Efficient and Accurate Algorithm for Cleaved Fragments Prediction (CFPA) in Protein Sequences Dataset Based on Consensus and Its Variants: A Novel Degradomics Prediction Application

Protein Degradome of Spinal Cord Injury: Biomarkers and Potential Therapeutic Targets

Degradomics is a proteomics sub-discipline whose goal is to identify and characterize protease-substrate repertoires. With the aim of deciphering and characterizing key signature breakdown products, degradomics emerged to define encryptic biomarker neoproteins specific to certain disease processes. Remarkable improvements in structural and analytical experimental methodologies as evident in research investigating cellular behavior in neuroscience and cancer have allowed the identification of specific degradomes, increasing our knowledge about proteases and their regulators and substrates along with their implications in health and disease. A physiologic balance between protein synthesis and degradation is sought with the activation of proteolytic enzymes such as calpains, caspases, cathepsins, and matrix metalloproteinases. Proteolysis is essential for development, growth, and regeneration; however, inappropriate and uncontrolled activation of the proteolytic system renders the diseased tissue susceptible to further neurotoxic processes. In this article, we aim to review the protease-substrate repertoires as well as emerging therapeutic interventions in spinal cord injury at the degradomic level. Several protease substrates and their breakdown products, essential for the neuronal structural integrity and functional capacity, have been characterized in neurotrauma including cytoskeletal proteins, neuronal extracellular matrix glycoproteins, cell junction proteins, and ion channels. Therefore, targeting exaggerated protease activity provides a potentially effective therapeutic approach in the management of protease-mediated neurotoxicity in reducing the extent of damage secondary to spinal cord injury.

Fate and Biological Activity of the Antimicrobial Lasso Peptide Microcin J25 Under Gastrointestinal Tract Conditions

The bacteriocin microcin J25 (MccJ25) inhibits the growth of Gram-negative pathogens including Salmonella and Shigella species, and Escherichia coli. This 21-amino acid peptide has remarkable stability to heat and extreme pH values and resistance to many proteases, thanks to a characteristic lasso structure. In this study, we used the dynamic simulator TIM-1 as gastro-intestinal tract model to evaluate the stability and antibacterial activity of MccJ25 during passage through the proximal portion of the human gastrointestinal tract. MccJ25 concentration was measured in the different simulator sections by HPLC, and inhibition of Salmonella enterica serotype Enteritidis was evaluated using qualitative and quantitative assays. LC-MS/MS analysis and subsequent molecular networking analysis on the Global Natural Product Social Molecular Networking platform (GNPS) and analysis of the peptide degradation in the presence of proteolytic enzymes mimicking the gastro-intestinal conditions permitted to delineate the fate of MccJ25 through identification of the main degradation products. MccJ25 was relatively stable under gastric conditions, but degraded rapidly in the compartment mimicking the duodenum, notably in the presence of pancreatin. Among pancreatin components, elastase I appeared primarily responsible for MccJ25 breakdown, while α-chymotrypsin was less efficient.