Complete Model of Vinculin Suggests the Mechanism of Activation by Helical Super-Bundle Unfurling

The Protein Journal - To shed light onto the activation mechanism of vinculin, we carried out a detailed refinement of chicken vinculin and compared it to the human protein which is greater than...     

Fibers with polypyrrole and polythiophene phases for isolation and determination of adrenolytic drugs from human plasma by SPME-HPLC

In this study, polypyrrole (PPy) and polythiophene (PTh) SPME coatings and their ability to extract selected adrenolytic drugs with different physico-chemical properties from standard solutions and human plasma samples were evaluated. In measurements metoprolol, oxprenolol, mexiletine, propranolol, and propaphenon were investigated. The main parameters such as extraction time, desorption conditions and pH influence were examined. Inter-day precisions were in range 0.1–2.0%, 1.1–2.9%, 1.3–2.6%, 0.1–2.6% and 0.3–2.1% for metoprolol, oxprenolol, mexiletine, propranolol and propaphenon, respectively. Accuracies were less than 15%, which was evaluated by analyzing preparation samples of five replicates. The method was successfully applied to human plasma samples spiked with selected adrenolytic drugs. The method was linear in the concentration range from 1 to 10 μg/ml for all of studied adrenolytic drugs using human plasma samples. The PTh-SPME coating displayed higher extraction efficiency towards the target analytes in comparison to PPy-SPME. The reproducibility of the extraction using polypyrrole and polythiophene fibers was confirmed by variation coefficients lower than 8% and 3%, respectively.     

A novel method for quantified, superresolved, three-dimensional colocalisation of isotropic, fluorescent particles

Colocalisation, the overlap of subcellular structures labelled with different colours, is a key step to characterise cellular phenotypes. We have developed a novel bioimage informatics approach for quantifying colocalisation of round, blob-like structures in two-colour, highly resolved, three-dimensional fluorescence microscopy datasets. First, the algorithm identifies isotropic fluorescent particles, of relative brightness compared to their immediate neighbourhood, in three dimensions and for each colour. The centroids of these spots are then determined, and each object in one location of a colour image is checked for a corresponding object in the other colour image. Three-dimensional distance maps between the centroids of differently coloured spots then display where and how closely they colocalise, while histograms allow to analyse all colocalisation distances. We use the method to reveal sparse colocalisation of different human leukocyte antigen receptors in choriocarcinoma cells. It can also be applied to other isotropic subcellular structures such as vesicles, aggresomes and chloroplasts. The simple, robust and fast approach yields superresolved, object-based colocalisation maps and provides a first indication of protein–protein interactions of fluorescent, isotropic particles.     

The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity

Cas4 nucleases constitute a core family of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) associated proteins, but little is known about their structure and activity. Here we report the crystal structure of the Cas4 protein Pcal_0546 from Pyrobaculum calidifontis, which revealed a monomeric protein with a RecB-like fold and one [2Fe-2S] cluster coordinated by four conserved Cys residues. Pcal_0546 exhibits metal-dependent 5′ to 3′ exonuclease activity against ssDNA substrates, whereas the Cas4 protein SSO1391 from Sulfolobus solfataricus can cleave ssDNA in both the 5′ to 3′ and 3′ to 5′ directions. The active site of Pcal_0546 contains a bound metal ion coordinated by the side chains of Asp123, Glu136, His146, and the main chain carbonyl of Ile137. Site-directed mutagenesis of Pcal_0546 and SSO1391 revealed that the residues of RecB motifs II, III and QhXXY are critical for nuclease activity, whereas mutations of the conserved Cys residues resulted in a loss of the iron-sulfur cluster, but had no effect on DNA cleavage. Our results revealed the biochemical diversity of Cas4 nucleases, which can have different oligomeric states, contain [4Fe-4S] or [2Fe-2S] clusters, and cleave single stranded DNA in different directions producing single-stranded DNA overhangs, which are potential intermediates for the synthesis of new CRISPR spacers.     

Efficient elution of purified proteins from polyvinylidene difluoride membranes (immobilon) after transfer from SDS-PAGE and their use as immunogenes

Following separation of proteins by SDS-PAGE, they are electroblotted onto polyvinylidene difluoride membranes (Immobilon). Protein bands of interest are excised, and the proteins are eluted from the membrane with detergent-containing buffers at pH 9.5. The method routinely yields recovery of 70–90%, and this is independent of protein molecular weight.