Sequence-Specific Rates of Interaction of Target Peptides with the Molecular Chaperones DnaK and DnaJ

The kinetics of complex formation between nine different fluorescence-labeled peptides (7−22 amino acid residues) and DnaK (Hsp70 homologue of Escherichia coli) in the nucleotide-free R state and in the ATP-liganded T state were measured. R-state DnaK (1 μM) formed high-affinity complexes (K d = 0.06−2 μM) and bound all peptides (22−50 nM) in slow one- or two-step processes with apparent rate constants for the first phase, varying only by a maximum factor of 30 (k obs1 = 0.003−0.084 s-1 at pH 7.0 and 25 °C). In contrast, the rates of complex formation between DnaK−ATP and the same peptides (K d = 2.2−107 μM) have been found previously to vary by 4 orders of magnitude [one- or two-step processes with k obs1 = 0.001−7.9 s-1; Gisler, S. M., Pierpaoli E. V., and Christen, P. (1998) J. Mol. Biol. 279, 833−840]. The slow and relatively uniform rates of peptide binding to the R state might be determined by the fraction of time during which the α-helical lid above the peptide-binding site is open. The faster and widely divergent rates of binding to the open T state might reflect sequence-specific conformational rearrangements in the peptide-binding site and perhaps of the peptide itself. The different rates of association with DnaK−ATP suggest a kinetic partitioning of target sequences in which only slowly interacting segments of polypeptides are channeled into the chaperone cycle.