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Chaperonins are cage-like complexes in which nonnative polypeptides prone to aggregation are thought to reach their native state optimally. However, they also may use ATP to unfold stably bound misfolded polypeptides and mediate the out-of-cage native refolding of large proteins. Here, we show that even without ATP and GroES, both GroEL and the eukaryotic chaperonin containing t-complex polypeptide 1 (CCT/TRiC) can unfold stable misfolded polypeptide conformers and readily release them from the access ways to the cage. Reconciling earlier disparate experimental observations to ours, we present a comprehensive model whereby following unfolding on the upper cavity, in-cage confinement is not needed for the released intermediates to slowly reach their native state in solution. As over-sticky intermediates occasionally stall the catalytic unfoldase sites, GroES mobile loops and ATP are necessary to dissociate the inhibitory species and regenerate the unfolding activity. Thus, chaperonin rings are not obligate confining antiaggregation cages. They are polypeptide unfoldases that can iteratively convert stable off-pathway conformers into functional proteins.

Proteins prone to aggregation in yeast are imported into mitochondria under stress conditions, suggesting that mitochondrial import and proteolysis may help to disaggregate proteins in the cytoplasm. Mitochondria import stressed proteins Cellular defects associated with ageing and neurodegenerative disorders include accumulation of protein aggregates and mitochondrial dysfunction. Disease-associated proteins can also be found inside mitochondria and, in yeast, ageing or stress can lead to the tethering of protein aggregates to mitochondria. Rong Li and colleagues provide evidence that implicate a role for mitochondria in cellular quality control. They find that, when exposed to heat shock stress, yeast proteins that are prone to aggregation are imported from the cytoplasm into mitochondria through interaction with the mitochondrial import machinery. This process, which can also occur in the absence of stress, allows aggregation-prone proteins to reside in the mitochondrial intermembrane space and matrix. Blocking mitochondrial import prevented protein disaggregation in the cytoplasm, which suggests that mitochondrial import may facilitate disaggregation by actively removing dissociated proteins. Loss of proteostasis underlies ageing and neurodegeneration characterized by the accumulation of protein aggregates and mitochondrial dysfunction 1 , 2 , 3 , 4 , 5 . Although many neurodegenerative-disease-associated proteins can be found in mitochondria 4 , 6 , it remains unclear how mitochondrial dysfunction and protein aggregation could be related. In dividing yeast cells, protein aggregates that form under stress or during ageing are preferentially retained by the mother cell, in part through tethering to mitochondria, while the disaggregase Hsp104 helps to dissociate aggregates and thereby enables refolding or degradation of misfolded proteins 7 , 8 , 9 , 10 . Here we show that, in yeast, cytosolic proteins prone to aggregation are imported into mitochondria for degradation. Protein aggregates that form under heat shock contain both cytosolic and mitochondrial proteins and interact with the mitochondrial import complex. Many aggregation-prone proteins enter the mitochondrial intermembrane space and matrix after heat shock, and some do so even without stress. Timely dissolution of cytosolic aggregates requires the mitochondrial import machinery and proteases. Blocking mitochondrial import but not proteasome activity causes a marked delay in the degradation of aggregated proteins. Defects in cytosolic Hsp70s leads to enhanced entry of misfolded proteins into mitochondria and elevated mitochondrial stress. We term this mitochondria-mediated proteostasis mechanism MAGIC (mitochondria as guardian in cytosol) and provide evidence that it may exist in human cells.

Formation of inclusion bodies in bacterial hosts poses a major challenge for large scale recovery of bioactive proteins. The process of obtaining bioactive protein from inclusion bodies is labor intensive and the yields of recombinant protein are often low. Here we review the developments in the field that are targeted at improving the yield, as well as quality of the recombinant protein by optimizing the individual steps of the process, especially solubilization of the inclusion bodies and refolding of the solubilized protein. Mild solubilization methods have been discussed which are based on the understanding of the fact that protein molecules in inclusion body aggregates have native-like structure. These methods solubilize the inclusion body aggregates while preserving the native-like protein structure. Subsequent protein refolding and purification results in high recovery of bioactive protein. Other parameters which influence the overall recovery of bioactive protein from inclusion bodies have also been discussed. A schematic model describing the utility of mild solubilization methods for high throughput recovery of bioactive protein has also been presented.

