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processes. The rate of turnover of some proteins has been correlated with their
amino acid N-terminal residue sequences (N-end rule pathway), which appar-
ently favor ubiquitination of the protein and its subsequent proteasomal
digestion. It has been reported that N-terminal Cys of certain proteins must
first be arginylated in order to be degraded in a ubiquitin-dependent pathway.
However, arginylation of N-terminal Cys requires its prior oxidation, a process
that is controlled and rate limited by NO and oxygen (862).
In general, the level of a modified protein is always the result of the balance
between the relative rates of protein modification and degradation. For
example, oxidized proteins may accumulate in muscle tissues due to the slower
repair or degradation (863). Some mechanisms of protein aging, that is, race-
mization of aspartyl residues (647) or nonenzymatic glycosylation (601), occur
slowly and are therefore found predominantly in long-lived proteins.
Correlations between protein structure and degradation rates have been
thought to explain the basis of protein turnover. Degradation rates have been
correlated with thermal stability, dissociation of stabilizing ligands, and suscep-
tibility to proteolytic cleavage (824). Bachmair et al. (864) suggest that the
rate-limiting step in the degradation of long-lived proteins is slow aminopep-
tidase cleavage, which exposes a destabilizing amino acid. The destabilizing
element is rapidly recognized and leads to degradation according to the N-end
rule. Other observations are not consistent with a simple proteolytic mecha-
nism of degradation. For example, acidic proteins are generally degraded more
rapidly than are neutral or basic ones, the rate of degradation is nearly pro-
portional to the amount of apolar surface area of the folded protein, and
proteins composed of large polypeptide chains are degraded more rapidly
than those composed of small chains. It was proposed that proteins that are
rapidly degraded in eukaryotic cells contain regions rich in proline (P), glu-
tamic acid (E), serine (S), and threonine (T)—the PEST sequence (865). The
PEST hypothesis appears to be consistent with observations that acidic pro-
teins are generally degraded more rapidly than basic proteins, as PEST pro-
teins tend to be acidic.
Metal-Catalyzed Oxidation (MCO)
Since 1981, Stadtman and colleagues have examined the inactivation of pro-
teins in cell-free systems involving the metal ion-catalyzed autoxidation of
ascorbate and/or hydrogen peroxide; in some cases, the metal ions were
derived from metalloproteins. These systems are now termed “metal-catalyzed
oxidation systems” instead of the previous confusing term “mixed-function
oxidation systems” (44).
Under normal conditions, the MCO systems are the major source of oxida-
tive damage, requiring hydrogen peroxide or organic hydroperoxides (8) and
a transition metal (61) modifying preferentially amino acid residues at the
metal-binding site (254, 866).
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