Density Functional Investigation of Methoxy-Substituted p-Benzoquinones: Conformational Analysis and Harmonic Force Fields of 2-Methoxy- and 2,3-Dimethoxy-1,4-benzoquinone

Conformational differences between the methoxy groups of QA and QB 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 in vivo 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, QA and QB. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones (13)C-labeled at the headgroup methyl and methoxy substituents, and have measured the (13)C 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 QA and QB sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with QB more out of plane by 20-25°. This corresponds to an ≈50 meV larger electron affinity for the QB 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.

Does different orientation of the methoxy groups of ubiquinone-10 in the reaction centre of Rhodobacter sphaeroides cause different binding at QA and QB?

The different roles of ubiquinone-10 (UQ10) at the primary and secondary quinone (QA and QB) binding sites of Rhodobacter sphaeroides R26 reaction centres are governed by the protein microenvironment. The 4C=O carbonyl group of QA is unusually strongly hydrogen-bonded, in contrast to QB. This asymmetric binding seems to determine their different functions. The asymmetric hydrogen-bonding at QA can be caused intrinsically by distortion of the methoxy groups or extrinsically by binding to specific amino-acid side groups. Different X-ray-based structural models show contradictory orientations of the methoxy groups and do not provide a clear picture. To elucidate if distortion of the methoxy groups induces this hydrogen-bonding, their (ring-)C-O vibrations were assigned by use of site-specifically labelled [5-13C]UQ10 and [6-13C]UQ10 reconstituted at either the QA or the QB binding site. Two infrared bands at 1288 cm(-1) and 1264 cm(-1) were assigned to the methoxy vibrations. They did not shift in frequency at either the QA or QB binding sites, as compared with unbound UQ10. As the frequencies of these vibrations and their coupling are sensitive to the conformations of the methoxy groups, different conformations of the C(5) and C(6) methoxy groups at the QA and QB binding sites can now be excluded. Both methoxy groups are oriented out of plane at QA and QB. Therefore, hydrogen-bonding to His M219 combined with electrostatic interactions with the Fe2+ ion seems to determine the strong asymmetric binding of QA.

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.

Resonance Raman and infrared spectral studies on radical anions of model photosynthetic reaction center quinones (naphthoquinone derivatives)

Quinones play a vital role in the processes of electron transfer in bacterial photosynthetic reaction centers. It is of interest to investigate photochemical reactions involving quinones with a view to elucidate structure-function relationships in biological processes. Resonance Raman and FTIR spectra of electrochemically generated radical anions of 2-methyl-1,4-naphthoquinone, and 2-methyl-3-phytyl-1,4-naphthoquinone, also known as Vitamin K3 and Vitamin K1, respectively, (model compound for QA in Rhodopseudomonas viridis, a bacterial photosynthetic reaction center) have been reported. The same study has also been extended to 1,4-naphthoquinone for comparison. The vibrational assignments were carried out on the basis of comparison with our earlier time resolved resonance Raman studies on photochemically generated radical anions of 1,4-naphthoquinone and 2-methyl-1,4-naphthoquinone (Balakrishnan et al., J. Phys. Chem., 100, (1996), 16472-16478). These in vitro results have been compared with the reported vibrational spectral data under in vivo conditions.