Binding mode of 1,4-naphthoquinones at the QA-site of the reaction centre from Rhodobacter sphaeroides investigated by light-induced FTIR difference spectroscopy

Abstract

Recently, methyl substituted 1,4-naphthoquinone compounds have gained substantial interest since those compounds bind tightly to the QA site of the bacterial reaction center (RC) from Rhodobacter sphaeroides enabling its functional reconstitution while retaining the native ubiquinone at QB. We reported the synthesis of 29 naphthoquinone derivatives containing different numbers of methyl groups in various positions of the ring system and a systematically altered tail structure. To investigate the binding mode of these quinones at QA we measured QA-/QA-FTIR difference spectra. In the non quinonic regions the band shapes and vibrational frequencies exhibited a high similarity for all quinones. This indicates that no larger structural changes of the binding site occur upon quinone binding. Based on the well characterized QA-/QA-FTIR difference spectra for vitamin K1 some of the quinone signals were tentatively assigned to specific vibrational modes. Accordingly, those quinones carrying methyl groups in position 6 and/or 7 exhibit asymmetric hydrogen bonds between the two quinone oxygens and the protein binding pocket in both the oxidized and the reduced form, whereas in case of vitamin K1 these hydrogen bonds become symmetric upon photoreduction. Work is in progress to assign all relevant vibrational modes of the quinones by means of isotopically labelled compounds. A detailed knowledge of the quinone spectral contributions is a prerequisite for using these naphthoquinones to elucidate the complex coupling mechanism of electron transfer, proton transfer and conformational changes in the RC protein.