A computational study of alginate lyases and homology modeling of AlyPA: Implications for treatment of cystic fibrosis

ABSTRACT Alginate Lyase is an enzyme intended to catalyze the degradation of alginate, which facilitate to have its medical importance being useful to reduce cystic fibrosis complications, along with its industrial use. Although some sources of alginate lyase were found to be effective during laboratory test but they were inappropriate for medical use, mainly due to the complexity of their insufficient production. In this study, we were deliberate to find new efficient sources to solve the problem, and thus alginate lyases from different source of organisms were analyzed through bioinformatics tools for phylogenetic analysis, homology & motif analysis for both therapeutic and industrial purposes. We also found a conserved “alginate_lyase2” domain uniformly observed in alginate lyase sequences. Among the alginate lyase-producing bacterial strain, suggesting that Pseudoalteromonas sp. SM0524 is a good producer of alginate lyases and also showed activities toward both poly G (α-L-guluronic acid) and poly M (β-D-mannuronic acid), indicating that it is a bifunctional alginate lyase. So the homology model of the wild type alginate lyase (AlyPA) of marine bacterium