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Autonomous folding of a peptide corresponding to the N‐terminal β‐hairpin from ubiquitin
Author(s) -
Zerella Rosa,
Evans Philip A.,
Ionides JOHN M.C.,
Packman Len C.,
Trotter B. Wesley,
Mackay Joel P.,
Williams Dudley H.
Publication year - 1999
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.8.6.1320
Subject(s) - random coil , folding (dsp implementation) , protein folding , population , crystallography , ubiquitin , chemistry , sequence (biology) , phi value analysis , native state , biophysics , protein structure , protein secondary structure , biology , biochemistry , demography , sociology , electrical engineering , gene , engineering
The N‐terminal 17 residues of ubiquitin have been shown by 1 H 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.