Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I
Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster F<sub>X</sub>, which is...
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MDPI AG
2022-02-01
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| Online Access: | https://www.mdpi.com/2079-7737/11/3/362 |
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| author | Fedaa Ali Medhat W. Shafaa Muhamed Amin |
| author_facet | Fedaa Ali Medhat W. Shafaa Muhamed Amin |
| author_sort | Fedaa Ali |
| collection | DOAJ |
| description | Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster F<sub>X</sub>, which is followed by two terminal iron–sulfur clusters F<sub>A</sub> and F<sub>B</sub>. Experiments have shown that F<sub>X</sub> has lower oxidation potential than F<sub>A</sub> and F<sub>B</sub>, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>E</mi><mi>m</mi></msub></mrow></semantics></math></inline-formula> potentials of the F<sub>X</sub>, F<sub>A</sub> and F<sub>B</sub> clusters. Our calculations show that F<sub>X</sub> has the lowest oxidation potential compared to F<sub>A</sub> and F<sub>B</sub> due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for F<sub>X</sub> compared to F<sub>A</sub> and F<sub>B</sub>. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for F<sub>X</sub> compared to both F<sub>A</sub> and F<sub>B.</sub> These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics. |
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| language | English |
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| spelling | doaj.art-a099027776a74d53a345349b414009932023-11-30T20:51:15ZengMDPI AGBiology2079-77372022-02-0111336210.3390/biology11030362Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem IFedaa Ali0Medhat W. Shafaa1Muhamed Amin2Medical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, EgyptMedical Biophysics Division, Department of Physics, Faculty of Science, Helwan University, Cairo 11795, EgyptDepartment of Sciences, University College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The NetherlandsPhotosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster F<sub>X</sub>, which is followed by two terminal iron–sulfur clusters F<sub>A</sub> and F<sub>B</sub>. Experiments have shown that F<sub>X</sub> has lower oxidation potential than F<sub>A</sub> and F<sub>B</sub>, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><msub><mi>E</mi><mi>m</mi></msub></mrow></semantics></math></inline-formula> potentials of the F<sub>X</sub>, F<sub>A</sub> and F<sub>B</sub> clusters. Our calculations show that F<sub>X</sub> has the lowest oxidation potential compared to F<sub>A</sub> and F<sub>B</sub> due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for F<sub>X</sub> compared to F<sub>A</sub> and F<sub>B</sub>. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for F<sub>X</sub> compared to both F<sub>A</sub> and F<sub>B.</sub> These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.https://www.mdpi.com/2079-7737/11/3/362photosystem Iiron–sulfur clustercontinuum electrostaticsbroken symmetry DFTelectron transferMCCE |
| spellingShingle | Fedaa Ali Medhat W. Shafaa Muhamed Amin Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I Biology photosystem I iron–sulfur cluster continuum electrostatics broken symmetry DFT electron transfer MCCE |
| title | Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I |
| title_full | Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I |
| title_fullStr | Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I |
| title_full_unstemmed | Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I |
| title_short | Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I |
| title_sort | computational approach for probing redox potential for iron sulfur clusters in photosystem i |
| topic | photosystem I iron–sulfur cluster continuum electrostatics broken symmetry DFT electron transfer MCCE |
| url | https://www.mdpi.com/2079-7737/11/3/362 |
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