The folding pathway of the cell-cycle regulatory protein p13suc1: clues for the mechanism of domain swapping

Background: The 113-residue alpha+beta protein suc1 is a member of the cyclin-dependent kinase subunit (cks) family of proteins that are involved in regulation of the eukaryotic cell cycle, in vitro, suc1 undergoes domain swapping to form a dimer by the exchange of a C-terminal beta strand. We have analysed the folding pathway of suc1 in order to determine the atomic details of how strand-exchange occurs in vitro and thereby obtain clues as to the possible mechanism and functional role of dimerisation in vivo. Results: The structures of the rate-determining transition state for the folding/unfolding of suc1 and of the intermediate that is populated during refolding were probed using phi values determined for 57 mutants with substitutions at 43 sites throughout the protein. The majority of values are fractional in the intermediate and transition state, indicating that interactions build up in a concerted manner during folding, In the transition state, phi values of greater than 0.5 are clustered around the inner strands beta 2 and beta 4 of the beta sheet. This part of the structure constitutes the nucleus for folding according to a nucleation-condensation mechanism. Molecular dynamics simulations of unfolding of suc1, performed independently in a blind manner, are in excellent agreement with experiment (proceeding paper). Conclusions: Strand beta 4 is the exchanging strand in the dimer and yet it forms an integral pair of the folding nucleus. This suggests that association is an early event in the folding reaction of the dimer, Therefore, interchange between the monomer and dimer must occur via an unfolded state, a process that may be facilitated in vivo by accessory proteins.