The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins

To investigate the sequence dependence in the molecular mechanism of urea induced denaturation, molecular dynamics denaturing simulations of two beta-hairpin peptides, a fast folding peptide 1 (SESYINPDGTWTVTE) and a slow folding TRPZIP4 (GEWTWDDATKTWTWTE), were performed in urea aqueous solutions. It was found that beta-hairpin denaturation by urea is highly dependent on the hydrophobicity of the side chains. The two beta-hairpin peptides studied here and the GB1 studied previously display three different denaturant processes in urea solution by which the breaking of backbone native hydrogen bonds takes different orders. The variation of their denaturing mechanism is well correlated to the variation in their structural properties. In peptide 1, which has only a loosely packed hydrophobic core formed by residues Trp11 and Ile5, all backbone native hydrogen bonds (1 to 5) are broken in a short period of time. Whereas for TRPZIP4 with a compact hydrophobic core of four tryptophan residues, the backbone native hydrogen bonds (1 to 6) are considerably more stable, with the middle hydrogen bonds protected well by the hydrophobic core being the most stable. The comparison of different beta-hairpin peptides shows that the side-chain packing on each face of the strands plays a major role in the stability of the backbone native hydrogen bonds in urea solution, and indicates that protein denaturation by urea can be highly sequence dependent.