Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant

Protein folding and unfolding reactions invariably appear to be highly cooperative reactions, but the structural and sequence determinants of cooperativity are poorly understood. Importantly, it is not known whether cooperative structural change occurs throughout the protein, or whether some parts change cooperatively and other parts change noncooperatively. In the current study, hydrogen exchange mass spectrometry has been used to show that the mechanism of unfolding of the PI3K SH3 domain is similar in the absence and presence of 5 M urea. The data are well described by a four state N <-> I-N <-> I-2 <-> U model, in which structural changes occur noncooperatively during the N <-> IN and I-N <-> I-2 transitions, and occur cooperatively during the I-2 <-> U transition. The nSrc-loop and RT-loop, as well as beta strands 4 and 5 undergo noncooperative unfolding, while beta strands 1, 2, and 3 unfold cooperatively in the absence of urea. However, in the presence of 5 M urea, the unfolding of beta strand 4 switches to become cooperative, leading to an increase in the extent of cooperative structural change. The current study highlights the relationship between protein stability and cooperativity, by showing how the extent of cooperativity can be varied, using chemical denaturant to alter protein stability.