C. The magnitude of the latter facilitating action was positively correlated with both the temperature and the tumor-promoting potency of the phorbol esters. Thus, the existence of a parallelism between the biological potency of phorbol esters and their biophysical effect in this artificial system tightly depended on such factors as the lipid composition of the liposomal matrix and the ambient temperature.     

Investigations of the possible role of proteases in altering surface proteins of virally transformed hamster fibroblasts

Virally transformed fibroblasts have on their surfaces zero or reduced amounts of a large external transformation-sensitive (LETS) glycoprotein. This protein is extremely sensitive to proteolysis. When prelabeled normal fibroblasts are cocultivated with transformed cells, the LETS glycoprotein of the normal cells shows an increased rate of turnover. Experiments are described which investigate the possibility that this phenomenon and the absence of LETS glycoprotein are due to proteolysis by the transformed cells. In particular, the role of plasminogen activation is examined by the use of protease inhibitors and plasminogen-depleted serum. It is concluded that activation of plasminogen is not required for the disappearance of the LETS glycoprotein although the involvement of other proteases cannot be ruled out. The role of proteases in affecting cell growth and behavior is discussed.     

希瓦氏菌Shewallena oneidensis MR-1合成硒纳米棒

摘要:【目的】探索采用希瓦氏菌合成硒(Se)纳米棒,并阐明合成底物Se(IV)的浓度与细菌培养时间对生物合成的影响。【方法】将希瓦氏菌Shewallena oneidensis MR-1 接种至Luria-Bertani(LB)液体培养基,分别以Se(IV)浓度0.1、1、10和100 mmol/L的Na2 SO3作为电子受体,厌氧培养并绘制生长曲线。再将希瓦氏菌接种到含最适Se( IV)浓度的LB 培养基中,在厌氧培养后第24和72 h离心获取沉淀。采用扫描电镜、X射线能谱和X射线衍射对沉淀进行分析。【结果】在Se(IV)浓度1 mmol/L的培养基中培养24 h形成的纳米棒沉淀截面直径约80 nm,长度2－3 μm。而培养72 h形成的沉淀较大,超出纳米物质范畴。采用X射线能谱和X射线衍射确定纳米棒组成为单质Se。【结论】本研究为生物合成Se纳米棒提供了一种可行的方法。希瓦氏菌最适宜在1 mmol/L Se(IV)浓度下以及在对数生长期大量合成Se纳米棒,具有潜在应用价值。     

A Structural Model for Apolipoprotein C-II Amyloid Fibrils: Experimental Characterization and Molecular Dynamics Simulations

The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple ‘letter-G-like’ β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops.     

NaCl-dependent formation of the highly crystalline phase in sufficiently hydrated dimyristoylphosphatidylglycerol bilayers

We investigated the low-temperature phase behavior of dimyristoylphosphatidylglycerol (DMPG) bilayers in the presence of high concentration of NaCl (≥100 mM). Differential scanning calorimetry showed that the highly crystalline (HC) phase grew after an initial delay period when DMPG bilayers were sufficiently hydrated and incubated at 1 °C in the presence of more than 100 mM NaCl. The HC phase formation reached a plateau, the level of which depended on NaCl concentration; all the lipids were unable to be in the HC phase at the plateau stage without a quite high concentration of NaCl. Since electron microscopic observations suggested that the HC phase formed coexists with the precursor phases in a closed vesicle, elastic constrain and/or shortage of free sodium ions in the inside of the closed vesicle may prevent the complete transition into the HC phase.     

Reconstituted P2/Myelin-Lipid Multilayers

A complex forms when bovine P2 protein is added to single-bilayer vesicles created by sonicating myelin lipids. The complex was studied by biochemical analysis, freeze-fracture (FF) and thin-section electron microscopy (EM), and by X-ray diffraction. Smaller amounts of P2 cause the vesicles to aggregate and fuse whereas larger amounts (greater than or equal to 4 wt%) cause multilayers to form. Binding saturates at 15 wt% P2. FF EM shows that large, flat multilayers form within 15 min of addition of P2. Only smooth fracture faces are seen, as expected for a peripheral membrane protein. X-ray diffraction shows a constant repeating distance in the multilayers: 86.0 +/- 0.7 A between the centers of bilayers in the range 4 wt% less than or equal to P2/(P2 + lipid) less than or equal to 15 wt%. Assuming a 53 A-thick bilayer, the space between bilayers is 33 A wide. This is a wider space than for myelin basic protein (MBP) (20-25 A wide). The respective widths are consistent with a compact, globular structure for P2 and a flattened shape for MBP. Calculated electron-density profiles of the lipids with and without P2 reveal the protein largely in the interbilayer spaces, with a small part possibly inserted into the lipid headgroup layers. The different proportions of P2 in the sciatic nerve of various species are tentatively correlated with the different average widths observed by X-ray diffraction for the cytoplasmic space (major period line) between bilayers in the respective sciatic myelins.     

