Three-dimensional structures, dynamics and calcium-mediated interactions of the exopolysaccharide, Infernan, produced by the deep-sea hydrothermal bacterium Alteromonas infernus

Abstract

The exopolysaccharide Infernan, from the bacterial strain GY785, has a complex repeating unit of nine monosaccharides established on a double-layer of sidechains. A cluster of uronic and sulfated monosaccharides confers to Infernan functional and biological activities. We characterized the 3-dimensional structures and dynamics along Molecular Dynamics trajectories and clustered the conformations in extended two-fold and five-fold helical structures. The electrostatic potential distribution over all the structures revealed negatively charged cavities explored for Ca²⁺ binding through quantum chemistry computation. The transposition of the model of Ca²⁺complexation indicates that the five-fold helices are the most favourable for interactions. The ribbon-like shape of two-fold helices brings neighbouring chains in proximity without steric clashes. The cavity chelating the Ca²⁺ of one chain is completed throughout the interaction of a sulfate group from the neighbouring chain. The resulting is a 'junction zone' based on unique chain-chain interactions governed by a heterotypic binding mode.

Keywords: 3 dimensional structures; Calcium binding; Exopolysaccharides, Alteromonas infernus; Gel forming; Molecular dynamics; Quantum chemistry.