Molecular Dynamics Unlocks Atomic Level Self-Assembly of the Exopolysaccharide Matrix of Water-Treatment Granular Biofilms

Abstract

Biofilm formation, in which bacteria are embedded within an extracellular matrix, is the default form of microbial life in most natural and engineered habitats. In this work, atomistic molecular dynamics simulations were employed to examine the self-assembly of the polysaccharide Granulan to provide insight into the molecular interactions that lead to biofilm formation. Granulan is a major gel forming matrix component of granular microbial biofilms found in used-water treatment systems. Molecular dynamics simulations showed that Granulan forms an antiparallel double helix stabilized by complementary hydrogen bonds between the β-glucosamine of one strand and the N-acetyl-β-galactosamine-2-acetoamido-2-deoxy-α-galactopyranuronic pair of the other in both the presence and absence of Ca(2+). It is shown that Ca(2+) binds primarily to the carboxyl group of the terminal hexuronic acid of the sugar branch and that interactions between branches mediated by Ca(2+) suggest a possible mechanism for strengthening gels by facilitating interhelical bridging.