Probing residual interactions in unfolded protein states using NMR spin relaxation techniques:: An application to Δ131Δ

Residual interactions in Delta131Delta, a large disordered fragment of staphylococcal nuclease, have been probed at two different pHs using backbone N-15 and side-chain methyl H-2 NMR spin relaxation techniques. The amplitudes of picosecond time-scale motions of both the backbone and side chains do not change considerably at either pH value, although they are significantly larger than those observed for folded proteins. In contrast, dramatic increases in the amplitudes of motions occurring on a nanosecond time scale are observed throughout Delta131Delta at pH 3 relative to pH 5. This is consistent with a picture in which residual hydrophobic contacts at pH 5 are disrupted by electrostatic repulsions that dominate at the lower pH.