Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
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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 <TDA2>t and <REE>t or <RCC>t. Plotting the 1000/t sets of log10 <TDA2>t as a function of <REE>t or <RCC>t, we made a principal coordinate analysis for these distributions. The slopes <βE>t and <βC>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 <TDA2>tvs <REE>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 <TDA2>tvs <RCC>t. These results indicate that only the correlation between <TDA2>t and <REE>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”. No MeSH data available. Related in: MedlinePlus |
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Mentions: In Figure 5 we plotted the correlation diagram of log TDA2 and RCC calculated by same way as Figure 4. We find that the values of TDA2 distribute over more than 5 orders of magnitude for the distribution of about 1.8 Å of RCC. In this case also we find very little correlation between the values of log TDA2 and RCC calculated for the instantaneous conformations of fluctuating protein. |
View Article: PubMed Central - PubMed
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 <TDA2>t and <REE>t or <RCC>t. Plotting the 1000/t sets of log10 <TDA2>t as a function of <REE>t or <RCC>t, we made a principal coordinate analysis for these distributions. The slopes <βE>t and <βC>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 <TDA2>tvs <REE>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 <TDA2>tvs <RCC>t. These results indicate that only the correlation between <TDA2>t and <REE>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”.
No MeSH data available.