Anchimeric assistance effect on regioselective hydrolysis of branched PEGs: a mechanistic investigation

Branched poly(ethylene glycols) (PEG2) are nowadays widely used for protein and peptides bioconjugation, for their favourable properties (such as the ability to protect the protein surface in an 'umbrella like' fashion). The discovery that mPEG(2)-LysMetbeta AlaOEt lost one mPEG chain during standard base-catalysed ester hydrolysis conditions prompted us to investigate the hydrolytic stability of such systems and the mechanism involved in the PEG chain loss. A series of branched PEGs, substituted with different aminoacids and dipeptides, have been prepared to test the influence of steric hindrance, chain lengths, ramification and Lys-AA amide substitution on hydrolysis. Unexpected results reveal an anchimeric assistance of the Lys-AaA amide proton to the hydrolysis of the carbamoyl moiety joining mPEG to the alpha-amino group of lysine through the formation of an hydantoin system.     

A conformational model of per-O-acetyl-cyclomaltoheptaose (-beta-cyclodextrin) in solution: detection of partial inversion of glucopyranose units by NMR spectroscopy

The stereochemical features of per-O-acetyl-cyclomaltoheptaose (-beta-cyclodextrin) have been investigated in solution by NMR spectroscopy, and the deviation of functionalised glucopyranose rings from 4C(1) chairs to skew-type conformations has been detected.     

Measurement of DNA breaks and oxidative damage in polymorphonuclear and mononuclear white blood cells: a novel approach using the comet assay

DNA damage is thought to play a relevant role in degenerative diseases and aging. Therefore, measuring DNA damage in living cells without artifacts is a critical issue, especially with very sensitive methods, such as the comet assay, which can detect very low levels of DNA damage. We show here that the procedures of cell subtype isolation increase DNA damage measured in human white blood cells (WBC) with the comet assay. We describe a novel and simple method to measure DNA strand breaks and oxidative damage separately in polymorphonuclear and mononuclear leukocytes, using whole blood without previous cell isolation. This method can be useful for measuring DNA damage in different subtypes of human peripheral leukocytes, avoiding the artifacts and the time involved in the cell separation procedures.     

New therapies for muscular dystrophy: cautious optimism

The quest for a therapy for muscular dystrophy has been the driving force behind the past 40 years of advances in this field. Numerous results, such as the identification of satellite cells and gene mutations that are responsible for most forms of dystrophies, advances in gene transfer and modification technology and, more recently, stem cells, have fueled hopes. However, administering corticosteroids still remains the only effective treatment available. Several recent advances have uncovered a diversity of possible therapeutic approaches, from pharmacological treatments to gene therapy (exon-skipping and adeno-associated viruses) and cell therapy with different types of newly identified stem cells. Importantly, a combination of these strategies might greatly enhance the possibility of successful therapy.     

Vav mediates Ras stimulation by direct activation of the GDP/GTP exchange factor Ras GRP1

Here we describe a new signaling cross-talk between the Vav/Rac1 and Ras pathways that is established through the stimulation of RasGRP1, an exchange factor for Ras subfamily GTPases. This interaction is crucial for Ras activation in lymphoid cells, since this GTPase cannot become activated in the absence of Vav proteins. The activation of RasGRP1 requires both the generation of diacylglycerol via phospho lipase C-gamma and the induction of actin polymerization, two responses induced by Vav and Rac1 that facilitate the translocation of RasGRP1 to juxtamembrane areas of the cell. Consistent with this, the cross-talk can be activated by tyrosine-phosphorylated wild-type Vav, oncogenic Vav and constitutively active Rac1. Conversely, Ras activation can be blocked in lymphocytes and ectopic systems using inhibitors affecting either phospholipase C-gamma or F-actin polymerization. These results indicate that a relay mechanism exists in lymphoid and other cells helping in the generation of robust signaling responses by the Rac/Rho and Ras pathways upon receptor engagement.     

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites

SUMMARY: SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting signals and predicts their cleavage sites. The accuracy in cross-validation is similar to that of other available programs: the rate of false positives is 4 and 6%, for prokaryotes and eukaryotes respectively and that of false negatives is 3% in both cases. When a set of 409 prokaryotic lipoproteins is predicted, SPEPlip predicts 97% of the chains in the signal peptide class. However, by integrating SPEPlip with a regular expression search utility based on the PROSITE pattern, we can successfully discriminate signal peptide-containing chains from lipoproteins. We propose the method for detecting and discriminating signal peptides containing chains and lipoproteins. AVAILABILITY: It can be accessed through the web page at http://gpcr.biocomp.unibo.it/predictors/     

In silico prediction of the structure of membrane proteins: is it feasible?

In the 'omic' era, hundreds of genomes are available for protein sequence analysis, and some 30 per cent of all sequences are of membrane proteins. Unlike globular proteins, a 3D model for membrane proteins can hardly be computed starting from the sequence. Why is this so? What can we really compute and with what reliability? These and other matters are outlined.