Protein Conformational Gate Controlling Binding Site Preference and Migration for Ubiquinone-B in the Photosynthetic Reaction Center ofRhodobactersphaeroides

A convergence of research effort in a number of scientific disciplines in the early 1980s resulted in a rapid expansion of knowledge of the structure and function of the photosynthetic reaction center in bacteria and higher plants. The structure of the reaction center from photosynthetic bacteria was determined by X-ray analysis. The herbicide binding protein (the D1 protein) was identified by photoaffinity labelling and found to be an integral part of the photosynthetic reaction center complex in higher plants. Studies using herbicide-resistant mutants enabled the location of the herbicide binding niche on D1 to be determined. Quantitative Structure Activity Relationships (QSAR) of families of inhibitors and their effect on photosynthetic electron transport helped elucidate the nature of the interaction between inhibitors and receptor. Binding appeared to be predominantly hydrophobic with hydrogen bonding also having an important role. Studies with a series of highly potent inhibitors, the 2-cyanoacrylates, identified certain steric constraints in the interaction of these molecules with the binding site. The activity of these inhibitors was particularly sensitive to minor structural change and they proved to be useful probes of receptor topography. The results of structure-activity studies of the 2-cyanoacrylates combined with a refined knowledge of the three-dimensional structure of the inhibitor binding site has enabled computer-based molecular modelling of interactions of these inhibitors with the receptor. The spatial arrangement of the inhibitor functional groups within the binding domain was shown to be a critical factor in determining binding affinity.

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The Singlet-Triplet Splitting of the Primary Radical Pair in the Bacterial Photosynthetic Reaction Center*

Zeitschrift für Physikalische Chemie ◽

10.1524/zpch.1992.1.part_1.193 ◽

1992 ◽

Vol 1 (Part_1) ◽

pp. 193-208

Author(s):

M. Bixon ◽

J. Jortner ◽

M. E. Michel-Beyerle

Keyword(s):

Reaction Center ◽

Radical Pair ◽

Photosynthetic Reaction Center ◽

Primary Radical ◽

Triplet Splitting ◽

Primary Radical Pair ◽

Bacterial Photosynthetic Reaction Center

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Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

10.26434/chemrxiv.11980119.v1 ◽

2020 ◽

Author(s):

Denis Artiukhin ◽

Patrick Eschenbach ◽

Johannes Neugebauer

Keyword(s):

Spin Density ◽

Reaction Center ◽

Density Functional ◽

Photosynthetic Reaction Center ◽

Chem Phys ◽

Molecular Structures ◽

Error Characteristic ◽

Molecular Systems ◽

Density Distributions ◽

The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from Synechococcus elongatus, Thermococcus vulcanus, and Rhodobacter sphaeroides, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

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