Conformational Differences between the Methoxy Groups of Q_A and Q_B Site Ubisemiquinones in Bacterial Reaction Centers: A Key Role for Methoxy Group Orientation in Modulating Ubiquinone Redox Potential

Ubiquinone is an almost universal, membrane-associated redox mediator. Its ability to accept either one or two electrons allows it to function in critical roles in biological electron transport. The redox properties of ubiquinone <i>in vivo</i> are determined by its environment in the binding sites of proteins and by the dihedral angle of each methoxy group relative to the ring plane. This is an attribute unique to ubiquinone among natural quinones and could account for its widespread function with many different redox complexes. In this work, we use the photosynthetic reaction center as a model system for understanding the role of methoxy conformations in determining the redox potential of the ubiquinone/semiquinone couple. Despite the abundance of X-ray crystal structures for the reaction center, quinone site resolution has thus far been too low to provide a reliable measure of the methoxy dihedral angles of the primary and secondary quinones, Q_A and Q_B. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones ¹³C-labeled at the headgroup methyl and methoxy substituents, and have measured the ¹³C isotropic and anisotropic components of the hyperfine tensors. Hyperfine couplings were compared to those derived by DFT calculations as a function of methoxy torsional angle allowing estimation of the methoxy dihedral angles for the semiquinones in the Q_A and Q_B sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with Q_B more out of plane by 20–25°. This corresponds to an ≈50 meV larger electron affinity for the Q_B quinone, indicating a substantial contribution to the experimental difference in redox potentials (60–75 mV) of the two quinones. The methods developed here can be readily extended to ubiquinone-binding sites in other protein complexes