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

The N-terminal 17 residues of ubiquitin have been shown by H-1 NMR to fold autonomously into a beta-hairpin structure in aqueous solution. This struct ure has a specific, native-like register, though side-chain contacts differ in detail from those observed in the intact protein. An autonomously foldi ng hairpin has previously been identified in the case of streptococcal prot ein G, which is structurally homologous with ubiquitin, but remarkably, the two are not in topologically equivalent positions in the fold. This sugges ts that the organization of folding may be quite different for proteins sha ring similar tertiary structures. Two smaller peptides have also been studi ed, corresponding to the isolated arms of the N-terminal hairpin of ubiquit in, and significant differences from simple random coil predictions observe d in the spectra of these subfragments, suggestive of significant limitatio n of the backbone conformational space sampled, presumably as a consequence of the strongly beta-structure favoring composition of the sequences. This illustrates the ability of local sequence elements to express a propensity for beta-structure even in the absence of actual sheet formation. Attempts were made to estimate the population of the folded start of the hairpin, i n terms of a simple two-state folding model. Using published "random coil" values to model the unfolded state, and values derived from native ubiquiti n for the putative unique, folded state, it was found that the apparent pop ulation varied widely for different residues and with different NMR paramet ers. Use of the spectra of the subfragment peptides to provide a more reali stic model of the unfolded state led to better agreement in the estimates t hat could be obtained from chemical shift and coupling constant measurement s, while making it clear that some other approaches to population estimatio n could not give meaningful results, because of the tendency to populate th e beta-region of conformational space even in the absence of the hairpin st ructure.