Protein folding: Origami with Jellyfish

PDBe calendar 2020 May
01 May 2020

 

The featured structure for May in the PDBe calendar draws inspiration from the protein prefoldin, a chaperone protein that helps other proteins to fold correctly. 

Protein folding is a fundamental concept to the field of structural biology, describing the morphological journey nascent proteins take en route to their mature three-dimensional form.

Under standard conditions, the interactions between a protein’s amino acids, and between these amino acids and the solvent, are generally understood to be the prime driving force of protein folding. However, there are many complex exceptions to this, for example: some proteins require chemical modification; some must be brought together with other protein components; some only need assistance if they incorrectly fold; many require shielding from external stresses (i.e. temperature); while some proteins do not fully fold at all. Whilst we lack a comprehensive theory of protein folding, its significance and complexity can perhaps be appreciated from the vast array of processes and components it involves and, unfortunately, the often severe consequences when it goes awry.

Proteins which function to facilitate the folding of other proteins are termed molecular chaperones and are classified based on the specific mechanisms they employ. Chaperonins, or “foldases”, are one such class that work by directly capturing substrate proteins within a cavity and then promoting their correct structural rearrangement. Whilst the capture of the substrate protein is seemingly well-understood, the precise (or dominant) mechanism which drives substrate folding is still hotly debated. The prominent hypotheses support either a “passive” mechanism (where the formation of undesired folds is prohibited), or an “active” mechanism (where specific interactions are encouraged to direct correct folding). 

Chaperonins themselves can be classified into subgroups based upon their structural organisation.

Group I chaperonins include the well-studied GroEL/ES system from E.coli (Figure 1), and are principally comprised of two homo-heptameric stacked rings, each of which form a chamber in a barrel-like complex. After binding both ATP and the substrate protein, these chaperones recruit a co-chaperone capping complex (in the case of GroEL, this is GroES) that binds the chamber opening, releasing the substrate further inside the folding cavity. Formation of the whole complex is concomitant with a large conformational change of the GroEL chamber, that nearly doubles the volume of the cavity and makes it considerably more hydrophilic. It is this change which is associated with substrate folding. Following ATP hydrolysis, a second conformational change causes readjustment of the GroEL ring, releasing the folded protein and allowing the alternate half of the barrel to accept a substrate.

 

Figure 1. The group I GroEL/ES molecular chaperone from E.coli. Side view (bottom-left) of the free homo-tetradecameric GroEL barrel, with an end view (top-left) showing the seven constituent subunits that comprise the top ring (PDB ID: 1SS8). Side view (bottom-right) of the homo-tetradecameric GroEL barrel in complex with ADP and GroES (cyan), with an end view (top-right) showing the same upper ring following the conformational change of the complexed state (PDB ID: 1PF9).

 

 

 

 

 

  

 

 

 

 

  

Figure 1. The group I GroEL/ES molecular chaperone from E.coli. Side view (bottom-left) of the free homo-tetradecameric GroEL barrel, with an end view (top-left) showing the seven constituent subunits that comprise the top ring (PDB ID: 1SS8). Side view (bottom-right) of the homo-tetradecameric GroEL barrel in complex with ADP and GroES (cyan), with an end view (top-right) showing the same upper ring following the conformational change of the complexed state (PDB ID: 1PF9).

 

Each GroEL/ES chamber can bind and fold one substrate protein of up to 60 kDa, with an approximate turnover of one protein every ~10 seconds. Some proteins however require multiple processing cycles to reach their functional fold. Group I chaperonins also include eukaryotic Heat Shock Proteins (HSPs) which are expressed in response to extreme environmental stimuli to help stabilise protein folding in the face of extreme conditions. 

 In comparison, group II chaperonins have not been well described in the scientific literature, at least in terms of their mechanism of action. Prefoldin is one such group II chaperonin, the structure of which (Figure 2), was the inspiration for this month’s artwork. Group II chaperonins can be found in many species, including ancient Archaean single-celled organisms and Eukaryotes (including Humans), although interestingly not in bacteria. 

 

Figure 2. The jellyfish-like prefoldin chaperone from Methanococcus maripaludis (PDB ID: 1FXK)

Structurally, many parallels can be made to group I chaperonins. They are also primarily formed from two multimeric (albeit usually heterooligomeric) rings. However, instead of a separate capping-complex, they employ additional flexible alpha-helical regions which act to seal their own cavity after substrate binding (Figure 3). This conformational change is also driven by ATP-hydrolysis, however unlike group I chaperonins, it is not thought to be required for initiating the folding cycle of the reciprocal chamber.

Figure 3. The hexadecameric prefoldin chaperone from Methanococcus maripaludis in the open(PDB ID: 3IYF, left) and closed (PDB ID: 3LOS, right) states.

Chaperonins are however just one class of molecular chaperone. Whilst the full extent of the proteome requiring chaperone activity has not been ultimately determined, it will no doubt be extensive. Nearly 200 chaperones have so far been identified in Humans, and the group II chaperonin TriC is thought to facilitate folding for 10% of the entire genome alone. Chaperones are therefore essential for the maintenance of healthy cells and very little genetic variation is tolerated. Hereditary spastic paraplegia and hereditary cataracts are two diseases directly related to chaperone mutations.

Likewise, the importance of correct protein folding can also be seen from so-called protein-misfolding diseases which include neurological conditions like Alzheimer’s and Parkinson’s disease, as well as type 2 diabetes. Generally speaking, these conditions arise from the damage which results from the uncontrolled formation of rigid fibrils – which themselves are aggregates of misfolded proteins (Figure 4).

 

Figure 4. The amyloid fibrils of amyloid-beta (Osaka mutation, PDB ID: 2MVX, A)  and islet amyloid peptide (PDB ID: 6Y1A, B), as implicated in Alzheimer’s disease and type 2 diabetes, respectively. Individual chains are coloured differently. (Bottom) Top down views highlighting the repeating structure of each chain through the fibril, with core hydrophobic residues shown as sticks. 

An understanding of protein folding, misfolding, and the part that molecular chaperones play is therefore of great significance to the future of human health. Perhaps, if we can start by learning how nature has evolved to deal with the complexities of protein folding, we can begin to unpick a wide range of pathologies and open avenues for the development of future treatments.

 

About the artwork

May’s artwork utilises structural elements of the protein chaperone prefoldin from the methane-producingmethanothermobacter family of bacteria. The artwork was realised with print and Brusho by Erin Baker from Impington Village College Cambridge, drawing inspiration from PDB entry 1FXK. This structure was determined by X-ray crystallography in 2000 from the lab of Ismail Moarefi, working at the Max Planck Institute.

 James Tolchard