Multiple-Site Exchange in Proteins Studied with a Suite of Six NMR Relaxation Dispersion Experiments: An Application to the Folding of a Fyn SH3 Domain Mutant

Abstract

The three-site exchange folding reaction of an ¹⁵N-labeled, highly deuterated Gly48Met mutant of the Fyn SH3 domain has been characterized at 25 °C using a suite of six CPMG-type relaxation dispersion experiments that measure exchange contributions to backbone ¹H and ¹⁵N transverse relaxation rates in proteins. It is shown that this suite of experiments allows the extraction of all the parameters of this multisite exchange process in a robust manner, including chemical shift differences between exchanging states, from a data set recorded at only a single temperature. The populations of the exchanging folded, intermediate, and unfolded states that are fit are 94, 0.7, and 5%, respectively. Despite the small fraction of the intermediate, structural information is obtained for this state that is consistent with the picture of SH3 domain folding that has emerged from other studies. Taken together, the six dispersion experiments facilitate the complete reconstruction of ¹H−¹⁵N correlation spectra for the unfolded and intermediate states that are “invisible” in even the most sensitive of NMR experiments.