IOPs: irreversibly oxidized proteins; T6SS: type VI secretion system. 4. in bacteria under stress conditions [15,16,17,18]. ClpB can remodel some protein substrates without the DnaK assistance, but cooperation of ClpB and DnaK produces the most efficient disaggregation [19,20,21]. Interestingly, the ClpB-DnaK cooperation in Etifoxine protein disaggregation is species-specific, i.e., ClpB efficiently cooperates only with DnaK from the same microorganism [22,23,24]. Like other Hsp100 family members, ClpB forms ring-shaped hexamers in the presence of ATP [25,26,27,28] with a narrow central channel (pore), wide enough to accommodate extended unfolded polypeptides (Figure 1). Each protomer of ClpB consists of multiple domains: N-terminal domain (NTD), two ATP-binding modules, i.e., nucleotide-binding domain 1 (NBD-1) and nucleotide-binding domain 2 (NBD-2) and a unique coiled-coil middle domain (MD) inserted at the end of NBD-1 (Figure 1A). Each NBD domain contains all the characteristic and highly conserved motifs of AAA+ ATPases, namely Walker A, Walker B, arginine finger, sensor-1, and sensor-2 (Figure 1A). The NTD of ClpB is responsible for the recognition and binding of protein substrates. NBDs generate energy from ATP for polypeptide translocation through the ClpB channel. The MD mediates the interactions with DnaK that are required for bacterial thermotolerance and efficient protein disaggregation [23,24,29] and is also involved in coordinating the communication between NBDs [19]. Of note, the presence of the coiled-coil MD distinguishes ClpB from such Hsp100/Clp proteins as ClpA, ClpX or HslU that are associated with a peptidase (ClpP or HslV) and do not display disaggregase activity. Open in a separate window Figure 1 (A) Structural organization of the ClpB monomer. Four domains are Etifoxine indicated: N-terminal domain (NTD), two nucleotide-binding domains (NBD-1 and NBD-2), and middle domain (MD). Each NBD contains the characteristic AAA+ motifs: Walker A (GX4GKT/S) (A), Walker B (Hy2DE) (B), sensor-1 (S-1), sensor-2 (S-2, GAR), and the arginine fingers (in the closed conformation (PDB entry 6N8T) [30]. Left panel: side view with the structural domains indicated for one Hsp104 subunit: NTD (red), NBD-1 (blue), MD (magenta), and NBD-2 (green). Right panel: top view with each subunit shown in a different color. The substrate-processing channel is visible at the center of the structure. Three out of six MDs were resolved in this cryo-EM image analysis, which highlights the highly dynamic properties and Etifoxine structural asymmetry of the hexameric complex. Images generated using PyMol 1.3 (Schr?dinger LLC, www.pymol.com accessed on 2010). Elegant studies of Bukaus group demonstrated that protein disaggregation mediated by ClpB is linked to the ATP hydrolysis-coupled substrate translocation through the central channel [31]. Recent advances in Rabbit Polyclonal to LFNG high-resolution cryo-electron microscopy and single-molecule force spectroscopy provided critical insights into the mechanism of ClpB activity. Most significantly, recent cryo-EM image reconstructions revealed the subunits of hexameric ClpB/Hsp104 (Number 1B) are arranged inside a spiral construction and undergo dynamic conformational rearrangements which support ratcheting of substrates through the central channel [30,32,33,34]. Optical tweezer experiments shown that ClpB is definitely a powerful source of a mechanical push capable of extracting polypeptides from aggregated particles and possibly acting upon surface-exposed loops (Number 2) [35]. In contrast to a directional push generation by ClpB, DnaK and additional Hsp70 chaperones modulate the conformation of their substrates by applying entropic pulling and stochastic relationships [36,37]. Open in a separate windowpane Number 2 Assistance of ClpB and DnaK during aggregate reactivation based on ref. [35]. (1) The aggregate-bound DnaK recruits ClpB to a protein aggregate and exposes ClpB-accessible fragments of the aggregate; (2) ClpB initiates substrate translocation from an revealed polypeptide loop; (3) stably folded domains can become hurdles for ClpB-mediated polypeptide extraction; (4) resistance during the translocation stalls ClpB-mediated disaggregation; (5) switching to single-strand translocation can launch stalled ClpB; (6) extracted unfolded polypeptide exits the ClpB channel; (7) extracted polypeptide refolds while ClpB can engage in another polypeptide extraction cycle. In summary, ClpB is definitely a pivotal component of protein quality control which maintains protein homeostasis (proteostasis) in bacterial cells and supports their survival under environmental tensions by mediating the reactivation of protein aggregates. Because of the unique protein disaggregation activity, ClpB and its candida ortholog Hsp104 were postulated to become tools in the development of novel therapies for.