Selective stabilization of a partially unfolded protein by a metabolite

When proteins fold in vivo, the intermediates that exist transiently on their folding pathways are exposed to the potential interactions with a plethora of metabolites within the cell. However, these potential interactions are commonly ignored. Here, we report a case in which a ubiquitous metabolite interacts selectively with a nonnative conformation of a protein and facilitates protein folding and unfolding process. From our previous proteomics study, we have discovered that Escherichia coli glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is not known to bind ATP under native conditions, is apparently destabilized in the presence of a physiological concentration of ATP. To decipher the origin of this surprising effect, we investigated the thermodynamics and kinetics of folding and unfolding of GAPDH in the presence of ATP. Equilibrium unfolding of the protein in urea showed that a partially unfolded equilibrium intermediate accumulates in the presence of ATP. This intermediate has a quaternary structure distinct from the native protein. Also, ATP significantly accelerates the unfolding of GAPDH by selectively stabilizing a transition state that is distinct from the native state of the protein. Moreover, ATP also significantly accelerates the folding of GAPDH. These results demonstrate that ATP interacts specifically with a partially unfolded form of GAPDH and affects the kinetics of folding and unfolding of this protein. This unusual effect of ATP on the folding of GAPDH implies that endogenous metabolites may facilitate protein folding in vivo by interacting with partially unfolded intermediates.