Favoured carbonyl binding regions around the QA and Q B sites of Rps. viridis.

The factors governing quinone protein binding in the photosynthetic bacterium Rps. viridis are investigated via use of empirical intermolecular energy calculations using the GRID method (PJ Goodford (1985) J Med Chem 28: 849-854). A probe atom corresponding to a carbonyl oxygen atom is used to investigate regions exhibiting preference for carbonyl binding in the QA and QB sites of Rps. viridis. Two distinct regions at the top and bottom of the sites are revealed to be most favourable for carbonyl binding. Overlay of the crystallographically determined positions for the quinone carbonyl groups shows that they lie within the regions predicted theoretically. The method is also shown to be able to give qualitative insight into the affect of amino acid mutations of quinone binding.