Communication between the domains of the DnaK chaperone characterized by single molecule force spectroscopy

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DnaK is a Hsp70 chaperone of E. coli which consists of an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate binding domain (SBD). NBD binds ATP or ADP and displays very weak ATPase activity. SBD recognizes hydrophobic stretches in the polypeptide chain of protein substrates. DnaK shows negative cooperativity between the binding of ATP to NBD and protein substrates to the remote SBD. This bidirectional allosteric communication is mediated through the conserved linker between the domains. Notably, the underlying physical principles of the communication pathways are still not know. Recent progress in atomic force microscopy (AFM) allows molecular forces to be measured at sub-pico-Newton resolution and at variable dimensions what could be particularly interesting for allosteric proteins. Using these techniques, my major goals will be to elucidate: (1) the interdomain dynamics of DnaK in different states; (2) the mechanics of the allosteric transitions upon nucleotide and substrate binding; and (3) the movements of DnaK subdomains induced by the concerted action of the co-chaperone DnaJ and the nucleotide exchange protein GrpE.