On the Specificity of Heparin/Heparan Sulfate Binding to Proteins. Anion-Binding Sites on Antithrombin and Thrombin Are Fundamentally Different

Background

The antithrombin–heparin/heparan sulfate (H/HS) and thrombin–H/HS interactions are recognized as prototypic specific and non-specific glycosaminoglycan (GAG)–protein interactions, respectively. The fundamental structural basis for the origin of specificity, or lack thereof, in these interactions remains unclear. The availability of multiple co-crystal structures facilitates a structural analysis that challenges the long-held belief that the GAG binding sites in antithrombin and thrombin are essentially similar with high solvent exposure and shallow surface characteristics.

Methodology

Analyses of solvent accessibility and exposed surface areas, gyrational mobility, symmetry, cavity shape/size, conserved water molecules and crystallographic parameters were performed for 12 X-ray structures, which include 12 thrombin and 16 antithrombin chains. Novel calculations are described for gyrational mobility and prediction of water loci and conservation.

Results

The solvent accessibilities and gyrational mobilities of arginines and lysines in the binding sites of the two proteins reveal sharp contrasts. The distribution of positive charges shows considerable asymmetry in antithrombin, but substantial symmetry for thrombin. Cavity analyses suggest the presence of a reasonably sized bifurcated cavity in antithrombin that facilitates a firm ‘hand-shake’ with H/HS, but with thrombin, a weaker ‘high-five’. Tightly bound water molecules were predicted to be localized in the pentasaccharide binding pocket of antithrombin, but absent in thrombin. Together, these differences in the binding sites explain the major H/HS recognition characteristics of the two prototypic proteins, thus affording an explanation of the specificity of binding. This provides a foundation for understanding specificity of interaction at an atomic level, which will greatly aid the design of natural or synthetic H/HS sequences that target proteins in a specific manner.     

一种简便经济的凝胶电泳同工酶特异染色方法

介绍一种简单、经济的同工酶染色方法：用熔化的0．4％琼脂糖处理滤纸备用,染色前将滤纸浸于同工酶染色液中,染色时将滤纸盖在聚丙烯酸胺胶上,然后将胶放在有盖塑料盒中保温染色,染色时间要比普通方法略长。染色后将胶和滤纸移入固定液中用镊子除去滤纸．     

A Simple Method for Making Tetrahedra to Illustrate Stereochemicai Principles

Actin and myosin, the major proteins of the contractile complex actomyosin, have now been demonstrated to be important constituents of many eukaryotic cells. As in muscle, their role is primarily that of a contractile system. This system is thought to underly all aspects of cellular motility: locomotion, shape change, mitosis and meiosis, cell division, cytoplasmic streaming, organelle motion, endo-cytosis (pinocytosis, phagocytosis), and exocytosis.

We describe here a simple experimental system to demonstrate quantitatively aspects of motility and its regulation in the slime mould Physarum polycephalum     

A Simple Biosynthetic Method for Preparation of High Specific Radioactivity Phosphatidyl-choline

Chemical changes in lysozyme during heating at 150~250°C for 20min were investigated by means of IR, ESR, and CD spectroscopies and gel permeation chromatography, and further a tryptic hydrolysate from the lysozyme heated at 200°C was analyzed by ion exchange chromatography. At 150°C, polymerization through disulfide linkages was observed, and at180°C, both polymerization and degradation occurred. When the temperature was raised to 200°C, remarkable changes in the structure of lysozyme, such as cleavage and recombination of peptide bonds, occurred. Over 200°C, polymerization and degradation occurred more violently.     

A Simple Method for Predicting Transmembrane Proteins Based on Wavelet Transform

The increasing protein sequences from the genome project require theoretical methods to predict transmembrane helical segments (TMHs). So far, several prediction methods have been reported, but there are some deficiencies in prediction accuracy and adaptability in these methods. In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG is chosen as an example to describe the prediction process by this method. 80 proteins with known 3D structure from Mptopo database are chosen at random as data sets (including 325 TMHs) and 80 sequences are divided into 13 groups according to their function and type. TMHs prediction is carried out for each group of membrane protein sequences and obtain satisfactory result. To verify the feasibility of this method, 80 membrane protein sequences are treated as test sets, 308 TMHs can be predicted and the prediction accuracy is 96.3%. Compared with the main prediction results of seven popular prediction methods, the obtained results indicate that the proposed method in this paper has higher prediction accuracy.     

