Computer Simulation of the Structure of Efflux Pumps to Increase Whole-Cell Biocatalytic Efficiency for Reactions Involving Aromatic Compounds

Bioconversion reactions often produce higher yields than traditional chemical processes, but are not always as productive. Low rates may be caused by the cell's ability to actively expel reactants before they can be converted. One large family of transport proteins called root-nodulation division (RND) efflux pumps exhibit a broad substrate range, including various antibiotics and aromatic hydrocarbons. One particular efflux pump from P. putida is Ttg, which exports toluene - a toxic solvent - is relatively unselective. Because of its low selectivity Ttg is useful as a baseline for comparison of other types of efflux pumps. Computer simulations enable one to gain a better understanding of the structure-function relationship in efflux pumps. The amino acid sequence of Ttg and eight other efflux pump proteins were compared to a consensus sequence. Residues at select non-consensus sites were identified and correlations attempted between residue charge, size and substrate specificity. Regions that are identified as binding sites can be modified to eliminate or enhance the selectivity of the pump toward that molecule. This would allow the reactant to remain in the cell longer or the product released more quickly, increasing productivity.