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.     

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 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.     

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.     

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.     

A Simple Method for Selective Isolation of Stenotrophomonas maltophilia from Environmental Samples

Stenotrophomonas maltophilia is a commonly found environmental bacterium that is associated with the plant rhizosphere. It shows increasing prevalence in immunocompromised patients. We report a simple method for selective isolation of S. maltophilia from soils which makes use of both its resistance to imipenem and its requirement for methionine.     

A Simple, Efficient Method for the Separation of Humic Substances and DNA from Environmental Samples

Three different gels (Sepharose 4B, Sephadex G-200, and Sephadex G-50) were evaluated as a means of removing humic contaminants from DNA extracts of environmental samples. Sepharose 4B gave superior separation of DNA from humics, and DNA purified in this way showed consistently greater amplification than DNA purified by the other materials.     

A Rapid and Efficient Method for the Isolation of Proteins from Polyacrylamide Gels

A procedure is described for the rapid and efficient electrophoretic elution of protein from polyacrylamide gels which is then collected in a dialysis bag tied to the end of a tube containing the gel slices. To illustrate the method a heterogeneous preparation of alkaline phosphatase was used from which a single homogeneous component was isolated in six hours with a recovery of 86%. The eluted protein is collected in a volume which can easily be kept below 1.5 ml, thus eliminating the need for subsequent concentration. The method has also been used successfully in two other systems in which a human lung tumor-associated antigen and glycogen synthetase from yeast were isolated. Since the method utilizes a standard analytical gel electrophoresis apparatus with no modifications or accessories, it should be immediately applicable for the isolation of many different proteins from polyacrylamide gels.     

A Simple Silica-based Method for Metagenomic DNA Extraction from Soil and Sediments

A new method is described for extraction of metagenomic DNA from soil and sediments which is based on DNA adsorption to silica without the use of phenol, ethanol precipitation or a cesium chloride gradient. High-quality DNA was obtained, and PCR inhibition was overcome by adding bovine serum albumin and adjusting magnesium concentration. By using PCR-DGGE with Firmicutes and lactic acid bacteria-specific primers the extracted metagenomic DNA was shown to contain a mixture of bacterial genomes. This method can be used for screening bacterial diversity in soil and sediment samples.     

A Simple Method for the Purification of Nisin

Nisin, an antimicrobial peptide showing activity against a broad range of Gram-positive bacteria, is widely used as a food preservative and has potential as a therapeutic for a range of infectious diseases. Here, we present a simple purification method, based on a salting-out approach, which can produce a powder containing ～33% nisin, from a nisin-producing culture in a whey permeate-based medium. This process removes over 99% of the lactic acid, NaCl, lactose and non-nisin proteins from the cell-free culture supernatant. The approach can also enrich a commonly used commercial nisin preparation over 30-fold to a purity of ～58%. These are higher purities than comparable published methods. The simplicity of this approach facilitates its use in research and also its scale-up.