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Autonomous folding of a peptide corresponding to the N-terminal β-hairpin from ubiquitin

Published online by Cambridge University Press:  01 June 1999

ROSA ZERELLA
Affiliation:
Cambridge Centre for Molecular Recognition and University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
PHILIP A. EVANS
Affiliation:
Cambridge Centre for Molecular Recognition and Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
JOHN M.C. IONIDES
Affiliation:
Cambridge Centre for Molecular Recognition and MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
LEN C. PACKMAN
Affiliation:
Cambridge Centre for Molecular Recognition and Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
B. WESLEY TROTTER
Affiliation:
Cambridge Centre for Molecular Recognition and University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138.
JOEL P. MACKAY
Affiliation:
Cambridge Centre for Molecular Recognition and University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom Present address: University of Sydney, Department of Biochemistry, Sydney, New South Wales 2006, Australia.
DUDLEY H. WILLIAMS
Affiliation:
Cambridge Centre for Molecular Recognition and University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Abstract

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.

Type
Research Article
Copyright
© 1999 The Protein Society

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