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Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

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 (18)O 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 (18)O 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.

SUBMITTER: Zhao N

PROVIDER: S-EPMC3757576 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

Zhao Nan N Lamichhane Hari P HP Hastings Gary G

Frontiers in plant science 20130830

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 (18)O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated f ...[more]

PMID: 24009618

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Project description:BACKGROUND:The availability of photon and electron spectra in digital form from current accelerators and Monte Carlo (MC) systems is scarce, and one of the packages widely used refers to linacs with a reduced clinical use nowadays. Such spectra are mainly intended for the MC calculation of detector-related quantities in conventional broad beams, where the use of detailed phase-space files (PSFs) is less critical than for MC-based treatment planning applications, but unlike PSFs, spectra can easily be transferred to other computer systems and users. METHODS:A set of spectra for a range of Varian linacs has been calculated using the PENELOPE/PRIMO MC system. They have been extracted from PSFs tallied for field sizes of 10 cm × 10 cm and 15 cm × 15 cm for photon and electron beams, respectively. The influence of the spectral bin width and of the beam central axis region used to extract the spectra have been analyzed. RESULTS:Spectra have been compared to those by other authors showing good agreement with those obtained using the, now superseded, EGS4/BEAM MC code, but significant differences with the most widely used photon data set. Other spectra, particularly for electron beams, have not been published previously for the machines simulated in this work. The influence of the bin width on the spectrum mean energy for 6 and 10 MV beams has been found to be negligible. The size of the region used to extract the spectra yields differences of up to 40% for the mean energies in 10 MV beams, but the maximum difference for TPR 20,10 values derived from depth-dose distributions does not exceed 2% relative to those obtained using the PSFs. This corresponds to kQ differences below 0.2% for a typical Farmer-type chamber, considered to be negligible for reference dosimetry. Different configurations for using electron spectra have been compared for 6 MeV beams, concluding that the geometry used for tallying the PSFs used to extract the spectra must be accounted for in subsequent calculations using the spectra as a source. CONCLUSIONS:An up-to-date set of consistent spectra for Varian accelerators suitable for the calculation of detector-related quantities in conventional broad beams has been developed and made available in digital form.

Dataset Information

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

Publications

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

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