Ferricytochrome structures

G. Fiandaca, E. Vitrano, and A. Cupane, Ferricytochrome c encapsulated in silica nanoparticles structural stability and functional properties. Biopolymers 74, 55—59 (2004). 

In a bulk silica matrix that differs from the silica nanomatrix regarding only the matrix size but has a similar network structure of silica, several kinetic parameters have been studied and the results demonstrated a diffusion controlled mechanism for penetration of other species into the silica matrix [89-93]. When the silica is used as a catalyst matrix in the liquid phase, slow diffusion of reactants to the catalytic sites within the silica rendered the reaction diffusion controlled [90]. It was also reported that the reduction rate of encapsulated ferricytochrome by sodium dithionite decreased in a bulk silica matrix by an order of magnitude compared to its original reaction rate in a homogeneous solution [89], In gas-phase reactions in the silica matrix, diffusion limitations were observed occasionally [93],... 

Figure 1. (a) X-ray crystal structure of horse-heart ferricytochrome c.8 All protein atoms are shown in the C.-P.-K. form, while the heme group is shown in the stick form. All Arg and Lys residues are colored blue, while Glu and Asp are colored in red, to contrast the destribution of the most ionizable side chains, (b) The X-ray crystal structure of horse heart ferricytochrome c in complex with horse cytochrome c peroxidase (cep).9 The peroxidase is shown as a molecular surface model, with blue regions depicting positive and red representing negative electrostatic potential. Note the cluster of negative potential on ccp that surrounds the contact interface. 

Water arrangements essentially similar to those for lysozyme have been found for various other high-resolution structures of proteins, for example, penicillopepsin (James and Sielecki, 1983), ferricytochrome c (Finzel et al., 1985), glyceraldehyde-3-phosphate dehydrogenase (Skar-zynski et al., 1987), and bacteriophage T4 lysozyme (Weaver tuid Matthews, 1987). Wlodawer et al. (1988) described the solvent about phosphate-free ribonuclease A, at 1.26 A, and have compared their results with those for other high-resolution structures of this protein. 

Solution Structures of Horse Ferro- and Ferricytochrome c using 2D and 3D IH NMR and Restrained Simulated Annealing... 

The X-ray crystal structure of D. vulgaris (Hildenborough) ferricytochrome c3 is known [51] and a preliminary solution structure for the ferrocytochrome has been obtained by NMR [58]. Also, the reduction potentials for each of its four hemes, as well as the specific assignment to their position in the structure... 

Cytochrome c exhibits several pH-dependent conformational states. In particular, an alkaline transition with a pXa —9.1 has been observed for ferricy-tochrome c. This transition is believed to be associated with the dissociation of Met-80 the reduetion potential decreases dramatically, and the 695-nm absorption band, associated with a sulfur iron charge-transfer transition, disappears. The NMR resonance due to ( H3C-) Met-80 in deuterium-enriched ferricytochrome c disappears from its hyperfine-shifted upheld position without line broadening, and reappears coincident with the ( H3C-)Met-65 resonance. In contrast, ferrocytochrome c maintains an ordered structure over the pH range 4 to 11. The heme iron in ferricytochrome c remains low-spin throughout this... 

The last of the critical eight aromatic rings is phenylalanine-82, totally invariant over all 60 eukaryotic sequences and the two bacterial cytochromes whose three-dimensional structures are known. It is found nested against the heme, closing the upper left of the heme crevice as shown in Fig. 6. Although this residue was formerly believed from the two-derivative, 2.8 A resolution electron density map of horse oxidized cytochrome to be swung out and away from the heme in ferricytochrome (12-1J ), the four-derivative, 2.0 A map of tuna ferricytochrome has revealed this to be incorrect (15). In both oxidation states, phenylalanine-82 appears to lie next to the heme, and the crevice remains "closed in the sense observed in Fig. 7. 

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