From protein engineering to folding pathways: folding of PDZ domain at atomic level

Gianni, S., Travaglini-Allocatelli, C., C.losci, N., Brunori, M.

Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università di Roma “La Sapienza”

Understanding the mechanism by which a polypeptide chain folds into its unique native structure requires a complete and detailed description of all the species populated in the folding process. Experimentally the best strategy to unravel the folding mechanism of a protein is to employ basic rules of chemistry: identify all the intermediates of the reaction and the transition states between them and characterize their structure. To this aim, kinetic and equilibrium measurements on the unfolding and refolding of mutant proteins can be used to map the formation of structure in transition states and folding intermediates. We report a complete characterization of the kinetic folding mechanism of PDZ2 from PTP-BL, investigated at a variety of different experimental conditions. Furthermore, by using some 30 suitable mutants we depict a detailed folding pathway for PDZ2 from PTP-BL at nearly atomic resolution. Finally, we present evidence that folding proceeds via the formation of a localized nucleus whose local structure drives the denatured state to its functional native conformation.

Email: stefano.gianni@uniroma1.it

Address: Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”,, Università di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Rome, Italy