A Simple and Non-destructive Method of Direct-PCR for Plant Systems

To date, PCR is a fundamental tool for most of the research concerning plant diversity analysis, marker-assisted selection, genetic purity testing, disease diagnostics, and transgene analysis. In all of these analyses, good-quality DNA serves as a template for amplification of target sequences. Extraction of good-quality DNA requires many steps, making the whole process time consuming, tedious, labor intensive, and expensive due to costlier and toxic chemicals. To overcome these preparatory steps from PCR-based DNA amplification, we have developed a direct-PCR amplification method for plants without isolating DNA. The method is unique and beneficial over some previously described methods of direct-PCR which fail due to inefficient amplification of target DNA in the presence of PCR inhibitors and crop specificity. Moreover, such methods are non-specific and, being destructive, cannot be replicated; one cannot completely rely on them due to lack of reproducibility. This method was streamlined from our earlier observation that alcohol-desiccated tissues maintain intact DNA for a long time. This method is specific, rapid, and, being non-destructive, allows replication, giving advantages over existing methods. The method was tested over a wide range of plant species and found very effective and quick in generating data. The method was successfully used to test the genetic purity of pearl millet hybrid (RHB-127) and its restorer (RIB 3135-18) and CMS line (ICMA 93333A). Our method is especially important for developing inexpensive and high-throughput non-invasive genetic analyses.     

A Simple Method for the Reconstitution of Membrane Proteins into Giant Unilamellar Vesicles

A simple method for the reconstitution of membrane protein from submicron proteoliposomes into giant unilamellar vesicles (GUVs) is presented here: This method does not require detergents, fusion peptides or a dehydration step of the membrane protein solution. In a first step, GUVs of lipids were formed by electroformation, purified and concentrated; and in a second step, the concentrated GUV solution was added to a small volume of vesicles or proteoliposomes. Material transfer from submicron vesicles and proteoliposomes to GUVs occurred spontaneously and was characterized with fluorescent microscopy and patch-clamp recordings. As a functional test, the voltage-dependent, anion-selective channel protein was reconstituted into GUVs, and its electrophysiological activity was monitored with the patch clamp. This method is versatile since it is independent of the presence of the protein, as demonstrated by the fusion of fluorescently labeled submicron vesicles and proteoliposomes with GUVs.     

Simple and Efficient Method for Heterologous Expression of Clostridial Proteins

Many clostridial proteins are poorly produced in Escherichia coli. It has been suggested that this phenomena is due to the fact that several types of codons common in clostridial coding sequences are rarely used in E. coli and the quantities of the corresponding tRNAs in E. coli are not sufficient to ensure efficient translation of the corresponding clostridial sequences. To address this issue, we amplified three E. coli genes, ileX, argU, and leuW, in E. coli; these genes encode tRNAs that are rarely used in E. coli (the tRNAs for the ATA, AGA, and CTA codons, respectively). Our data demonstrate that amplification of ileX dramatically increased the level of production of most of the clostridial proteins tested, while amplification of argU had a moderate effect and amplification of leuW had no effect. Thus, amplification of certain tRNA genes for rare codons in E. coli improves the expression of clostridial genes in E. coli, while amplification of other tRNAs for rare codons might not be needed for improved expression. We also show that amplification of a particular tRNA gene might have different effects on the level of protein production depending on the prevalence and relative positions of the corresponding codons in the coding sequence. Finally, we describe a novel approach for improving expression of recombinant clostridial proteins that are usually expressed at a very low level in E. coli.     

一种简易高效的小麦叶片胞间液蛋白提取方法的建立

植物细胞间液中的蛋白在植物生长发育和抗病抗逆反应及其信号传导过程中发挥着重要作用,是植物学研究的新热点.由于细胞间液含量低,容易因组织细胞损伤性受到胞内成分污染,高纯度的细胞间液蛋白的提取相对困难,参考相关文献报道,建立了一种简易高效的小麦叶片细胞间液蛋白的提取方法.选取小麦品种“铭贤169”幼苗叶片为材料,用50mmol/L NaAc缓冲液充分浸润,负压处理20 min后,30 × g离心5 min除去叶片表面缓冲液,随后2 000×g离心15 min,收集小麦叶片胞间液.将获得的小麦叶片胞间液冷冻干燥后,进行SDS-PAGE分离分析.电泳胶图上显示出细胞间液提取物与叶片组织提取物的蛋白质组成有极显著差异,使用MALD-TOF/TOF MS技术分析SDS胶上的细胞间液蛋白条带,共鉴定到9种非高丰度或假定的蛋白,其中有两种是已报道过的植物细胞间液蛋白.试验结果表明,本方法简易高效,适用于小麦蛋白质组学研究中高纯度的细胞间液蛋白的提取.     

