Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
NCBI PubMed ID: 34823768Publication DOI: 10.1016/j.carbpol.2021.118732Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: S. Perez <serge.perez
cermav.cnrs.fr>
Institutions: Ifremer, Laboratoire Ecosystemes Microbiens et Molecules Marines pour les Biotechnologies, 44311 Nantes, France, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russian Federation, Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France, Centre de Recherches sur les Macromolécules Végétales, Université de Grenoble Alpes, Centre National de la Recherche Scientifique, Grenoble, France
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.
molecular dynamics, exopolysaccharides, Alteromonas infernus, 3 dimensional structures, calcium binding, gel forming, Quantum chemistry
Structure type: polymer chemical repeating unit
Location inside paper: Fig. 1
Trivial name: infernan
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_423153,IEDB_983931,SB_192,SB_7
Methods: MD simulations, MM3 force field, DFT computations, mechanics calculations, potential energy surfaces (PES)
Comments, role: the repeating unit of Infernan (GY785 EPS)
3D data: molecular modeling
NCBI Taxonomy refs (TaxIDs): 179275Reference(s) to other database(s): GTC:G33666QQ, GlycomeDB:
27442
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There is only one chemically distinct structure:
Found 
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