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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”.

No MeSH data available.


General view of the coordination of donor (bacterio-pheophytin), acceptor (quinone), and the three amino acids (TrpM252, MetM218, and HisM219) which we investigate in this paper. The molecular structure of donor and acceptor is represented by a ball and stick model. The molecular structure of the three amino acids is represented by a stick model. Blue balls, red balls, deep blue balls, and white balls indicate carbon atoms, oxygen atoms, nitrogen atoms, and hydrogen atoms, respectively. The gold stick in the MetM218 represents the sulfur atom.
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f1-4_19: General view of the coordination of donor (bacterio-pheophytin), acceptor (quinone), and the three amino acids (TrpM252, MetM218, and HisM219) which we investigate in this paper. The molecular structure of donor and acceptor is represented by a ball and stick model. The molecular structure of the three amino acids is represented by a stick model. Blue balls, red balls, deep blue balls, and white balls indicate carbon atoms, oxygen atoms, nitrogen atoms, and hydrogen atoms, respectively. The gold stick in the MetM218 represents the sulfur atom.

Mentions: The procedures for the quantum chemistry (QC) calculations of TDA are the same as before6,9. Here, we briefly describe it. The chemical structures of donor and acceptor which we adopted in calculating the molecular orbitals of donor and acceptor are shown in Figure 1. In these calculations, long hydrocarbon chains of native bacteriopheophytin a and the native ubiquinone 10 are truncated to hydrogen atoms. It has been shown that the similar result of the time variation of TDA is obtained in both cases when 60 amino acids surrounding donor and acceptor are considered and when 3 amino acids between donor and acceptor are considered9. Then we consider the three amino acids TrpM252, MetM218, and HisM219 in the present calculations. The coordination of the three amino acids is shown in Figure 1. The electronic structure of donor and acceptor were calculated by the PM3 method30 in the Gaussian package31. To save the computation time, we fix the atomic orbital coefficients in the molecular orbitals which are solved in the isolated state of BPhe and QA. The electronic structures of the pruned protein are solved at the extended Hückel level. We referred to the FORTICON8 program32. We take into account the variable hyperconjugation effect of the methyl group with the π-conjugated part of quinone in the course of rotation of the methyl group33. The tunneling matrix element TDA is calculated for each protein conformation by the same method as before6,9. The tunneling energy is chosen at −9.5 eV.


Correlation between square of electron tunneling matrix element and donor-acceptor distance in fluctuating protein media
General view of the coordination of donor (bacterio-pheophytin), acceptor (quinone), and the three amino acids (TrpM252, MetM218, and HisM219) which we investigate in this paper. The molecular structure of donor and acceptor is represented by a ball and stick model. The molecular structure of the three amino acids is represented by a stick model. Blue balls, red balls, deep blue balls, and white balls indicate carbon atoms, oxygen atoms, nitrogen atoms, and hydrogen atoms, respectively. The gold stick in the MetM218 represents the sulfur atom.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036608&req=5

f1-4_19: General view of the coordination of donor (bacterio-pheophytin), acceptor (quinone), and the three amino acids (TrpM252, MetM218, and HisM219) which we investigate in this paper. The molecular structure of donor and acceptor is represented by a ball and stick model. The molecular structure of the three amino acids is represented by a stick model. Blue balls, red balls, deep blue balls, and white balls indicate carbon atoms, oxygen atoms, nitrogen atoms, and hydrogen atoms, respectively. The gold stick in the MetM218 represents the sulfur atom.
Mentions: The procedures for the quantum chemistry (QC) calculations of TDA are the same as before6,9. Here, we briefly describe it. The chemical structures of donor and acceptor which we adopted in calculating the molecular orbitals of donor and acceptor are shown in Figure 1. In these calculations, long hydrocarbon chains of native bacteriopheophytin a and the native ubiquinone 10 are truncated to hydrogen atoms. It has been shown that the similar result of the time variation of TDA is obtained in both cases when 60 amino acids surrounding donor and acceptor are considered and when 3 amino acids between donor and acceptor are considered9. Then we consider the three amino acids TrpM252, MetM218, and HisM219 in the present calculations. The coordination of the three amino acids is shown in Figure 1. The electronic structure of donor and acceptor were calculated by the PM3 method30 in the Gaussian package31. To save the computation time, we fix the atomic orbital coefficients in the molecular orbitals which are solved in the isolated state of BPhe and QA. The electronic structures of the pruned protein are solved at the extended Hückel level. We referred to the FORTICON8 program32. We take into account the variable hyperconjugation effect of the methyl group with the π-conjugated part of quinone in the course of rotation of the methyl group33. The tunneling matrix element TDA is calculated for each protein conformation by the same method as before6,9. The tunneling energy is chosen at −9.5 eV.

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 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.