Recent advances in the structural and mechanistic aspects of Hsp70 molecular chaperones

Abstract

Hsp70 chaperones are central hubs of the protein quality control network and collaborate with co-chaperones having a J-domain (an ∼70-residue-long helical hairpin with a flexible loop and a conserved His-Pro-Asp motif required for ATP hydrolysis by Hsp70s) and also with nucleotide exchange factors to facilitate many protein-folding processes that (re)establish protein homeostasis. The Hsp70s are highly dynamic nanomachines that modulate the conformation of their substrate polypeptides by transiently binding to short, mostly hydrophobic stretches. This interaction is regulated by an intricate allosteric mechanism. The J-domain co-chaperones target Hsp70 to their polypeptide substrates, and the nucleotide exchange factors regulate the lifetime of the Hsp70-substrate complexes. Significant advances in recent years are beginning to unravel the molecular mechanism of this chaperone machine and how they treat their substrate proteins.

Keywords: 70-kilodalton heat shock protein (Hsp70); J-domain; allosteric regulation; chaperone DnaJ (DnaJ); chaperone DnaK (DnaK); molecular chaperone; nanomachine; protein folding; protein homeostasis.

Figure 1.

Hsp70 functions and ATPase cycle. a, JDPs target Hsp70s to a diverse set of substrates, including nascent polypeptide chains at the ribosome or translocation pore, to misfolded, aggregated, or amyloidic proteins, to oligomeric protein complexes, and to certain native proteins. b, structures of E. coli DnaK in the ATP-bound open conformation (PDB code 4B9Q, (16)) and the ADP-bound closed conformation (PDB code 2KHO (13)) with NBD lobe I in dark blue, lobe II in light blue, the conserved interdomain linker in yellow, SBDβ in dark green, and SBDα in light green. Substrates (dark red) targeted by JDPs bind with high association rates to the open conformation of Hsp70·ATP (indicated as transparent peptide from the aligned 1DKX structure (10)) and in synergism with the JDP trigger ATP hydrolysis and transition to the ADP-bound closed high-affinity state. NEFs accelerate ADP release, and rebinding of ATP converts Hsp70 back to the low-affinity ATP-bound state with subsequent substrate release. c, schematic illustrating ATP-induced conformational changes in Hsp70s; colors as in b.

Figure 2.

Hsp70–substrate interaction and helical lid dynamics. a, on the left is shown the substrate-binding domain of the E. coli Hsp70, DnaK, with the model peptide NRLLLTG (in cyan) bound to the binding cleft (10) (PDB code 1DKZ). This side view of the crystal structure shows how the β-subdomain cradles the model substrate in an extended conformation, with the helical lid serving as a cover over the peptide substrate. On the right is shown a top view of the SBD–NRLLLTG complex (with the helical lid removed) to illustrate the five pockets that comprise the canonical binding site (numbered). The structure shows the extended backbone of the peptide substrate model and the fit of side chains into the pockets on the chaperone. b, on the left is shown the ADP- and substrate-bound conformation of DnaK (PDB code 2KHO (13)), including a bound model peptide substrate (NRLLLTG) (in red), with a schematic representation of the potential movements of the helical lid that have been observed to occur by a variety of methods (34–36). On the right is shown how the lifting of the helical lid away from the β-subdomain enables the binding of a partially folded client protein to the canonical binding groove in the SBD. The protein depicted here, a mutant form of apoflavodoxin, illustrates a representative ensemble of unfolded states as determined by NMR (PDB code 2KQU) (121).

Figure 3.

Structure and function of JDPs. a, domain organization of JDPs; JD, J-domain; G/F, glycine-phenylalanine–rich region; Zn, zinc finger; β1, first β-sandwich domain; β2, second β-sandwich domain; DD, dimerization domain. b, NMR structure of the J-domain of E. coli DnaJ (PDB code 1XBL (122)) indicating the four helices of the helical hairpin and the HPD motif. c, structure of the ATP-bound open conformation of E. coli DnaK in complex with the J-domain of E. coli DnaJ (PDB code 5NRO (82)); NBD lobe I, dark blue; NBD lobe II, light blue; linker, yellow; SBDβ, dark green; SBDα, light green; J-domain, purple. The SBDβ was aligned with the structure of the SBD in complex with a substrate peptide (PDB code 1DKX (10)) to show how peptides (dark red) bind to the ATP-bound open conformation. d, zoom into the structure presented in c showing residues involved in J-domain–DnaK interactions and in substrate and DnaJ-mediated stimulation of the ATPase activity as sticks, polar contacts as black dashed lines, and hydrophobic interactions as gray hatched lines. e, cartoon representation of the β-sandwich domains and the zinc finger of the class A JDP Saccharomyces cerevisiae Ydj1 (PDB code 1NLT (86); dimerization domain is missing in the structure) and the full structure of the class B JDP T. thermophilus DnaJ (PDB code 4J80 (123); J-domain, purple; G/F region, cyan; zinc, dark teal; β1, light green; β2, yellow; dimerization domain, orange.

Figure 4.

Mode of action of NEFs. Cartoon and surface representations of crystal structures of different NEFs (orange and yellow) in complex with an Hsp70 NBD (IA, dark blue; IB, cyan; IIA, light blue; IIB, dark teal), overlaid onto the full-length solution structure of DnaK (PDB code 2KHO (13), only SBD shown) to illustrate the position of the SBD. From top to bottom: E. coli GrpE in complex with E. coli DnaK–NBD (a, PDB code 1DKG (91)); Bag-domain of human Bag1 in complex with the NBD of bovine Hsc70 (b, PDB code 1HX1 (124)); yeast Sse1 in complex with the NBD of bovine Hsc70 (c, PDB code 3D2E (125)); yeast Sil1 in complex with the NBD of yeast Kar2 (d, PDB code 3QML (126)); yeast Sil1 in complex with the NBD of yeast Kar2 overlaid to bovine Hsc70 and rotated as indicated (yellow arrow indicates the displacement of subdomain IIB); e, NBD of bovine Hsc70 in complex with ADP, phosphate, Mg²⁺, and two K⁺ ions (PDB code 1HPM (68)). The NBDs of all structures are aligned to subdomains IA, IB, and IIA of the NBD of bovine Hsc70. Dashed lines at the N termini of GrpE and Sil1 indicate the unstructured regions not present in the crystal structure and proposed to bind into the substrate-binding pocket of Hsp70 (115, 116). The N-terminal methionine (M1) and the first residue in the structure are indicated.