Understanding the lectin-sugar recognition process is essential in the structure-based design of proteins for specific purposes. Here we investigated the sugar binding ability of a double trefoil carbohydrate-binding/recognition domains (CRD) found in several plant protein toxins. By performing molecular dynamics simulations on the apo form and various ligand-bound forms of the protein ricin chain B, we examine the binding ability differences among possible sites of ricin-like CRD. A detailed picture of the sugar recognition of the ricin-like CRD was obtained by evaluating structural stability, hydrogen bond dynamics, flexibility, as well as binding free energy. Results from the structural correlation matrix showed that the two subdomains are structurally one entity. Unlike previously believed, we found that the binding ability of one site is positively affected by the other site, a cooperativity phenomenon. Site 2?, the stronger binding site identified from previous experimental data, has a more rigid recognition pocket than site 1a and can maintain a set of essential hydrogen bonds. The order of the stability of these essential hydrogen bonds is similar for the mono-ligand and the double-ligand complex forms, though the stability is much higher in the latter form due to cooperativity. The most critical sugar binders in both site 1a and site 2? are the 4-OH and 3-OH hydroxy groups.

Sugar recognition ability of ricin-like carbohydrate binding domains

241st National Meeting (2011)

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