Structure of the phylloquinone-binding (Q.vphi.) site in green plant photosystem I reaction centers: the affinity of quinones and quinonoid compounds for the Q.vphi. site

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Abstract
The dissociation constants (Kd) between the phylloquinone-binding site (designated as the Q phi site) and 23 quinones and 2 quinonoid compounds were measured in spinach photosystem I reaction centers. Kd values were calculated from the dependency of the recovery of the flash-induced stable oxidation of the primary donor chlorophyll P700 in the phylloquinone-extracted reaction center on the concentration of added compounds. The binding free energy, calculated from the Kd value of quinones with nonpolar substituted groups, linearly depended on their partition coefficients between water and cyclohexane, but only if their molecular sizes are smaller than anthraquinone. The quinones with larger molecular sizes showed a lower affinity than expected from their hydrophobicities. This suggests that the quinone-binding domain is hydrophobic and that its size is similar to that of anthraquinone. The interaction other than the hydrophobic one was also estimated to stabilize the binding by -5.7 kcal/mol for alkylated quinones. Deletion of one of the carbonyls of p-quinones significantly decreased the binding affinity. This suggests a hydrogen bond or a pi-pi electronic interaction between quinone and the Q phi site. Effects of halogens and amino substitutions on the binding affinity were also studied. The structure of the quinone-binding site in the photosystem I reaction center is deduced from these results.

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