Turning Polysaccharides into Injectable and Rapid Self-Healing Antibacterial Hydrogels for Antibacterial Treatment and Bacterial-Infected Wound Healing.

Great efforts have been devoted to the development of novel and multifunctional wound dressing materials to meet the different needs of wound healing. Herein, we covalently grafted quaternary ammonium groups (QAGs) containing 12-carbon straight-chain alkanes to the dextran polymer skeleton. We then oxidized the resulting product into oxidized quaternized dextran (OQD).

Insights into protease sequence similarities by comparing substrate sequences and phylogenetic dynamics.

Based on substrate sequences, we proposed a novel method for comparing sequence similarities among 68 proteases compiled from the MEROPS online database. The rank vector was defined based on the frequencies of amino acids at each site of the substrate, aiming to eliminate the different order variances of magnitude between proteases. Without any assumption on homology, a protease specificity tree is constructed with a striking clustering of proteases from different evolutionary origins and catalytic types.

Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites.

Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites.

DCGR: feature extractions from protein sequences based on CGR via remodeling multiple information.

Background: Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on graphical representation is one of the most effective and efficient ways. However, most existing methods suffer limitations from their method design.

Block-based characterization of protease specificity from substrate sequence profile.

Background: The mechanism of action of proteases has been widely studied based on substrate specificity. Prior research has been focused on the amino acids at a single amino acid site, but rarely on combinations of amino acids around the cleavage bond.

Results: We propose a novel block-based approach to reveal the potential combinations of amino acids which may regulate the action of proteases.