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Molecules 2005, 10(10), 1263-1271; doi:10.3390/10101263
Article

Theoretical Study of Molecular Determinants Involved in Signal Binding to the TraR Protein of Agrobacterium tumefaciens

1, 2 and 1,*
1 School of Chemistry, The University of New South Wales, Australia 2 The Centre for Marine Biofouling and Bio-Innovation, The University of New South Wales, Australia
* Author to whom correspondence should be addressed.
Received: 1 December 2004 / Accepted: 20 April 2005 / Published: 31 October 2005
(This article belongs to the Special Issue 2004 RACI One-day Natural Products Group Symposium)
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Abstract

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.
Keywords: Quorum sensing; TraR; N-acyl homoserine lactone; Molecular modeling; AHL receptor binding. Quorum sensing; TraR; N-acyl homoserine lactone; Molecular modeling; AHL receptor binding.
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Goh, W.; Rice, S.; Kumar, N. Theoretical Study of Molecular Determinants Involved in Signal Binding to the TraR Protein of Agrobacterium tumefaciens. Molecules 2005, 10, 1263-1271.

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