Interaction of the N‐terminal domain of Escherichia coli heat‐shock protein ClpB and protein aggregates during chaperone activity

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Abstract
The Escherichia coli heat‐shock protein ClpB reactivates protein aggregates in cooperation with the DnaK chaperone system. The ClpB N‐terminal domain plays an important role in the chaperone activity, but its mechanism remains unknown. In this study, we investigated the effect of the ClpB N‐terminal domain on malate dehydrogenase (MDH) refolding. ClpB reduced the yield of MDH refolding by a strong interaction with the intermediate. However, the refolding kinetics was not affected by deletion of the ClpB N‐terminal domain (ClpBΔN), indicating that MDH refolding was affected by interaction with the N‐terminal domain. In addition, the MDH refolding yield increased 50% in the presence of the ClpB N‐terminal fragment (ClpBN). Fluorescence polarization analysis showed that this chaperone‐like activity is explained best by a weak interaction between ClpBN and the reversible aggregate of MDH. The dissociation constant of ClpBN and the reversible aggregate was estimated as 45 μM from the calculation of the refolding kinetics. Amino acid substitutions at Leu 97 and Leu 110 on the ClpBN surface reduced the chaperone‐like activity and the affinity to the substrate. In addition, these residues are involved in stimulation of ATPase activity in ClpB. Thus, Leu 97 and Leu 110 are responsible for the substrate recognition and the regulation of ATP‐induced ClpB conformational change.