The ‘light’ and ‘medium’ subunits of the photosynthetic reaction centre from <i>Rhodopseudomonas viridis</i>
: isolation of the genes, nucleotide and amino acid sequence

Michel, Hartmut; Weyer, Karl Aloys; Gruenberg, H; Dunger, Irmtraud; Oesterhelt, Dieter; Lottspeich, Friedrich

doi:10.1002/j.1460-2075.1986.tb04340.x

Cited by 314 publications

(167 citation statements)

References 36 publications

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“…The transmembrane segments are thus identified as a-Val-21:a-Ala-40 and P-Thr-22:p-Trp-41. It is worth mentioning that, although hydropathy analysis has been successfully applied to identifying transmembrane helices, the method cannot determine the ends of helices precisely (Michel et al, 1986). The accuracy of the prediction relies on a proper choice of the window size and the cut-off value for identifying membrane-spanning residues that have been calibrated against known structures of membrane proteins (Kyte & Doolittle, 1982 …”

Section: Discussionmentioning

confidence: 99%

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Predicting the structure of the light-harvesting complex II ofrhodospirillum molischianum

Hamer

et al. 1995

Protein Sci.

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We attempted to predict through computer modeling the structure of the light-harvesting complex II (LH-Ii) of Rhodospirillum molischianum, before the impending publication of the structure of a homologous protein solved by means of X-ray diffraction. The protein studied is an integral membrane protein of 16 independent polypeptides, 8 a-apoproteins and 8 @-apoproteins, which aggregate and bind to 24 bacteriochlorophyll-a's and 12 lycopenes. Available diffraction data of a crystal of the protein, which could not be phased due to a lack of heavy metal derivatives, served to test the predicted structure, guiding the search. In order to determine the secondary structure, hydropathy analysis was performed to identify the putative transmembrane segments and multiple sequence alignment propensity analyses were used to pinpoint the exact sites of the 20-residue-long transmembrane segment and the 4-residue-long terminal sequence at both ends, which were independently verified and improved by homology modeling. A consensus assignment for the secondary structure was derived from a combination of all the prediction methods used. Three-dimensional structures for the cy-and the @-apoprotein were built by comparative modeling. The resulting tertiary structures are combined, using X-PLOR, into an a@ dimer pair with bacteriochlorophyll-a's attached under constraints provided by site-directed mutagenesis and spectral data. The a@ dimer pairs were then aggregated into a quaternary structure through further molecular dynamics simulations and energy minimization. The structure of LH-I1 so determined is an octamer of a@ heterodimers forming a ring with a diameter of 70 A.

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Section: Discussionmentioning

confidence: 99%

“…In addition, transmembrane helices are not always 20 residues long. All the transmembrane helices in the photosynthetic reaction center of Rhodopseudomunus viridis, for example, are 24-30 residues long (Michel et al, 1986). In our approach, we utilized hydropathy analysis solely to identify the hydrophobic core of transmembrane helices.…”

Section: Imentioning

confidence: 99%

Predicting the structure of the light-harvesting complex II ofrhodospirillum molischianum

Hamer

et al. 1995

Protein Sci.

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“…Since R. viridis, in contrast to Rhodobacter sphaeroides, belongs to the group of purple bacteria with a tightly bound cytochrome subunit of the reaction center (13,28) Southern blot analysis. Total genomic DNA from R. viridis was isolated as described previously (29). After electrophoresis on agarose gels, the DNA fragments were transferred onto nylon membranes (42 (20).…”

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confidence: 99%

Sequence analysis and transcriptional organization of the Rhodopseudomonas viridis cytochrome c2 gene

1990

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The cytochrome c2 gene (cycA) of the purple nonsulfur bacterium Rhodopseudomonas viridis was isolated from a genomic library by using two degenerate oligonucleotides containing all possible DNA sequences predicted from the published amino acid sequence of this protein (Ambler et al., Proc. Natl. Acad. Sci. USA 73:472-475, 1976). Cloning and sequence analysis of the cytochrome c2 gene indicated the presence of a typical procaryotic 20-residue signal peptide, suggesting that this periplasmic protein in synthesized in vivo as a precursor. In addition, four amino acids were found to be different by comparing the published sequence of the mature protein with that deduced from the isolated cycA gene (Lys-14----Leu, Ser-46----Ala, Ile-84----Val, Leu-97----Ile). Northern (RNA) blot analysis and fine mapping of the 5' and 3' ends of the cycA gene transcript from photoheterotrophically grown R. viridis cells revealed one abundant transcript of 523 to 530 nucleotides in length, with the transcription start site at position -39 relative to the coding region of cytochrome c2. A low-abundance transcript with an extended 3' end (about 600 bases in length) is thought to be processed by exonucleases, resulting in the slightly shorter main transcript.

