Reaction center proteins, modeling

Figure 3. The bacterial reaction-center protein model from Rhodopseudomonas sphaeroides the structure and positioning of components are highly speculative.

Most of the interest in mimicing aspects of photosynthesis has centered on a wide variety of model systems for electron transfer. Among the early studies were experiments involving photoinduced electron transfer in solution from chlorophyll a to p-benzoquinone (21, 22) which has been shown to occur via the excited triplet state of chlorophyll a. However, these solution studies are not very good models of the in vivo reaction center because the in vivo reaction occurs from the excited singlet state and the donor and acceptor are held at a fixed relationship to each other in the reaction-center protein. 

Figure 23-31 (A) Stereoscopic ribbon drawing of the photosynthetic reaction center proteins of Rhodopseudomonas viridis. Bound chromophores are drawn as wire models. The H subunit is at the bottom the L and M subunits are in the center. The upper globule is the cytochrome c. The view is toward the flat side of the L, M module with the L subunit toward the observer. (B) Stereo view of only the bound chromophores. The four heme groups Hel-He4, the bacteriochlorophylls (Bchl) and bacteriopheophytins (BPh), the quinones QA and QB/ and iron (Fe) are shown. The four hemes of the cytochrome are not shown in...

Molecular Modeling and Simulation of a Reaction Center Protein... 

Modeling the First Electron Transfer from Qa to Qb in Reaction Center Proteins from Rb, sphaeroides... 

Rees, D.C., et al. The bacterial photosynthetic reaction center as a model for membrane proteins. Anna. Rev. Biochem. 58 607-633, 1989. 

Deisenhofer, J., et al. X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. f. Mol. Biol. 180 385-398, 1984. 

FIGURE 22.18 Model of the R. viridis reaction center, (a, b) Two views of the ribbon diagram of the reaction center. Mand L subunits appear in purple and blue, respectively. Cytochrome subunit is brown H subunit is green. These proteins provide a scaffold upon which the prosthetic groups of the reaction center are situated for effective photosynthedc electron transfer. Panel (c) shows the spatial relationship between the various prosthetic groups (4 hemes, P870, 2 BChl, 2 BPheo, 2 quinones, and the Fe atom) in the same view as in (b), but with protein chains deleted. 

Another important result that was obtained recently concerns the evaluation of the contribution to the reorganization energy arising from the polarization of the medium, protein and solvent from a microscopic model including the residual charges and induced dipoles of the protein as well as bound water molecules, a value of about 0.2 eV was calculated for different eleetron transfer processes [97], This weak value results from the apolar character of the medium, and is compatible with the kinetic data which indicate that reorganization energies are small in the reaction center (Sect. 3.2.2)... 

While the results of this work are encouraging, it is clear that the structural definition of mutant proteins of this type is critical to development of rational interpretation of the results if for no other reason than that the structural perturbation introduced is presumably greater than for simple point mutations. Moreover, it would be particularly interesting to compare the functional properties of mutants compared in this manner in assays involving protein-protein reactions relevant to the species of cytochrome c on which the mutagenesis is based. For example, comparison of the activities of wild-type yeast cytochrome c with that of a loop-insertion mutant modelled on a photosynthetic cytochrome c in the reaction with the photosynthetic reaction center could help define the structural elements involved in the cytochrome c binding domain for the reaction center. 

Figure 23-28 (A) Model of a light-harvesting chlorosome from green photosynthetic sulfur bacteria such as Chlorobium tepidum and species of Prosthecochloris. The chlorosome is attached to the cytoplasmic membrane via a baseplate, which contains the additional antenna bacteriochlorophylls (795 BChl a) and is adjacent to the trimeric BChl protein shown in (B) and near the reaction center. After Li et al.302 and Remigy et a/.304 (B) Alpha carbon diagram of the polypeptide backbone and seven bound BChl a molecules in one subunit of the trimeric protein from the green photosynthetic bacterium Prosthecochloris. For clarity, the magnesium atoms, the chlorophyll ring substituents, and the phytyl chains, except for the first bond, are omitted. The direction of view is from the three-fold axis, which is horizontal, toward the exterior of the molecule. From Fenna and Matthews.305 See also Li et al.302...

The cobalt center in MeCbl, one of the two important B12 coenzymes, is clearly involved in key steps in catalytic methyl transfer processes. Here, the Co center cycles between Co(I) and Co(III)CH3. In methionine synthase, the proposed mechanism involves direct nucleophilic attack on the C of the Co(III)CH3 group. In model reactions, the thiolate most frequently simply binds tram to the alkyl group to give a product recently established by an x-ray study of a model system. The protein may block access to the Co, thus preventing this reaction common in models. It is likely that the reactive form of the bound cofactor is five-coordinate in the key point in the catalytic cycle. This reactive form will lead to a four-coordinate Co(I) species. The axial coordination of the cofactor by a protein imidazole allows for a finer tuning of the Cbl chemistry and may permit control of the coordination number. Thus, recoordination of Co in the Co(I) state may facilitate attack on methyltetrahydrofolate and re-formation of Co(III)CH3. 

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