A Simple Method for the Selection of Specific Small Areas of Central Nervous Tissue for Electron Microscopy

An improved modification of an area or cell-selection technique is described. The method involves cutting 2.5-5.0 μm thick plastic sections, mounting than on 0.2 mm acetate sheet, examining them by phase-contrast microscopy, remounting selected sections and cutting these into ultrathin sections. Simplicity and speed are achieved by using acetate sheet instead of the usual glass slides and cover-slips. The method is suitable for topographic localization in small areas of the tissue and especially for the selection of dispersed single cells which are to be examined by electron microscopy.     

一种简便、高效、经济的从凝胶中回收DNA的方法

目的:尝试一种简便、高效的从凝胶中回收DNA的方法。方法:在Eppendorf管的管底用注射器扎孔,将一小团用Eppendorf管融化后拉成的细丝放入管中,把含有DNA的凝胶放在细丝上,离心,收集从管底流出的液体,经酚氯仿抽提后用乙醇沉淀DNA。结果:经过简单的离心即可近乎100%地回收凝胶中的DNA。结论:使用该方法从琼脂糖凝胶回收DNA,操作简单,回收率高,无其他试剂污染。     

Specific Recognition of Influenza A/H1N1/2009 Antibodies in Human Serum: A Simple Virus-Free ELISA Method

Background

Although it has been estimated that pandemic Influenza A H1N1/2009 has infected millions of people from April to October 2009, a more precise figure requires a worldwide large-scale diagnosis of the presence of Influenza A/H1N1/2009 antibodies within the population. Assays typically used to estimate antibody titers (hemagglutination inhibition and microneutralization) would require the use of the virus, which would seriously limit broad implementation.

Methodology/Principal Findings

An ELISA method to evaluate the presence and relative concentration of specific Influenza A/H1N1/2009 antibodies in human serum samples is presented. The method is based on the use of a histidine-tagged recombinant fragment of the globular region of the hemagglutinin (HA) of the Influenza A H1N1/2009 virus expressed in E. coli.

Conclusions/Significance

The ELISA method consistently discerns between Inf A H1N1 infected and non-infected subjects, particularly after the third week of infection/exposure. Since it does not require the use of viral particles, it can be easily and quickly implemented in any basic laboratory. In addition, in a scenario of insufficient vaccine availability, the use of this ELISA could be useful to determine if a person has some level of specific antibodies against the virus and presumably at least partial protection.     

A Simple, Rapid Method for Demonstrating Bacterial Flagella

We developed a simple, rapid method for demonstrating flagellation of bacteria using the fluorescent protein stain NanoOrange (Molecular Probes, Eugene, Oreg.). The NanoOrange reagent binds to hydrophobic regions of proteins, which results in substantial enhancement of fluorescence. Unbound reagent is essentially nonfluorescent. NanoOrange fluorescently stained bacterial cell bodies, as well as flagella and other appendages, which could be directly observed by epifluorescence microscopy. Detection of flagella was further improved by using a charge-coupled device camera for image capture and processing. The reliability of the method was tested by using 37 pure cultures of marine bacteria. Detection of flagella on the isolates by NanoOrange staining was compared to detection by transmission electron microscopy (TEM). For 36 of 37 cultures, the two methods yielded the same results. In one case, flagella were detected by TEM but not by NanoOrange, although the difference may be attributable to differences between the culture preparations. NanoOrange staining is rapid (10 to 15 min) and does not require fixation or dehydration, so live samples can be stained. Since NanoOrange is a general protein stain and works directly in seawater, it may also prove to be useful for staining other proteinaceous material that is of interest to aquatic microbial ecologists.     

一种从人血凝块中提取基因组DNA的方法

介绍了一种新的从人血凝块中提取基因组DNA的方法,用该方法提取的DNA成功地应用于PCR和限制性酶切等后续实验中。基本过程为首先机械粉碎,然后高盐高EDTA溶液处理,含蛋白酶K和SDS的消化液变换温度消化,苯酚氯仿抽提。     

A Simple Method for Identifying Plant/T-DNA Junction Sequences Resulting from Agrobacterium-mediated DNA Transformation

Genomic integration of transferred T-DNA is traditionally analyzed by Southern hybridization; however, these analyses often do not provide sufficient information pertaining to the transformation event. Analysis of the junction sequences spanning the region between the T-DNA borders and plant genomic DNA, give a clear demonstration of genomic integration. The procedures available for border junction analysis can be problematic, therefore a simplified method was developed for plants transformed by Agrobacterium tumefaciens harboring the binary vector with pBI121 backbone.     

