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Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media.

ABSTRACT: Correlation between fluctuations of the square of electron tunneling matrix element TDA2 and the donor-acceptor distance RDA in the electron transfer (ET) reaction from bacteriopheophytin anion to the primary quinone of the reaction center in the photosynthetic bacteria Rhodobacter sphaeroides is investigated by a combined study of molecular dynamics simulations of the protein conformation fluctuation and quantum chemical calculations. We adopted two kinds of RDA ; edge-to-edge distance REE and center-to-center distance RCC . The value of TDA2 distributed over more than 5 orders of magnitude and the fluctuation of the value of RDA distributed over more than 1.8 Å for the 106 instantaneous conformations of 1 ns simulation. We made analysis of the time-averaged correlation step by step as follows. We divide the 106 simulation data into 1000/t parts of small data set to obtain the averaged data points of t and t or t . Plotting the 1000/t sets of log10 t as a function of t or t , we made a principal coordinate analysis for these distributions. The slopes t and t of the primary axis are very large at small value of t and they are decreased considerably as t becomes large. The ellipticity for the distribution of tvs t which can be a measure for the degree of correlation became very small when t is large, while it does not hold for the distribution of tvs t . These results indicate that only the correlation between t and t for large t satisfies the well-known linear relation ("Dutton law"), although the slope is larger than the original value 1.4 Å-1. Based on the present result, we examined the analysis of the dynamic disorder by means of the single-molecule spectroscopy by Xie and co-workers with use of the "Dutton law".

SUBMITTER: Nishioka H

PROVIDER: S-EPMC5036608 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media.

Nishioka Hirotaka H Ueda Nobuharu N Kakitani Toshiaki T

Biophysics (Nagoya-shi, Japan) 20081015

Correlation between fluctuations of the square of electron tunneling matrix element TDA2 and the donor-acceptor distance RDA in the electron transfer (ET) reaction from bacteriopheophytin anion to the primary quinone of the reaction center in the photosynthetic bacteria Rhodobacter sphaeroides is investigated by a combined study of molecular dynamics simulations of the protein conformation fluctuation and quantum chemical calculations. We ado ...[more]

PMID: 27857572

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Project description:Microbially-mediated uranium bioremediation has been demonstrated in uranium contaminated aquifers when acetate was artificially supplied and growth of the natural population of Geobacteraceae was stimulated. In order to mimic the environmental response to acetate, steady-state cells of G. sulfureducens were cultured in chemostats under conditions of either 1) acetate as the sole electron donor and limiting factor and fumarate as the sole electron acceptor or 2) acetate was supplied in excess with fumarate as sole electron acceptor and limiting factor. In silico fluxome modeling and transcriptome analysis were used as tools for investigating the cell response to the acetate availability. For global gene expression profiling, a DNA microarray of the complete G. sulfurreducens genome was used. Statistically significant results were obtained from two-color, dye swap hybridizations produced from a total of three biological replicates. Eight technical replicates were tested from two of the biological replicates and six technical replicates were tested from the third biological replicate. Major findings from this study are given as follows. The in silico model successfully predicted a higher TCA-cycle flux (ca. 2-fold) under acetate-excess conditions, suggesting that catabolism of acetate is favored with respect to anabolism, and thus more electrons are available for metal reduction. Transcriptome analyses offered a comprehensive picture of the regulation points subjected to the acetate availability. Under acetate-excess conditions, acetate transporters in the G. sulfurreducens genome were down-regulated. In addition the oxidation-related acetyl-CoA transferase was up-regulated approximately three-fold and the assimilatory-related acetate kinase was down-regulated approximately two-fold, respectively, indicating that the transcriptional regulation of acetate activation may be the key point for coping with the excess of acetate and increasing the TCA flux. The level of transcription for 10 c-type cytochromes was significantly increased in cells cultured with an excess of acetate. OmcS, an outer-membrane cytochrome which actively participates in electron transfer to Fe(III)-oxides and graphite electrodes from fuel cells, showed one of the highest fold increases in transcription. The integration of in silico modeling and genome-wide analysis shows for first time how G. sulffureducens adapts its metabolic flux and transcriptional network for optimizing the use of acetate as an electron donor for exocellular respiration instead of for use as a carbon source for biomass production. Keywords: Geobacter, gene expression, acetate limitation, fumarate limitation

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Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media.

Publications

Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media.

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