Novel 1:1 Labeling and Purification Process for C‑Terminal Thioester and Single Cysteine Recombinant Proteins Using Generic Peptidic Toolbox Reagents

We developed a versatile set of chemical labeling reagents which allow dye ligation to the C-terminus of a protein or a single internal cysteine and target purification in a simple two-step process. This simple process results in a fully 1:1 labeled conjugate suitable for all quantitative fluorescence spectroscopy and imaging experiments. We refer to a “generic labeling toolbox” because of the flexibility to choose one of many available dyes, spacers of different lengths and compositions which increase the target solubility, a variety of affinity purification tags, and different cleavage chemistries to release the 1:1 labeled proteins. Studying protein function in vitro or in the context of live cells and organisms is of vital importance in biological research. Although label free detection technologies gain increasing interest in molecular recognition science, fluorescence spectroscopy is still the most often used detection technique for assays and screens both in academic as well as in industrial groups. For generations, fluorescence spectroscopists have labeled their proteins of interest with small fluorescent dyes by random chemical linking on the proteins’ exposed lysines and cysteines. Chemical reactions with a certain excess of activated esters or maleimides of longer wavelength dyes hardly ever result in quantitative labeling of the target protein. Most of the time, more than one exposed amino acid side chain reacts. This results in a mixture of dye–protein complexes of different labeling stoichiometries and labeling sites. Only mass spectrometry allows resolving the precise chemical composition of the conjugates. In “classical” ensemble averaging fluorescent experiments, these labeled proteins are still useful, and quantification of, e.g., ligand binding experiments, is achieved via knowledge of the overall protein concentration and a fluorescent signal change which is proportional to the amount of complex formed. With the development of fluorescence fluctuation analysis techniques working at single molecule resolution, like fluorescence correlation spectroscopy (FCS), fluorescence cross correlation spectroscopy (FCCS), fluorescence intensity diffusion analysis (FIDA), etc., it became important to work with homogeneously labeled target proteins. Each molecule participating in a binding equilibrium should be detectable when it freely fluctuates through the confocal focus of a microscope. The measured photon burst for each transition contains information about the size and the stoichiometry of a protein complex. Therefore, it is important to work with reagents that contain an exact number of tracers per protein at identical positions. The ideal fluorescent tracer–protein complex stoichiometry is 1:1. While genetic tags such as fluorescent proteins (FPs) are widely used to detect proteins, FPs have several limitations compared to chemical tags. For example, FPs cannot easily compete with organic dyes in the flexibility of modification and spectral range; moreover, FPs have disadvantages in brightness and photostability and are therefore not ideal for most biochemical single molecule studies. We present the synthesis of a series of exemplaric toolbox reagents and labeling results on three target proteins which were needed for high throughput screening experiments using fluorescence fluctuation analysis at single molecule resolution. On one target, Hu-antigen R (HuR), we demonstrated the activity of the 1:1 labeled protein in ribonucleic acid (RNA) binding, and the ease of resolving the stoichiometry of an RNA-HuR complex using the same dye on protein and RNA by Fluorescence Intensity Multiple Distribution Analysis (FIMDA) detection

Chromatograms of Permeated MANT-Iota-Carrageenan Samples After 0, 1, 2 and 3 Hours (pH 7.5).

<p>The concentrations of the fluorescence marker MANT was determined by HPLC in order to derive amounts of iota-carrageenan that have permeated bovine mucosa after 0 hour (blue), 1 hour (purple), 2 hours (pink) and 3 hours (green) incubation with MANT-iota-carrageenan, at pH 7.5. A retention time of approx. 7 minutes was defined for MANT-iota-carrageenan (highlighted by black box) and approx. 15 minutes for free MANT.</p

The Intranasal Application of Zanamivir and Carrageenan Is Synergistically Active against Influenza A Virus in the Murine Model

<div><p>Background</p><p>Carrageenan is a clinically proven and marketed compound for the treatment of viral upper respiratory tract infections. As infections caused by influenza virus are often accompanied by infections with other respiratory viruses the combination of a specific anti-influenza compound with the broadly active antiviral polymer has huge potential for the treatment of respiratory infections. Thus, the combination of the specific anti-influenza drug Zanamivir together with carrageenan in a formulation suitable for intranasal application was evaluated <i>in-vitro</i> and <i>in-vivo</i>.</p><p>Principal Findings</p><p>We show <i>in-vitro</i> that carrageenan and Zanamivir act synergistically against several influenza A virus strains (H1N1(09)pdm, H3N2, H5N1, H7N7). Moreover, we demonstrate in a lethal influenza model with a low pathogenic H7N7 virus (HA closely related to the avian influenza A(H7N9) virus) and a H1N1(09)pdm influenza virus in C57BL/6 mice that the combined use of both compounds significantly increases survival of infected animals in comparison with both mono-therapies or placebo. Remarkably, this benefit is maintained even when the treatment starts up to 72 hours post infection.</p><p>Conclusion</p><p>A nasal spray containing carrageenan and Zanamivir should therefore be tested for prevention and treatment of uncomplicated influenza in clinical trials.</p></div

Therapeutic efficacy in influenza H1N1(09)pdm lethally infected mice.

<p>Mice (n = 20 per group) were lethally intranasally infected without anesthesia on day 0 and intranasally treated twice per day either with placebo or a combination of carrageenan and Zanamivir (1 mg/kg BW/day). Treatment started either 48 hpi or 72 hpi and continued for 5 days. On the y-axis the survival of mice [%] and on the x-axis the time post infection [days] is given. Placebo treated uninfected control mice showed 100% survival (data not shown). Statistical analyses were conducted using log rank test and are shown beneath the graphs. Values of p<0.05 were considered statistically significant.</p

Isobologram of compound interaction.

<p>Comparison of the combination of different doses of both compounds necessary to reach 50% replication inhibition of (A) H7N7 and (B) H1N1(09)pdm (◆) to a model of dose additivity that would represent a curve progression of 1 (□). Dose response was tested with an adapted plaque reduction assay with semi-liquid overlay in MDCK cells. On the x-axis the concentration of Zanamivir and on the y-axis the concentration of carrageenan is presented. The concentrations (determined as mean of 3 replicates) are given as the fraction of the respective IC₅₀ values of the different viruses with the particular compound (IC₅₀ = 1).</p

IC₅₀ values of carrageenan and Zanamivir for influenza A viruses of human and animal origin.

<p>^a IC₅₀ values were calculated in comparison to untreated infected cells. Each value represents the mean IC₅₀ of 6 replicates/assay and their standard deviation.</p><p>IC₅₀ values of carrageenan and Zanamivir for influenza A viruses of human and animal origin.</p