How do proteins fold, and why do they fold in that way? This Perspective integrates earlier and more recent advances over the 50-y history of the protein folding problem, emphasizing unambiguously clear structural information. Experimental results show that, contrary to prior belief, proteins are multistate rather than two-state objects. They are composed of separately cooperative foldon building blocks that can be seen to repeatedly unfold and refold as units even under native conditions. Similarly, foldons are lost as units when proteins are destabilized to produce partially unfolded equilibrium molten globules. In kinetic folding, the inherently cooperative nature of foldons predisposes the thermally driven amino acid-level search to form an initial foldon and subsequent foldons in later assisted searches. The small size of foldon units, ∼20 residues, resolves the Levinthal time-scale search problem. These microscopic-level search processes can be identified with the disordered multitrack search envisioned in the “new view” model for protein folding. Emergent macroscopic foldon–foldon interactions then collectively provide the structural guidance and free energy bias for the ordered addition of foldons in a stepwise pathway that sequentially builds the native protein. These conclusions reconcile the seemingly opposed new view and defined pathway models; the two models account for different stages of the protein folding process. Additionally, these observations answer the “how” and the “why” questions. The protein folding pathway depends on the same foldon units and foldon–foldon interactions that construct the native structure.

Talin, a force-bearing cytoplasmic adapter essential for integrin-mediated cell adhesion, links the actin cytoskeleton to integrin-based cell–extracellular matrix adhesions at the plasma membrane. Its C-terminal rod domain, which contains 13 helical bundles, plays important roles in mechanosensing during cell adhesion and spreading. However, how the structural stability and transition kinetics of the 13 helical bundles of talin are utilized in the diverse talin-dependent mechanosensing processes remains poorly understood. Here we report the force-dependent unfolding and refolding kinetics of all talin rod domains. Using experimentally determined kinetics parameters, we determined the dynamics of force fluctuation during stretching of talin under physiologically relevant pulling speeds and experimentally measured extension fluctuation trajectories. Our results reveal that force-dependent stochastic unfolding and refolding of talin rod domains make talin a very effective force buffer that sets a physiological force range of only a few pNs in the talin-mediated force transmission pathway. Talin is a mechanosensing cytoplasmic adaptor that links integrin cell adhesion receptors to the actin cytoskeleton. Here the authors measure the force-dependent folding and refolding kinetics of all talin rod domains to propose that talin can function as a force buffer under physiologically relevant conditions.

This chapter contains sections titled: Introduction Protein Folding In Vivo Molecular Simulation of Protein Refolding and Aggregation Refolding Methods Applications References

Recombinant proteins expressed as bacterial inclusion bodies (IBs) are now receiving tremendous attention for many diverse applications in the areas of industrial and medical biotechnology. Understanding the structure–function relationship of protein in IBs has recently created new possibilities in developing innovative isolation, solubilization, refolding, and purification processes for high-throughput recovery of bioactive protein from bacterial IBs. This opinion article describes the advantages, disadvantages, and major challenges presently associated with each of the processing steps. Finally, we conclude with the possible solutions for each operational step and the future direction of the basic and translational research to achieve maximum benefit from IB aggregates. In the past decade, considerable attention has been given to developing bioprocess methods that could plausibly decrease the number of operational steps and bring forth a universal strategy for recovering bioactive protein from any bacterial IB.Methods to isolate IBs are developed such that bacterial cells are disrupted effectively while maintaining the integrity of IBs.Novel mild-denaturing solubilization agents based on combinatorial approaches with high solubilization and refolding yield were recently reported.Screening for optimal refolding conditions and methods has become particularly important to ensure a good yield of correctly folded protein.Multimodal chromatography has offered the possibility of purifying the protein at laboratory and industrial scale based on the different protein properties.

