Abstract
Previously we have shown that ONIOM type (QM/MM) calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0), 2,3,5,6-tetramethyl-1, 4-benzoquinone (duroquinone, DQ), and 2,3-dimethyl-l,4-naphthoquinone (DMNQ) incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites. The normal modes that contribute to the bands in the calculated spectra, their composition, frequency, and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10–13 cm−1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry in H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are “tail-less.” Spectra were also calculated for reaction centers with corresponding “tail” containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated spectra.
Highlights
Quinones play an important role in biological proton and electron transfer processes that occur in both respiration and photosynthesis (Trumpower, 1982)
We show that the calculated spectra agree well with the experimental spectra, further supporting the notion that the ONIOM method is a useful approach for understanding complex Fourier transform infrared (FTIR) difference spectra associated with pigments in protein binding sites
Negative signs in the potential energy distribution (PED) refer to the relative phase of vibration of the internal coordinates
Summary
Quinones play an important role in biological proton and electron transfer processes that occur in both respiration and photosynthesis (Trumpower, 1982). In type II photosynthetic reaction centers two quinone molecules act as terminal electron acceptors (Ke, 2001a,b). The two quinones are often termed QA and QB. In this manuscript we will refer to the quinone binding site as QA and QB, . The quinones that occupy the QA and QB binding sites have very different functions.
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