The N-terminal 17 residues of ubiquitin have been
shown by 1H NMR to fold autonomously into a
β-hairpin structure in aqueous solution. This structure
has a specific, native-like register, though side-chain
contacts differ in detail from those observed in the intact
protein. An autonomously folding hairpin has previously
been identified in the case of streptococcal protein G,
which is structurally homologous with ubiquitin, but remarkably,
the two are not in topologically equivalent positions in
the fold. This suggests that the organization of folding
may be quite different for proteins sharing similar tertiary
structures. Two smaller peptides have also been studied,
corresponding to the isolated arms of the N-terminal hairpin
of ubiquitin, and significant differences from simple random
coil predictions observed in the spectra of these subfragments,
suggestive of significant limitation of the backbone conformational
space sampled, presumably as a consequence of the strongly
β-structure favoring composition of the sequences.
This illustrates the ability of local sequence elements
to express a propensity for β-structure even in the
absence of actual sheet formation. Attempts were made to
estimate the population of the folded state of the hairpin,
in terms of a simple two-state folding model. Using published
“random coil” values to model the unfolded
state, and values derived from native ubiquitin for the
putative unique, folded state, it was found that the apparent
population varied widely for different residues and with
different NMR parameters. Use of the spectra of the subfragment
peptides to provide a more realistic model of the unfolded
state led to better agreement in the estimates that could
be obtained from chemical shift and coupling constant measurements,
while making it clear that some other approaches to population
estimation could not give meaningful results, because of
the tendency to populate the β-region of conformational
space even in the absence of the hairpin structure.