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“…Current theories express the transfer rate in terms of a matrix element V(r) and a Franck-Condon factor F(Ax,): k I V(r)12F(Axd). [8] V(r) is due to the overlap ofthe electronic donor and acceptor wavefunctions and depends on the donor-acceptor distance r. To a first approximation, V(r) should be independent of the mass of the reacting species. F(Ax,) describes the coupling of the fluctuations in internuclear distances Axi for various vibrational modes of the system to the electronic energy for the reactants and products; this coupling depends on the temperature and nuclear masses.…”

Section: Resultsmentioning

confidence: 99%

“…The structure ofthe Rhodopseudomonas sphaeroides RC used in this study is assumed to be very similar to that of R. viridis. This assumption is based on the amino acid sequence homology between the two RCs (6)(7)(8) and the preliminary electron density mapping of the RC from R. sphaeroides by the molecular replacement method (9). The components of the electron-transfer chain (BChl dimer, BPh, and QA) are arranged in series across the membrane.…”

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confidence: 99%

Isotope effect on electron transfer in reaction centers from Rhodopseudomonas sphaeroides

Okamura

Fehér

1986

Proc. Natl. Acad. Sci. U.S.A.

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Previous ENDOR studies on reaction centers from Rhodopseudomonas sphaeroides have shown the presence of two hydrogen-bonded protons associated with the primary, ubiquinone, acceptor QA. These protons exchange with deuterons from solvent 2H20. The effect of this deuterium substitution on the charge-recombination kinetics (BCh nsl)Q-(BChl)2QA has been studied with a sensitive kinetic difference technique. The electron-transfer rate was found to increase with deuterium exchange up to a maximum Ak/k of 5.7 + 0.3%. The change in rate was found to have an exchange time of 2 hr, which matched the disappearance of the ENDOR lines due to the exchangeable protons. These results indicate that these protons play a role in the vibronic coupling associated with electron transfer. A simple model for the isotope effect on electron transfer predicts a maximum rate increase of 20%, which is consistent with the experimental results.The primary photochemistry in bacterial photosynthesis involves light-induced electron transfer in a bacteriochlorophyll (BChl) protein complex called the reaction center (RC) (for reviews, see refs. 1-3). The absorbed photon excites a primary donor species, a BChl dimer, which transfers an electron to a bacteriopheophytin (BPh) molecule. Subsequent electron transfer occurs from BPh to a primary quinone, QA, and then to a secondary quinone, QB.The structural basis for electron transfer in bacterial RCs has been investigated by a wide variety of biochemical and biophysical techniques, including the recent x-ray crystallographic structure determination by Deisenhofer et al. (4,5) of the RC from Rhodopseudomonas viridis. The structure ofthe Rhodopseudomonas sphaeroides RC used in this study is assumed to be very similar to that of R. viridis. This assumption is based on the amino acid sequence homology between the two RCs (6-8) and the preliminary electron density mapping of the RC from R. sphaeroides by the molecular replacement method (9). The components of the electron-transfer chain (BChl dimer, BPh, and QA) are arranged in series across the membrane. The secondary quinone, QB, is related to QA by an approximately 2-fold symmetry axis. An Fe2+ coordinated to four histidine residues is located between the two quinones.The success of the structural studies of bacterial RCs has motivated us to investigate the structural basis for the electron-transfer reactions. Theories of electron transfer require the coupling of electron transfer to vibrational motion (intermolecular or intramolecular) of the molecules involved in the reaction (10)(11)(12)(13)(14). This coupling is necessary to match the energies of the product and reactant state (i.e., to form the transition state for electron transfer). The coupling enables the excess energy of the reactant state to be given off to the lattice. The goal of this study was to identify the vibrational modes that play a role in the electron transfer. The approach that was adopted is based on the effect of isotope substitution on the rate of electron transfer.Rece...

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The ‘light’ and ‘medium’ subunits of the photosynthetic reaction centre from Rhodopseudomonas viridis : isolation of the genes, nucleotide and amino acid sequence

Cited by 314 publications

References 36 publications

Predicting the structure of the light-harvesting complex II ofrhodospirillum molischianum

Predicting the structure of the light-harvesting complex II ofrhodospirillum molischianum

Sequence analysis and transcriptional organization of the Rhodopseudomonas viridis cytochrome c2 gene

Isotope effect on electron transfer in reaction centers from Rhodopseudomonas sphaeroides

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