Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This paper reports studies of in-gel digestion procedures to generate MALDI-MS peptide maps of integral membrane proteins. The methods were developed for the membrane domain of the mannitol permease of E. coli. In-gel digestion of this domain with trypsin, followed by extraction of the peptides from the gel, yields only 44% sequence coverage. Since lysines and arginines are seldomly found in the membrane-spanning regions, complete tryptic cleavage will generate large hydrophobic fragments, many of which are poorly soluble and most likely contribute to the low sequence coverage. Addition of the detergent octyl-beta-glucopyranoside (OBG), at 0.1% concentration, to the extraction solvent increases the total number of peptides detected to at least 85% of the total protein sequence. OBG facilitates the recovery of hydrophobic peptides when they are SpeedVac dried during the extraction procedure. Many of the newly recovered peptides are partial cleavage products. This seems to be advantageous since it generates hydrophobic fragments with a hydrophilic solubilizing part. In-gel CNBr cleavage resulted in 5-10-fold more intense spectra, 83% sequence coverage, fully cleaved fragments and no effect of OBG. In contrast to tryptic cleavage sites, the CNBr cleavage sites are found in transmembrane segments; cleavage at these sites generates smaller hydrophobic fragments, which are more soluble and do not need OBG. With the results of both cleavages, a complete sequence coverage of the membrane domain of the mannitol permease of E. coli is obtained without the necessity of using HPLC separation. The protocols were applied to two other integral membrane proteins, which confirmed the general applicability of CNBr cleavage and the observed effects of OBG in peptide recovery after tryptic digestion.     

Application of carbon-based nanomaterials in sample preparation: A review

In this paper, a broad overview on the applications of different carbon-based nanomaterials, including nanodiamonds, fullerenes, carbon nanotubes, graphene, carbon nanofibers, carbon nanocones-disks and nanohorns, as well as their functionalized forms, in sample preparation is provided. Particular attention has been paid to graphene because many papers regarding its application in this research field are becoming available. The distinctive properties, derivatization methods and application techniques of these materials were summarized and compared. According to their research status and perspective, these nanomaterials were classified in four groups (I: graphene and carbon nanotubes; II: carbon nanofibers; III: fullerenes; and IV: nanodiamonds, carbon nanocones/disks and carbon nanohorns) and characteristics and future trends of every group were discussed.     

Characterization of carbon nanotubes and analytical methods for their determination in environmental and biological samples: A review

In the present paper, a critical overview of the most commonly used techniques for the characterization and the determination of carbon nanotubes (CNTs) is given on the basis of 170 references (2000–2014). The analytical techniques used for CNT characterization (including microscopic and diffraction, spectroscopic, thermal and separation techniques) are classified, described, and illustrated with applied examples. Furthermore, the performance of sampling procedures as well as the available methods for the determination of CNTs in real biological and environmental samples are reviewed and discussed according to their analytical characteristics. In addition, future trends and perspectives in this field of work are critically presented.     

A review on enzyme and ultrasound: A controversial but fruitful relationship

A critical review on the effect of ultrasound (US) on enzymes and their biocatalytic action is presented here. Discussion on the information users of US acquire before utilizing the different devices, and the importance they give to US frequency is constant along the review. The authors have gone into the different areas in which the US–enzyme binomial has been applied. The lack of enough information on the US–enzyme-working conditions under which each piece of research has been developed, and the necessity to provide complete information on the data and metadata to give enough light on each piece of research (and thus on the potential comparison of results from different studies) are critically exposed. With this aim, the study has been divided into the positive effect of US on enzymes to favor the production of metabolites, polymers or proteins; and the degradation, inhibition or activation of the biocatalyst under US application. Also the effect of US on enzyme production and the main fields of application of the US–enzyme binomial are discussed.