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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”.

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Plot of log10 <TDA2>Svs REE. <TDA2>S is calculated by averaging TDA2 which belongs to the bin of REE. The bin length is 0.02 Å. The green line represents the primary axis.
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f12-4_19: Plot of log10 <TDA2>Svs REE. <TDA2>S is calculated by averaging TDA2 which belongs to the bin of REE. The bin length is 0.02 Å. The green line represents the primary axis.

Mentions: In Figure 12, we plot the value of log10 <TDA2> S as a function of REE. Then, we make the principal coordinate analysis. The obtained primary axis is expressed as(10)ln<TDA2>S=−1.736REE−2.421Here, the value 1.736 Å−1 is the slope <βE>S in the stationary state. We also evaluate the ellipticity <ε>S as 0.058. This data point is plotted in Figure 10 by the red square named S. In Figure 10 we find that the value of <ε>t decreases rapidly and ceases to stop at the stationary state as t is increased from 100 ps. The value of <βE>t decreases slowly from about 2.1 Å−1 to the lower limit as t is increased from 100 ps.


Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
Plot of log10 <TDA2>Svs REE. <TDA2>S is calculated by averaging TDA2 which belongs to the bin of REE. The bin length is 0.02 Å. The green line represents the primary axis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036608&req=5

f12-4_19: Plot of log10 <TDA2>Svs REE. <TDA2>S is calculated by averaging TDA2 which belongs to the bin of REE. The bin length is 0.02 Å. The green line represents the primary axis.
Mentions: In Figure 12, we plot the value of log10 <TDA2> S as a function of REE. Then, we make the principal coordinate analysis. The obtained primary axis is expressed as(10)ln<TDA2>S=−1.736REE−2.421Here, the value 1.736 Å−1 is the slope <βE>S in the stationary state. We also evaluate the ellipticity <ε>S as 0.058. This data point is plotted in Figure 10 by the red square named S. In Figure 10 we find that the value of <ε>t decreases rapidly and ceases to stop at the stationary state as t is increased from 100 ps. The value of <βE>t decreases slowly from about 2.1 Å−1 to the lower limit as t is increased from 100 ps.

View Article: PubMed Central - PubMed

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 &Aring; 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 &lt;TDA2&gt;t and &lt;REE&gt;t or &lt;RCC&gt;t. Plotting the 1000/t sets of log10 &lt;TDA2&gt;t as a function of &lt;REE&gt;t or &lt;RCC&gt;t, we made a principal coordinate analysis for these distributions. The slopes &lt;&beta;E&gt;t and &lt;&beta;C&gt;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 &lt;TDA2&gt;tvs &lt;REE&gt;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 &lt;TDA2&gt;tvs &lt;RCC&gt;t. These results indicate that only the correlation between &lt;TDA2&gt;t and &lt;REE&gt;t for large t satisfies the well-known linear relation (&ldquo;Dutton law&rdquo;), although the slope is larger than the original value 1.4 &Aring;&minus;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 &ldquo;Dutton law&rdquo;.

No MeSH data available.


Related in: MedlinePlus