Vibrational modes of ubiquinone in cytochrome bo(3) from Escherichia coli identified by Fourier transform infrared difference spectroscopy and specific C-13 labeling

In this study we present the infrared spectroscopic characterization of the bound ubiquinone in cytochrome bo(3) from Escherichia coli, Electrochemica lly induced Fourier transform infrared (FTIR) difference spectra of Delta U biA (an oxidase devoid of bound ubiquinone) and Delta UbiA reconstituted wi th ubiquinone 2 and with isotopically labeled ubiquinone 2, where C-13 was introduced either at the 1- or at the 4-position of the ring (C=O groups), have been obtained. The vibrational modes of the quinone bound to the discu ssed high-affinity binding site (Q(H)) are compared to those from the synth etic quinones in solution, leading to the assignment of the C=O modes to a split signal at 1658/1668 cm(-1), with both carbonyls similarly contributin g. The FTIR spectra of Delta UbiA reconstituted with the labeled quinones i ndicate an essentially symmetrical and weak hydrogen bonding of the two C=O groups from the neutral quinone with the protein and distinct conformation s of the 2- and 3-methoxy groups. Perturbations of the vibrational modes of the 5-methyl side groups are discussed for a signal at 1452 cm(-1). Only n egligible shifts of the aromatic ring modes can be reported for the reduced and the protonated form of the quinone. Alterations of the protein upon qu inone binding are reflected in the electrochemically induced FTIR differenc e spectra. In particular, difference signals at 1640-1633 cm(-1) and 1700-1 670 cm(-1) indicate variations of beta-sheet secondary structure elements a nd loops, bands at 1706 and 1678 cm(-1) are tentatively attributed to indiv idual amino acids, and a difference signal a 1540 cm(-1) is discussed to re flect an influence on C=C modes of the porphyrin ring or on deprotonated pr opionate groups of the hemes. Further tentative assignments are presented a nd discussed. The C-13 labeling experiments allow the assignment of the vib rational modes of a bound ubiquinone 8 in the electrochemically induced FTI R difference spectra of wild-type bo(3).