A homologous series of apoptosis-inducing N‑acylserinols: Thermotropic phase behavior,interaction with cholesterol and characterization of cationic N‑myristoylserinol-cholesterol-CTAB niosomes

N?Acylserinols (NASOHs) exhibit anti-cancer activity by elevating ceramide levels, and/or by activating proapoptotic effectors. In the present work we investigated the thermotropic phase behavior and supramolecular organization of a homologous series of NASOHs (number of C-atoms in the acyl chain, n?=?8–18), and the interaction of N-myristoylserinol (NMSOH) with cholesterol, and characterized cationic niosomes made up of NMSOH, cholesterol and cetyltrimethylammonium bromide (CTAB). Differential scanning calorimetric studies revealed that NASOHs exhibit a major chain-melting phase transition in both dry and hydrated states. The thermodynamic parameters, transition enthalpy and entropy show linear dependence on the acyl chain length in the dry state, but exhibit odd-even alternation in the hydrated state. Powder X-ray diffraction studies revealed that NASOHs adopt a tilted bilayer structure, wherein the bilayer repeat distances (d-spacings) also showed odd-even alteration, with even-chainlength compounds exhibiting slightly higher d-spacings. Studies on the interaction between NMSOH and cholesterol revealed that both lipids mix well with up to 55?mol% cholesterol, whereas phase separation was observed at higher cholesterol content. The transition enthalpy corresponding to the NMSOH-cholesterol complex increases up to 55?mol% cholesterol and decreases at higher cholesterol content. Presence of the cationic surfactant CTAB affects the phase behavior, fluidity and size of the NMSOH-cholesterol (45,55, mol/mol) niosomes, with unilamellar vesicles of about 85 (±20) nm in diameter being obtained at 10?mol% CTAB. These results provide a thermodynamic and structural basis for further investigations on these cationic niosomes towards their use in drug delivery applications, especially for anticancer drugs.     

铁还原细菌Shewanella oneidensis MR-4诱导水合氧化铁形成蓝铁矿的过程

【目的】研究铁还原细菌Shewanella oneidensis MR-4在细胞外诱导形成含铁矿物的矿物相、化学成分和形貌结构等特性及其变化,深化对铁还原细菌细胞外诱导矿化过程的认识。【方法】在以30 mmol/L乳酸钠为电子供体,10 mmol/L水合氧化铁为电子受体,[HCO_3~–]为30 mmol/L,[PO_4~(3–)]为5 mmol/L条件下,30°C恒温下厌氧培养,进行细菌生长和细胞外诱导矿化实验,定期采样测量反应体系的pH、生物量、Fe(Ⅱ)浓度;采用激光拉曼光谱(Raman)、扫描电子显微镜(SEM)、透射电子显微镜(TEM)和X-射线衍射(XRD)等方法对不同时间点的矿化产物进行分析。【结果】MR-4在还原Fe(Ⅲ)的过程中,细胞快速生长,表明MR-4的Fe(Ⅲ)还原和乳酸氧化过程相互耦合,从而进行细胞生长,并在细胞外诱导矿物形成。对不同阶段矿化产物的综合分析表明,反应进行到约8 d时,无定形-弱结晶的水合氧化铁部分地转化为纳米尺寸的磁铁矿晶体颗粒;约16 d时,反应体系中开始出现蓝铁矿晶体颗粒;约20 d后,几乎所有矿物转化为纤维状或者叶片状的蓝铁矿。【结论】铁还原细菌Shewanella oneidensis MR-4细胞外诱导矿化过程受环境条件控制,当以乳酸钠和水合氧化铁分别作为电子供体和受体,相对高的[PO_4~(3–]/[HCO_3~–](1:6)时,水合氧化铁先转化为磁铁矿,最后大量转化为蓝铁矿。本研究为全面认识铁还原细菌的生物诱导矿化过程和评估其参与铁元素地球化学循环提供了新的数据。     

The structure and properties of different types of starch exposed to UV radiation: A comparative study

The effect of UV-irradiation on four different types of native starch (corn, waxy corn, wheat and potato) have been investigated. Although the changes in the chemical structure of starch specimens were small, indicating good photostability, the samples lost adsorbed water and their crystallinity degree decreased after irradiation. Moreover, a drop in average molecular weight occurred in samples (with the exception of potato starch) as a result of main chain scission. The variations in the properties of investigated specimens of various origin were related to the differences in their structure and macromolecular arrangement. The lowest photostability among the four starches was exhibited by potato starch.