Hsp70 binds unfolded protein segments in its groove, but can also bind and stabilize folded protein structures, owing to its moveable lid, with ATP hydrolysis and co-chaperones allowing control of these contrasting effects. A novel mechanism for Hsp70 action The protein-chaperone system centred on Hsp70 performs a variety of cellular control tasks, including folding assistance, protection against aggregation, trafficking and regulation of enzyme activity, a versatility that has been hard to reconcile with structural data, which suggest that Hsp70 only binds extended polypeptide segments. Now, using laser molecular tweezers, Sander Tans and colleagues show that the bacterial homolog of Hsp70, known as DnaK, relies on its 'groove' to bind unfolded proteins, but can also bind folded structures, thanks to its 'lid', with control of ATP hydrolysis by co-chaperones allowing regulation of such contrasting effects. Contrary to known stabilization mechanisms, through precise structural fit, Hsp70 can stabilize a vast repertoire of client proteins, through a clamp-like, ATP-driven conformational change. The Hsp70 system is a central hub of chaperone activity in all domains of life. Hsp70 performs a plethora of tasks, including folding assistance, protection against aggregation, protein trafficking, and enzyme activity regulation 1 , 2 , 3 , 4 , 5 , and interacts with non-folded chains, as well as near-native, misfolded, and aggregated proteins 6 , 7 , 8 , 9 , 10 . Hsp70 is thought to achieve its many physiological roles by binding peptide segments that extend from these different protein conformers within a groove that can be covered by an ATP-driven helical lid 11 , 12 , 13 , 14 , 15 . However, it has been difficult to test directly how Hsp70 interacts with protein substrates in different stages of folding and how it affects their structure. Moreover, recent indications of diverse lid conformations in Hsp70–substrate complexes raise the possibility of additional interaction mechanisms 15 , 16 , 17 , 18 . Addressing these issues is technically challenging, given the conformational dynamics of both chaperone and client, the transient nature of their interaction, and the involvement of co-chaperones and the ATP hydrolysis cycle 19 . Here, using optical tweezers, we show that the bacterial Hsp70 homologue (DnaK) binds and stabilizes not only extended peptide segments, but also partially folded and near-native protein structures. The Hsp70 lid and groove act synergistically when stabilizing folded structures: stabilization is abolished when the lid is truncated and less efficient when the groove is mutated. The diversity of binding modes has important consequences: Hsp70 can both stabilize and destabilize folded structures, in a nucleotide-regulated manner; like Hsp90 and GroEL, Hsp70 can affect the late stages of protein folding; and Hsp70 can suppress aggregation by protecting partially folded structures as well as unfolded protein chains. Overall, these findings in the DnaK system indicate an extension of the Hsp70 canonical model that potentially affects a wide range of physiological roles of the Hsp70 system.

The ability to reverse protein aggregation is vital to cells 1 , 2 . Hsp100 disaggregases such as ClpB and Hsp104 are proposed to catalyse this reaction by translocating polypeptide loops through their central pore 3 , 4 . This model of disaggregation is appealing, as it could explain how polypeptides entangled within aggregates can be extracted and subsequently refolded with the assistance of Hsp70 4 , 5 . However, the model is also controversial, as the necessary motor activity has not been identified 6 – 8 and recent findings indicate non-processive mechanisms such as entropic pulling or Brownian ratcheting 9 , 10 . How loop formation would be accomplished is also obscure. Indeed, cryo-electron microscopy studies consistently show single polypeptide strands in the Hsp100 pore 11 , 12 . Here, by following individual ClpB–substrate complexes in real time, we unambiguously demonstrate processive translocation of looped polypeptides. We integrate optical tweezers with fluorescent-particle tracking to show that ClpB translocates both arms of the loop simultaneously and switches to single-arm translocation when encountering obstacles. ClpB is notably powerful and rapid; it exerts forces of more than 50 pN at speeds of more than 500 residues per second in bursts of up to 28 residues. Remarkably, substrates refold while exiting the pore, analogous to co-translational folding. Our findings have implications for protein-processing phenomena including ubiquitin-mediated remodelling by Cdc48 (or its mammalian orthologue p97) 13 and degradation by the 26S proteasome 14 . A combination of optical tweezers and fluorescent-particle tracking is used to dissect the dynamics of the Hsp100 disaggregase ClpB, and show that the processive extrusion of polypeptide loops is the mechanistic basis of its activity.

Hsp70 chaperone systems are very versatile machines present in nearly all living organisms and in nearly all intracellular compartments. They function in many fundamental processes through their facilitation of protein (re)folding, trafficking, remodeling, disaggregation, and degradation. Hsp70 machines are regulated by co-chaperones. J-domain containing proteins (JDPs) are the largest family of Hsp70 co-chaperones and play a determining role functionally specifying and directing Hsp70 functions. Many features of JDPs are not understood; however, a number of JDP experts gathered at a recent CSSI-sponsored workshop in Gdansk (Poland) to discuss various aspects of J-domain protein function, evolution, and structure. In this report, we present the main findings and the consensus reached to help direct future developments in the field of Hsp70 research.