A Simple, Fast and Reliable Method for Obtaining Dopamine Histofluorescence from Mesencephalic Cultures

A modified glyoxylic acid technique for obtaining dopamine histofluorescence from cultured mesencephalic cells is described. This method requires only two solutions: one contains glyoxylic acid, sucrose and monobasic potassium phosphate and is used at room temperature, the other is a Hepes buffered solution used at 37 C. Relatively high concentrations of a monoamine oxidase inhibitor and dopamine are added to the cultures to load dopaminergic neurons; the cell bodies and their processes take up and hold dopamine quickly and evenly. The cultures are dipped in a glyoxylic acid solution, dried in air, heated for 5 min and coverslipped with mineral oil. Since the cultures remain in their culture dishes, the entire procedure takes less than 2 hr. The green histofluorescence characteristic of dopamine is seen when the cultures are viewed by standard fluorescence microscopy. Various cell body types and sizes can be distinguished, as well as the complete extent of their processes and varicosities.     

层析法去除A群流脑多糖疫苗粗糖中杂蛋白

目的:建立用层析法去除脑脊髓膜炎球菌A群荚膜多糖样品中的杂蛋白的方法,以替代传统的苯酚抽提。方法:A群流脑多糖粗糖经过新型多模式离子交换填料Capto adhere,使用低盐上样高盐洗脱,洗脱的目的峰再经过Sephardex G-25凝胶过滤脱盐换成水,即为流脑多糖精糖原液。结果:采用上述方法制备的精制多糖样品中杂蛋白占固总的比例低于0.2%,符合WHO现行规程中的杂蛋白比例低于1%的要求,核酸、内毒素等生化指标均符合现行规程,整个层析过程的回收率大于65%。结论:层析法去除A群流脑多糖粗糖中的杂蛋白是有效的,比传统的苯酚抽提的方法更有利于环保,易于操作,易于放大。     

A Simple Method for Separating Phenanthrene from Soil by Cloud-Point Extraction

Contamination of soil by polycyclic aromatic hydrocarbons (PAHs) is currently widespread in urban and industrial areas, and the decontamination of PAHs remains a challenge. In addition, recovering PAHs from large volumes of soil washings is costly. Therefore, in this study, we focused on cloud-point extraction (CPE) without centrifugation, which separates PAHs from the washing solution through gravitational sedimentation. Specifically, we examined the conditions for the separation of phenanthrene (a typical PAH pollutant) from soil using CPE. After evaluating the water and phenanthrene solubilities of 23 commercially available nonionic surfactants, Brij 30 was found to be optimal. We simulated contaminated soil by adding phenanthrene to three soils with different particle sizes and varying amounts of organic matter. We examined the Brij 30 washing conditions and the effects of salt additives that promote phase separation during CPE. The addition of either sodium chloride or sodium sulfate enabled CPE at 25°C, but sodium sulfate was found to be more effective at lower concentrations than sodium chloride. A phenanthrene recovery rate of 58–88% was observed for each laboratory-simulated contaminated soil by CPE using salt additives. This method is economical and effective for processing large amounts of contaminated soil.     

荔枝胚蛋白质的提取方法

以不同体积的Tris-HCl(0.1mol／L,pH8．8)为提取液,结合不同含量(以胚鲜重计)的PVP40,对怀枝、黑叶和桂味等荔枝(Lithi chinensis)品种的胚蛋白质进行提取。结果表明,提取液体积为胚鲜重的5倍(ml g-1 FW),并加入15％的 PVP40时,提取蛋白质的效果最好,可用于荔枝胚可溶性蛋白质含量的测定;胚乳蛋白质的提取则以等体积的提取液(内含2％的PVP40)为佳。加入10% PVP40的胚蛋白提取液可直接进行SDS-PAGE电泳,用10倍于蛋白质提取液体积的乙醇沉淀胚和胚乳的蛋白提取液,可得到最佳的SDS-PAGE电泳效果。     

一种简易快速高效提取麻疯树营养器官中RNA的方法

以麻疯树根、茎、叶为材料,用4种方法提取麻疯树中总RNA.琼脂糖凝胶电泳和紫外光谱分析结果表明,改良的张年辉法提取的RNA比张年辉法提取的完整性更好,时间更短,条件更粗放;试剂盒A提取的RNA多数降解;试剂盒B几乎不能提取其RNA.RT-PCR分析表明,以改良的张年辉法提取的根、茎、叶中RNA作模板也可成功地进行RT-PCR扩增.据此,我们认为用简易、快速、高效的改良张年辉法提取麻疯树根、茎、叶中RNA为最佳选择.