An expanded view of the protein folding landscape of PDZ domains

Most protein domains fold in an apparently co-operative and two-state manner with only the native and denatured states significantly populated at any experimental condition. However, the protein folding energy landscape is often rugged and different transition states may be rate limiting for the folding reaction under different conditions, as seen for the PDZ protein domain family. We have here analyzed the folding kinetics of two PDZ domains and found that a previously undetected third transition state is rate limiting under conditions that stabilize the native state relative to the denatured state. In light of these results, we have re-analyzed previous folding data on PDZ domains and present a unified folding mechanism with three distinct transition states separated by two high-energy intermediates. Our data show that sequence composition tunes the relative stabilities of folding transition states within the PDZ family, while the overall mechanism is determined by topology. This model captures the kinetic folding mechanism of all PDZ domains studied to date.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► An early transition state for folding of PDZ domains is demonstrated. ► The transition states for folding of PDZ domains can be selectively destabilized. ► Sequence composition tunes the relative stabilities of folding transition states within a protein family. ► A unified folding mechanism for PDZ domains includes three transition states.