Dead Proteins Tell No Tales

In July 2018, NASA made a big announcement, liquid water found on Mars! This could mean life!

But why does water mean life? Why is water essential for life? 

The answer is that water is a universal solvent, it can dissolve salts, DNA and proteins, enable their correct folding and act as a medium for their interaction. Without water, biomolecules cannot take shape, charge or move, and thus lose their capacity to act on their own or interact with each other. Without being hydrated or solubilized in water, salts, DNA and proteins are just dead powders, crystals, and stones. 

This is what happens proteins transform into the amyloid state. All the active sites from peptide side-chains become sequestered in the "dry steric zipper" between the two beta-sheets that form the backbone of any amyloid protofilament. 

The fundamental characters of the amyloid state can be summarized as follows:

1. It's physical. It denotes a physical solid state of proteins and not a particular protein. 

2. It's universal. Any protein can reach the amyloid state if pushed hard enough, even the most globular ones such as myoglobin. And we already know of about 40 different proteins of very diverse functions that form amyloids in different diseases (Fig. 1). 

Fig. 1

3. It's generic. Unlike functional soluble protein states, where each protein adopts a specific conformation for its function, all amyloids share the basic conformational unit the gives them their characteristic fibrillar architecture; the cross-β conformation. The protofilament subunit in all amyloids adopts the same conformation, where two beta-sheets are facing each other (cross-β), excluding water in between (hence the name dry steric zipper) and growing longitudinally with more peptide molecules added to the ends  (Fig. 2). 

Fig. 2

4. It's (very) stable. The amyloid state lies at the bottom of the free-energy landscape of any protein (Fig. 3). Once reached, it's very difficult to revert back to the soluble state. Also, it's difficult to get something this stable to interact with anything. 

Fig. 3

5. It's dead. It's dry inside, as water is excluded from the interface between the two β-sheets within the cross-β conformation. Additionally, it's insoluble in water, and due to its high stability, inert to most other interactions. That is why it is very difficult to solubilize them even with strong detergents. 

In that sense, amyloids are more like kidney or gallbladder stones,  which are also dead aggregates/crystals of salts and cholesterol, respectively. Being stone dead (literally), amyloids cannot replicate, transmit biological information or form strains, unless we can call the crystallization of kidney stones replication and their different shapes different strains (Fig. 4). Both amyloids and crystals/stones are governed by the same mechanisms of nucleation, and in both cases, the core crystalline architecture can lead to different final morphologies. 

Fig. 4. Different shapes of kidney stones. 

Based on these properties, the toxicity due to amyloid transformation is more likely to be dependent on loss-of-function (LOF) rather than gain-of-function (GOF) mechanisms. If something is so dry, insoluble and stable, it cannot interact to do any function (LOF), and is also too inert to be involved in toxic molecular interactions (GOF), unless it physically blocks the pathway of something useful. This is also similar to kidney or gallstones, which remain largely asymptomatic unless they block an important canal. The same occurs in systemic amyloidosis when huge amounts of amyloids physically disrupt organs. 

However, on the molecular level, if you cannot interact to do anything good, you probably cannot interact to do any harm either. That is why, due to this inert nature and lack of interactivity, the toxicity of amyloids is usually ascribed to a non-amyloid nanoparticulate species termed the oligomers, where some thermodynamic instability, and hence activity, can be assigned. 

Furthermore, the lack of amyloid fibril toxicity can be demonstrated in different contexts. For example, the infamous guardian of the genome, P53, forms amyloids that lead to LOF and consequent increased cellular proliferation and cancer, rather than cell death. Another example is bacterial amyloids, which are safely utilized by bacteria in biofilms without killing the bacterial cells. This also demonstrates that amyloid fibrils lack antimicrobial activity. 

Pirates of the Caribbean, Dead Men Tell No Tales, Disney, 2017 

It is important to highlight the physical nature of the amyloid phenomenon as a state any protein can reach where it adopts a generic, stable conformation that renders it both dehydrated and insoluble. It literally becomes stone dead. Dead proteins "tell no tales"  and cannot transmit biological information. They are also functionally dead, and we know about 40 of them already involved in diseases. Furthermore, they are too stable and inert to be toxic on the molecular level. Since it's difficult to resurrect the dead, the solution can be the injection of new life in the form of soluble functional proteins via replacement therapy. 

More info in our paper here and review here .