Bioinformatic resources for the investigation of proteins and proteomes

Experimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.

Bioinformatic resources for the investigation of proteins and proteomes

Experimental techniques in omics sciences need strong support of bioinformatics tools for the data management, analysis and interpretation. Scientific community develops continuously new databases and tools. They make it possible the comparison of new experimental data with the existing ones, to gain new knowledge. Bioinformatics assists proteomics scientists for protein identification from experimental data, management of the huge data produced, investigation of molecular mechanisms of protein functions, their roles in biochemical pathways, and functional interpretation of biological processes. This article introduces the main bioinformatics resources for investigation in the protein world, with references to analyses performed by means of free tools available on the net.

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

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.

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

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 .

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

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.

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

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.

Unravelling peptidomes by in silico mining

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

Peptidomics in veterinary science: focus on bovine paratuberculosis

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.