Recent advances of thiol-selective bioconjugation reactions

Proteins are the most abundant biomolecules within a cell and are involved in all biochemical cellular processes, fulfilling specific functions with unmatched precision. This unique specificity makes proteins an ideal scaffold to generate tools for the exploration of natural systems or for the construction of modern therapeutics. Thus, the chemoselective modification of proteins with functionalities that are not defined by the genetic code has become an indispensable approach for life science research and the development of therapeutics. Amongst site-selective strategies for protein modification, cysteine-selective approaches have long been used for the generation of functional protein conjugates and new reactions continue to emerge, offering solutions for diverse research questions. In this review, we are highlighting new strategies for the chemoselective modification of cysteine residues in peptides, proteins and antibodies with a particular focus on the most recent years. We lay special focus on new reagents for efficient cysteine conjugation that produce stable conjugation products with significant pharmaceutical application.     

An accurate fluorescent assay for quantifying the extent of RNA editing

Recent data suggest that small differences in editing efficiency can have significant functional consequences. Here we present a fluorescent poisoned primer extension assay that is capable of distinguishing editing efficiency differences as low as 5%. For a poison-primer extension assay to be accurate, the extension product must stop at the intended base. Sometimes, however, it runs beyond. We tested the effect of specific enzyme-terminator combinations on the amount of run through. In the worst cases it accounted for 70% of the total signal, and in the best cases <5%. In addition, the specific base can affect run through, with G producing the least. The accuracy of the assay was demonstrated on templates derived from mixed plasmids and then verified on two biological substrates. Using either a K(+) channel mRNA that contains a site for adenosine deamination or an ndhB mRNA that contains a site for cytidine deamination, the editing efficiency predicted by the assay closely matched that predicted by bulk sequencing of individual cDNA clones. This assay should prove useful for analyzing small changes in editing efficiency or for quantifying single nucleotide polymorphisms.     

Imaging and quantifying carbohydrate transport to the developing ovaries of maize

BACKGROUND AND AIMS: Shade or inadequate water can inhibit photosynthesis and limit the development of maize (Zea mays) ovaries around the time of pollination, potentially reducing the number of kernels at harvest. This study investigated whether the decreased photosynthesis diminished only the sugar supply or also altered the transport path to the ovaries. METHODS: Photosynthesis and water potentials (Psiw) were measured in the leaves while dry matter delivery was monitored in the ovaries. Ovary glucose, starch and acid invertase activities were measured in situ. Stems were fed xylem-mobile safranin or phloem-mobile carboxyfluorescein (CF), and the dye transport to the ovaries was determined. KEY RESULTS: Under normal conditions, the ovaries gained in dry mass, and starch accumulated in the pedicel and ovary wall. Glucose accumulated in the pedicel, apparently in the apoplast where insoluble (cell-wall-bound) acid invertase acted on the arriving sucrose. A glucose gradient developed from pedicel to nucellus. Safranin moved in the xylem and did not reach the ovary, but CF moved in the phloem and arrived at the ovary. CF also spread into the pedicel but unlike glucose it did not enter the nucellus. Low Psiw or shade decreased leaf photosynthesis, ovary dry mass accumulation, invertase activities, pedicel glucose, starch accumulation and CF delivery. Removal of these treatments reversed the effects. CONCLUSIONS: The success of CF in tracing the general path and rate of carbohydrate transport gave visual evidence that phloem transport to the ovary decreased at low Psiw or in the shade but otherwise remained functional. The decreases indicated that losses in carbohydrate delivery are central features of failed ovary development under these conditions. The selectivity of transport into the nucellus resembled the situation later when embryo and endosperm are present and selective uptake occurs from the apoplast.     

