Binding modes of PCBs to a degrading enzyme: a receptor-mapping study

The binding site of a PCB-degrading enzyme was mapped using the published data on biodegradation rates of individual PCB congeners by the Acinetobacter P6 strain. For this purpose an approach allowing for multiple binding modes of individual congeners, resulting from the symmetry of the biphenyl skeleton, was used. The effect of substitution patterns and conformational flexibility of individual congeners on their binding to a protein were investigated. The resulting map of the binding site is described by three parameters that indicate the importance of positions 4, 5', 5, 2' in a basic substitution pattern, the first two being favourable while the other two unfavourable for binding. An incorporation of conformational energy dependences of individual ligands into the model showed that ligand's conformation is either not a limiting factor for binding or that ligands bind in their relaxed conformations.