Molecular chaperones recognize unfolded or misfolded proteins by binding to
hydrophobic surface patches not normally exposed in the native proteins.
Members of the Clp/Hsp100 family of chaperones are present in eubacteria and
within organelles of all eukaryotes, promoting disaggregation and disassembly
of protein complexes and participating in energy-dependent protein
degradation. The ClpA, ClpB, and ClpC subfamilies of the Clp/Hsp100 ATPases
contain a conserved N-terminal domain of ~150 amino acids, which in turn
consists of two repeats of ~75 residues. Although the Clp repeat (R) domain
contains two approximate sequence repeats, it behaves as a single
cooperatively folded unit. The Clp R domain is thought to provide a means for
regulating the specificity of and to enlarge the substrate pool available to
Clp/Hsp100 chaperone or protease complexes. These roles can be assisted
through the binding of an adaptor protein. Adaptor proteins bind to the Clp R
domain, modulate the target specificity of the Clp/Hsp100 complex to a
particular substrate of interest, and may also regulate the activity of the
The Clp R domain is monomeric and partially α helical. It is a single
folding unit with pseudo 2-fold symmetry. The Clp R domain structure consists
of two four-helix bundles connected by a flexible loop [2,3,4].
The profile we developed covers the entire Clp R domain.
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