Collection strategies for quantifying protist assemblages in temperate headwater streams

We aimed at indicating some regularities of a constructed wetland treating agricultural runoff in China. The regularities, including the nitrogen removal capacity all year round, the nitrogen distribution pathways, and the nitrogen species removal kinetics, of a free water surface constructed wetland (2,800 m²) in the Dianchi Valley, which has been in operation for 27 months, were studied. The planted Phragmites australis and Zizania caduciflora were harvested biannually. The average inflow rate was recorded by an ultrasonic flow instrument, and then the hydraulic loading rate (HLR) and hydraulic retention time (HRT) were calculated. The average inflow and outflow concentrations of total nitrogen (TN), ammonia, and nitrate were measured, while the corresponding removal rates were calculated, showing better results than other constructed wetlands. Then the distribution pathways of nitrogen were analyzed, which indicated that plant harvesting was more important in wetland-treated agricultural runoff than in domestic wastewater. The reason for a good nitrogen removal capability and the obvious function of plants in the present wetland is the sound climate and intermittent inflow in the wetland. Results showed that inflow load had significant correction with both TN and ammonia removal efficiency. HLR, inflow rate, inflow nitrogen concentration, and temperature had significant and positive correction with both TN and ammonia removal. However, HRT had negative correction with both TN and ammonia removal, and the nitrate removal efficiency and parameters mentioned earlier were not significantly correlated. The rate constant values for nitrate and ammonia in summer were obviously larger than in winter. It is possible that bacterial and microbial activities were more active in summer than winter, and more conducive to bacterial and vegetative growth in summer than winter. Since this study was a pioneer for the implementation of constructed wetlands in China treating agricultural runoff, it has proved that this eco-technology could be used effectively for water quality enhancement in China and other areas with a similar climate.     

Use of stereo aerial photography for quantifying changes in the extent and height of mangroves in tropical Australia

The study investigated the use of aerial photographs, acquired in 1950 and1991, for assessing the temporal dynamics of mangroves along the WestAlligator River in Australia's Northern Territory. For both years,mangrove extent was mapped using an unsupervised classification of thedigital orthomosaic and Digital Elevation Models (DEMs), or height maps,of the mangrove canopy were derived from stereo pairs. Helicopter andfield observations in 1998 and 1999 respectively provided ground truthfor interpreting the derived datasets. The comparison of mangrove extentrevealed a substantial movement over the 41-year period, perhaps inresponse to hydrological changes that have resulted in a landward extensionof saline conditions. Changes in the height of mangroves were observedbut were difficult to quantify due to the reduced quality of the 1950 DEM. The study demonstrated the viability of using time-series of aerialphotography for monitoring and understanding the long-term response ofmangroves to environmental change, including hydrological variations andsea level rise.     

Gold nanoparticles and bioconjugation: a pathway for proteomic applications

In the last few years gold nanoparticles (AuNPs) became extremely interesting materials due to their enhanced optical, chemical and electrical properties. With the intention of taking advantage of those properties, the use of AuNPs has spread into a wide variety of areas such as physics, chemistry, biology, industry and medicine. More interestingly, their ability to form robust conjugates with biomolecules has given proteomics a new tool to improve aspects where the current methods to study proteins and their interactions in living cells cannot achieve the success required. In this review we present some of the current methods for AuNPs synthesis, the tailoring of their surface with ligands to improve stability and strategies to conjugate with biomolecules. Lastly, we also discuss their application in proteomic methods and recent developments in clinical diagnosis.     

Engineering of staphylococcal surfaces for biotechnological applications

Novel surface proteins can be introduced onto bacterial cell surfaces by recombinant means. Here, we describe various applications of two such display systems for the food-grade bacteria Staphylococcus carnosus and Staphylococcus xylosus, respectively. The achievements in the use of such staphylococci as live bacterial vaccine delivery vehicles will be described. Co-display of proteins and peptides with adhesive properties to enable targeting of the bacteria, have significantly improved the vaccine delivery potential. Recently, protective immunity to respiratory syncytial virus (RSV) could be evoked in mice by intranasal immunization using such 'second generation' vaccine delivery systems. Furthermore, antibody fragments and other 'affinity proteins' with capacity to specifically bind a certain protein, e.g. Staphylococcus aureus protein A-based affibodies, have been surface-displayed on staphylococci as initial efforts to create whole-cell diagnostic devices. Surface display of metal-binding peptides, or protein domains into which metal binding properties has been engineered by combinatorial protein engineering, have been exploited to create staphylococcal bioadsorbents for potential environmental or biosensor applications. The use of these staphylococcal surface display systems as alternatives for display of large protein libraries and subsequent affinity selection of relevant binding proteins by fluorescence-activated cell sorting (FACS) will be discussed.     

