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Three-dimensional structures, dynamics and calcium-mediated interactions of the exopolysaccharide, Infernan, produced by the deep-sea hydrothermal bacterium Alteromonas infernus
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.
Keyword(s)
Exopolysaccharides, Alteromonas infernus, 3 dimensional structures, Gel forming, Molecular dynamics, Quantum chemistry, Calcium binding
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File | Pages | Size | Access | |
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Publisher's official version | 11 | 3 Mo | ||
Supplementary material | - | 1 Mo | ||
Author's final draft | 20 | 999 Ko |