MCCE calculation of quinone dependent electron and proton transfers in Rhodobacter sphaeroides bacterial photosynthetic reaction centers.
Item
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Title
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MCCE calculation of quinone dependent electron and proton transfers in Rhodobacter sphaeroides bacterial photosynthetic reaction centers.
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Identifier
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AAI3159270
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identifier
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3159270
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Creator
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Zhu, Zhenyu.
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Contributor
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Adviser: Marilyn Gunner
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Date
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2005
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Language
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English
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Publisher
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City University of New York.
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Subject
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Biophysics, General
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Abstract
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To investigate the proton coupled electron transfers in membrane proteins such as photosynthetic reaction centers (RCs), Multiple Conformational Continuum Electrostatics (MCCE) was used to calculate the redox midpoint potentials and pKa of ubiquinone at QA and QB binding sites in the structures of Rhodobacter sphaeroides RCs.;By using 1AIJ(G) X-ray crystal structure, the calculated QA Em is -40 mV, the proximal QB Em is -10 mV, and the distal QB Em is -260 mV. In addition, the electrochemistry of the second reduction in the QB site was calculated. The reaction QA-QB - → QAQB-2 is about 200 meV less favorable than QA-Q B- → QA-QBH, supporting the Proton Transfer and Electron Transfer (PTET) mechanism where protonation of QB- precedes electron transfer. The calculations also confirm that the first protonation of QB occurs at the distal QB oxygen and the second binds to the proximal oxygen. SerL223 electrostatically stabilizes the semiquinone QBH and destabilizes QBH2.;By MCCE calculations on multiple X-ray crystal structures (1AIJ(G), 1M3X, 1PCR'), the average QA Em is -35 +/- 7 mV, and the average proximal QB Em is 24 +/- 27 mV. The Ems are relatively independent of and are in good agreement with the experimental data. However, MCCE simulations show significant differences in the ionization states of QB pocket residues AspL210, GluL212, AspL213 and G1uH173 in the ground state due to small changes in the different crystal structures. When QB is reduced the ionization states are identical in all structures. Thus, the intra-cluster proton transfers required for electron transfer vary with small changes in structure.
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Type
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dissertation
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Source
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PQT Legacy CUNY.xlsx
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degree
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Ph.D.
