Open Access Published by De Gruyter Open Access

Volume 1 Issue 1

January 2015

Issue of Peptidomics

Contents
Journal Overview

Open Access March 30, 2015

Peptidomics in veterinary science: focus on bovine paratuberculosis

Cristian Piras, Alessio Soggiu, Viviana Greco, Isabella Alloggio, Luigi Bonizzi, Paola Roncada

More Download PDF

Abstract

Bacterial infections represent a serious burden both for animal production and human health (zoonosis). Faster and more reliable diagnosis are mandatory in order to avoid economic losses and antibiotics misuse. The development of new potential diagnostic strategies for the immunodetection of pathogens is closely linked to the discovery of small polypeptides with immunogenic or immunoreactive activity. The candidate peptides used for this purpose must have several properties principally represented by their specificity and their location in the bacterial cell. Both proteomics, peptidomics and bioinformatics represent powerful complementary tools to discover specific immunoreactive peptides useful for diagnosis or vaccine. Peptidomics of Mycobacterium avium subsp. paratuberculosis (MAP) represents a good example of the potential of this discovery-phase. This review reports a comprehensive update of the current scientific knowledge about proteins and peptides of MAP with already documented humoral response. These findings, together with bioinformatics tools available, could be extremely useful to design a better strategy for subclinical bovine paratuberculosis diagnosis. The knowledge provided also represents a reliable example on the workflow to be followed in the direction of the diagnosis of other diseases through a peptidomic approach.

Open Access March 31, 2015

Unravelling peptidomes by in silico mining

Johannes Koehbach, Kathryn A.V. Jackson

More Download PDF

Abstract

Peptides of great number and diversity occur in all domains of life and exhibit a range of pharmaceutically relevant bioactivities. The complexity of biological samples including human cells or tissues, plant extracts or animal venom cocktails, often impedes the discovery of novel bioactive peptides using mass spectrometrybased peptidomics analysis. An increasing number of publicly available genome and transcriptome datasets, together with refined bioinformatics analysis, allows for rapid identification of novel peptides which may have been previously unrecognized. Moreover, a combination of information extracted from in silico mining approaches together with data derived from mass spectrometrybased studies provides new impetus for future peptidome analyses, including the discovery of novel bioactive peptides that can serve as starting points for drug development.

Topical Issue: FeS-2015, IUBMB Symposium FeS 2015 - Iron Sulfur Cluster Biogenesis and Regulation June 23-26, 2015 - Bergamo, Italy

Open Access January 20, 2016

FeS 2015, an IUBMB Symposium Gathering new information on the oldest cofactors in biology

Francesco Bonomi, Stefania Iametti

Download PDF

Open Access January 20, 2016

Serum metal evaluation in a small cohort of Amyotrophic Lateral Sclerosis patients reveals high levels of thiophylic species

Stefano De Benedetti, Giorgio Lucchini, Alessandro Marocchi, Silvana Penco, Christian Lunetta, Stefania Iametti, Elisabetta Gianazza, Francesco Bonomi

More Download PDF

Abstract

Amyotrophic Lateral Sclerosis (ALS) has often been associated with improper/altered metal metabolism. Analysis of thiophylic metals in serum from a small and geographically restricted cohort of ALS patients indicates contents of Pb and Ni much higher in patients than in controls (Ni, 5-fold; Pb, 2-fold). Se levels are also higher in the patients’ group, which has instead lower As levels than controls. Thiophylic metals may impair biogenesis of FeS clusters or substitute for iron, even in folded proteins; Se may non-functionally replace S. Thus, improper assembly/ function of FeS proteins could represent another possible issue to be considered in ALS pathogenesis.

Open Access January 20, 2016

Cysteine-containing peptides are produced by sequential clipping, but not released, from lupin 11S storage globulin during early germination

Jessica Capraro, Elisabetta Galanti, Mauro Marengo, Marcello Duranti, Alessio Scarafoni

More Download PDF

Abstract

The digestion of the seed storage proteins is a finely regulated process operated by several proteases whose action is influenced by the exposure of specific regions, which became progressively available upon their action. We focused our study on the initial stages of germination, where more subtle modifications to the storage proteins are expected. Small-size peptides containing cysteine residues and other possible metalbinding regions are de facto produced but are not released from the “parental” protein since they remain bound trough disulphide bridges. The meaning of these findings is discussed.

Open Access January 20, 2016

Functional investigation of Bacillus subtilis YrkF’s involvement in sulfur transfer reactions

Hannah L. Martin, Katherine A. Black, Patricia C. Dos Santos

More Download PDF

Abstract

Sulfur incorporation into the molybdenum cofactor (Moco) in the Gram-negative bacterium Escherichia coli involves six enzymes. The initial reaction includes the cysteine desulfurase IscS, the sulfurtransferase TusA, and the rhodanese domaincontaining protein YnjE. The Gram-positive bacterium Bacillus subtilis contains no direct homologs for IscS, but rather four distinct cysteine desulfurases (YrvO, NifS, NifZ, SufS) and YrkF, a two-domain rhodanese protein with an N-terminal domain similar to TusA. Bioinformatic analysis was used to identify potential enzymes involved in the B. subtilis Moco thiolation pathway and in vitro reactions demonstrated that YrkF can accept sulfur from and enhance the activity of YrvO.

Open Access January 20, 2016

Stabilization of the “open” conformer of apoIscU on the surface of polystyrene nanobeads accelerates assembly of a 2Fe2S structure

Alberto Barbiroli, Francesco Bonomi, Stefania Iametti, Mauro Marengo

More Download PDF

Abstract

The scaffold protein IscU is involved in the assembly/transfer of FeS clusters. IscU exists in both open and closed conformation. The clusterless open conformation of IscU adheres to the hydrophobic surface of polystyrene nanobeads, as observed for other proteins. Increased accessibility of the ligand cysteines in bound IscU facilitates assembly of a 2Fe2S cluster, and the cluster-bearing structured form of IscU does not interact with the nanobeads, thus ensuring turnover. The dependence of accelerated cluster assembly on the nanobeads concentration pointed to steric and crowding effects as for promoting cluster formation, and confirms the requirement for structural flexibility of IscU .

About this journal

The journal is closed for submissions.

Peptidomics was the very first journal devoted to the peptidome, i.e., the low molecular mass window of the proteome. The content presents the proteome, representing essential gene products in all organisms from the most primitive to the most evolved, carrying important biological information.

The journal was published in Open Access model and is archived in Portico.

All authors retain copyright, unless – due to their local circumstances – their work is not copyrighted. The copyrights are governed by the Creative-Commons license.