Simplified approach for developing the rate expressions for enzyme-catalyzed reactions

A Simplified version of rate equations for enzyme-catalyzed reactions has been developed in which the rate equation is analyzed with two different mechanisms: ordered bi–ter and Ping-Pong bi–bi mechanisms. This procedure is able to develop the rate expressions accurately. Random sequential order mechanism can be effectively explained by this approach.     

Hyaluronic acid-N-hydroxysuccinimide: a useful intermediate for bioconjugation.

Hyaluronic acid (HA) is an abundant nonsulfated glycosaminoglycan component of synovial fluid and the extracellular matrix. HA is an important building block for biocompatible and biointeractive materials with applications in drug delivery, tissue engineering, wound repair, and viscosupplementation. Herein we describe the synthesis and characterization of HA-N-succinimide, an activated ester of the glucuronic acid moiety. This HA-active ester intermediate is a precursor for fluorescent probes, drug-polymer conjugates, and cross-linked hydrogels. As a demonstration, we used HA-NHS to prepare HA-BODIPY by coupling with the hydrazide derivative of the fluor. Intracellular uptake of HA-BODIPY into human ovarian cancer cells, which overexpress cell-surface HA receptors, was visualized using confocal microscopy.     

Human hopping on damped surfaces: strategies for adjusting leg mechanics

Fast-moving legged animals bounce along the ground with spring-like legs and agilely traverse variable terrain. Previous research has shown that hopping and running humans maintain the same bouncing movement of the body's centre of mass on a range of elastic surfaces by adjusting their spring-like legs to exactly offset changes in surface stiffness. This study investigated human hopping on damped surfaces that dissipated up to 72% of the hopper's mechanical energy. On these surfaces, the legs did not act like pure springs. Leg muscles performed up to 24-fold more net work to replace the energy lost by the damped surface. However, considering the leg and surface together, the combination appeared to behave like a constant stiffness spring on all damped surfaces. By conserving the mechanics of the leg-surface combination regardless of surface damping, hoppers also conserved centre-of-mass motions. Thus, the normal bouncing movements of the centre of mass in hopping are not always a direct result of spring-like leg behaviour. Conserving the trajectory of the centre of mass by maintaining spring-like mechanics of the leg-surface combination may be an important control strategy for fast-legged locomotion on variable terrain.     

Bacterial adsorption to smooth surfaces: Rate, extent, and spatial pattern

The influence of bulk-water bacterial cell concentration and specific growth rate history on bacterial adsorption rates to surfaces was investigated using response surface analysis. A pure culture of Pseudomonas sp. 224S was grown in a chemostat and pumped into a continuous flow reactor where the bacteria were exposed to clean, glass surfaces under turbulent flow conditions for a period of six hours. Adsorption rate decreased approximately linearly with increasing specific growth rate history. Glass surfaces became saturated with 224S at ca. 0.1% coverage and the resulting spatial pattern of the adsorbed cells deviated from random in the direction of uniformity.     

Dual display of proteins on the yeast cell surface simplifies quantification of binding interactions and enzymatic bioconjugation reactions

Yeast surface display, a well‐established technology for protein analysis and engineering, involves expressing a protein of interest as a genetic fusion to either the N‐ or C‐terminus of the yeast Aga2p mating protein. Historically, yeast‐displayed protein variants are flanked by peptide epitope tags that enable flow cytometric measurement of construct expression using fluorescent primary or secondary antibodies. Here, we built upon this technology to develop a new yeast display strategy that comprises fusion of two different proteins to Aga2p, one to the N‐terminus and one to the C‐terminus. This approach allows an antibody fragment, ligand, or receptor to be directly coupled to expression of a fluorescent protein readout, eliminating the need for antibody‐staining of epitope tags to quantify yeast protein expression levels. We show that this system simplifies quantification of protein‐protein binding interactions measured on the yeast cell surface. Moreover, we show that this system facilitates co‐expression of a bioconjugation enzyme and its corresponding peptide substrate on the same Aga2p construct, enabling enzyme expression and catalytic activity to be measured on the surface of yeast.     

