Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies

Abstract

Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms’ lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.

Keywords

• lipoxygenase
• diatoms
• protein modelling
• sequence clustering
• docking analysis