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The role of a ß-bulge in the folding of the ß-hairpin structure in ubiquitin

¹ Cambridge Center for Molecular Recognition and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
² Institute of Chemistry, Academia Sinica, Taipei, Taiwan, R.O.C.

Reprint requests to: Sunney I. Chan, Institute of Chemistry, Academia Sinica, Taipei, 11529, Taiwan, R.O.C.; e-mail: chans{at}chem.sinica.edu.tw; fax: 886-2-2783-1237.

It is known that the peptide corresponding to the N-terminal ß-hairpin of ubiquitin, U(1–17), can populate the monomeric ß-hairpin conformation in aqueous solution. In this study, we show that the Gly-10 that forms the bulge of the ß-turn in this hairpin is very important to the stability of the hairpin. The deletion of this residue to desG10(1–16) unfolds the structure of the peptide in water. Even under denaturing conditions, this bulge appears to be important in maintaining the residual structure of ubiquitin, which involves tertiary interactions within the sequence 1 to 34 in the denatured state. We surmise that this residual structure functions as one of the nucleation centers in the folding process and is important in stabilizing the transition state. In accordance with this idea, deleting Gly-10 slows down the refolding and unfolding rate by about one half.

Keywords: Ubiquitin; hairpin; bulge; turn; peptide; structure; folding; stability; kinetics

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