Principles and strategies for developing network models in cancer

The flood of genome-wide data generated by high-throughput technologies currently provides biologists with an unprecedented opportunity: to manipulate, query, and reconstruct functional molecular networks of cells. Here, we outline three underlying principles and six strategies to infer network models from genomic data. Then, using cancer as an example, we describe experimental and computational approaches to infer "differential" networks that can identify genes and processes driving disease phenotypes. In conclusion, we discuss how a network-level understanding of cancer can be used to predict drug response and guide therapeutics.     

An extraction free modified o-phthalaldehyde assay for quantifying residual protein and microbial biofilms on surfaces

Abstract

Biological contamination of surfaces in industry and healthcare is an important vector of disease transmission. Current assays for detecting surface-adherent contamination require extraction of biological soil. However, physical inaccessibility or poor solubility may limit recovery. Here, how the o-phthalaldehyde (OPA) protein assay can be modified to measure residual protein (modeled with bovine serum albumin) or biofilm on a surface without extraction is described. The assay limit of detection (LOD) for protein was 1.6 µg cm^?2. The detection threshold for Staphylococcus epidermis biofilm was 117 µg cm^?2. The clinical utility of the method was demonstrated for measurements taken from clinically used endoscopes. Since this method is more sensitive than extraction-based testing, clinical results should not be compared with conventional benchmarks. By enabling direct detection and quantification of soils in complex or hard-to-reach areas, this method has potential to improve the margin of safety in medical and industrial cleaning processes.     

Dynamic metabolic engineering: New strategies for developing responsive cell factories

Metabolic engineering strategies have enabled improvements in yield and titer for a variety of valuable small molecules produced naturally in microorganisms, as well as those produced via heterologous pathways. Typically, the approaches have been focused on up‐ and downregulation of genes to redistribute steady‐state pathway fluxes, but more recently a number of groups have developed strategies for dynamic regulation, which allows rebalancing of fluxes according to changing conditions in the cell or the fermentation medium. This review highlights some of the recently published work related to dynamic metabolic engineering strategies and explores how advances in high‐throughput screening and synthetic biology can support development of new dynamic systems. Dynamic gene expression profiles allow trade‐offs between growth and production to be better managed and can help avoid build‐up of undesired intermediates. The implementation is more complex relative to static control, but advances in screening techniques and DNA synthesis will continue to drive innovation in this field.     

Novel method for in vitro O-glycosylation of proteins: application for bioconjugation

Here, we describe a new method for the bioconjugation of a nonglycoprotein with biomolecules. Using polypeptide-alpha- N-acetylgalactosaminyltransferase II (ppGalNAc-T2), we transfer a C2-modified galactose that has a chemical handle, such as ketone or azide, from its respective UDP-sugars to the Ser/Thr residue(s) of an acceptor polypeptide fused to the nonglycoprotein. The protein with the modified galactose is then coupled to a biomolecule that carries an orthogonal reactive group. As a model system for the nonglycoprotein, we engineered glutathione- S-transferase (GST) protein with a 17-amino-acid-long fusion peptide at the C-terminal end that was expressed as a soluble protein in E. coli. The ppGalNAc-T2 protein, the catalytic domain with the C-terminal lectin domain, was expressed as inclusion bodies in E. coli, and an in vitro folding method was developed to produce milligram quantities of the active enzyme from a liter of bacterial culture. This ppGalNAc-T2 enzyme transfers from the UDP-sugars not only GalNAc but also C2-modified galactose with a chemical handle to the Ser/Thr residue(s) in the fusion peptide. The chemical handle at the C2 of galactose is used for conjugation and assembly of bionanoparticles and preparation of immuno-liposomes for a targeted drug delivery system. This novel method enables one to glycosylate, using ppGalNAc-T2, the important biological nonglycoproteins, such as single-chain antibodies, growth factors, or bacterial toxins, with an engineered 17-residue peptide sequence at the C-terminus of the molecule, for conjugation and coupling.