Theoretical study of molecular determinants involved in signal binding to the TraR protein of Agrobacterium tumefaciens.

N-acylated homoserine lactone (AHL) mediated cell-cell communication in bacteria is dependent on the recognition of the cognate signal by its receptor. This interaction allows the receptor-ligand complex to act as a transcriptional activator, controlling the expression of a range of bacterial phenotypes, including virulence factor expression and biofilm formation. One approach to determine the key features of signal- binding is to model the intermolecular interactions between the receptor and ligand using computational-based modeling software (LigandFit). In this communication, we have modeled the crystal structure of the AHL receptor protein TraR and its AHL signal N-(3- oxooctanoyl)-homoserine lactone from Agrobacterium tumefaciens and compared it to the previously reported antagonist behaviour of a number of AHL analogues, in an attempt to determine structural constraints for ligand binding. We conclude that (i) a common conformation of the AHL in the hydrophobic and hydrophilic region exists for ligand-binding, (ii) a tail chain length threshold of 8 carbons is most favourable for ligand-binding affinity, (iii) the positive correlation in the docking studies could be used a virtual screening tool.