Quantifying the role of water in protein-carbohydrate interactions.

ABSTRACT: Water-mediated interactions play a key role in carbohydrate-lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed a

SUBMITTER: Tschampel SM 

PROVIDER: S-EPMC1538976 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature