BIOINORGANIC CHEMISTRY A Short Course Second Edition

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424 IRON-CONTAINING PROTEINS AND ENZYMES


systems immediately after dilution (concurrent with folding initiation) using
NMR and circular dichroism (CD). The CD spectra show that elements of
secondary structure, probably compact structures, begin forming shortly after
folding initiation and NMR spectra show that these are short - lived (milli-
seconds). All the experimental evidence suggests that the compact and
extended nonnative structures are in rapid equilibrium immediately after
denaturant dilution. This conclusion agrees with computational experiments
contending that global hydrophobic collapse is not an obligatory step in protein
folding. Normally, collapsed intermediates are favored by more hydrophobic
and less optimized protein primary sequences, while less hydrophobic and
strongly optimized sequences favor extended structures collapsing to native
protein conformation. The primary sequence and stability of cytochrome c
place it between the two limits, making the extended and collapsed structures
degenerate in energy. The relative instability of nonnative collapsed structures
prevents misfolded protein structures during self - assembly and reduces
the probability that the native protein will transiently adopt an incorrect
conformation.
Many other research groups have studied the cytochrome c folding problem.
One perspective that addresses some of the controversy surrounding cyto-
chrome c folding pathways is found in a Rousseau group perspective published
in 2000. 127a Readers interested in pursuing this topic should consult reference
127b , in which Akiyama, Morishima, and co - workers studied stepwise forma-
tion ofα - helices during cytochrome c folding using CD spectroscopy.


7.7.4.2 Electron Transfer in Cytochrome c and Its Redox Partners. Electron
transfer (eT) between cytochrome c and its redox partners has been studied
by many researchers using many different experimental techniques. For spe-
cifi c recognition between redox partners, complementary protein surfaces are
necessary and conformational changes may be required. Two different theories
predominate the protein electron transfer discussion: (1) Electron transfer is
mediated by the polypeptide backbone and specifi c amino acid side chains,^128
and (2) rapid electron transfer requires redox cofactors to approach each other
at a minimal distance without a requirement for a specifi c path through the
protein.^129 One area that has yielded information is electron transfer between
cytochrome c and cytochrome c peroxidase as studied by X - ray crystallogra-
phy and photochemically induced eT. Cytochrome c peroxidase (CcP) reacts
with H 2 O 2 and two equivalents of ferrocytochrome c to produce water, ferri-
cytochrome c, and regenerated CcP. In a multistep process, and before receiv-
ing electrons from cytochrome c, CcP forms compound I, then compound II,
intermediates of unknown structure. Native, resting state CcP contains a
Fe(III) ion in its cytochrome b cofactor. Compound I would nominally contain
a Fe(V) ion; however, M ö ssbauer and other studies have identifi ed a ferryl
(Fe(IV)) ion. The other electron lost in forming compound I has been shown
to come from a tryptophan side chain, in the species being discussed here, a
trp191 cation radical is formed. In mid - 2006, no detailed structural information

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