Neurologists have been interested in TDP43 (Tar Dna binding Protein of 43 kiloDaltons) for a long time. Mutants cause some cases of ALS (Amyotrophic Lateral Sclerosis — Lou Gehrig disease) and FTD (FrontoTemporal Dementia). Some 50 different mutations in the protein have been found in cases of these two diseases. Intracellular inclusions containing TDP are found in > 90% of sporadic ALS (no mutations) and 45% of FTD.
TDP43 contains 414 amino acids (as you might expect for a protein with a 43 kiloDalton mass). There is an amino terminal ubiquitinlike fold, two RNA Recognition Motifs (RRMs) followed by a glycine rich low complexity sequence prion-like domain at the other (carboxy) end. The disease causing mutations are found in the low complexity sequence.
A phase separated structure (the anisosome) never seen before involves mutant TDP43 [ Science vol. 371 pp. 585, abb4309 pp. 1 –> 15 ’21 ]. It is a phase separated mass with liquid spherical shells and liquid cores. The shells showed birefringence — evidence of a liquid crystal. The cores show the HSP70 chaperone bound to TDP43 (which wasn’t binding RNA).
ATP is required to maintain the chaperone activity of HSP70. When ATP levels are reduced, the anisosome is converted into the protein aggregates seen in ALS and FTD. So the anisosome is a protective mechanism.
Biology is clearly leading chemistry around by the nose. No chemist would ever have predicted something like this, or received a grant to mix all this stuff in a test tube not even thinking about stoichiometry and see what happened. For more details on phase separation please see an old post — https://luysii.wordpress.com/2020/12/20/neuroscience-can-no-longer-ignore-phase-separation/
Here’s some stuff from that post to whet your appetite
Advances in cellular biology have largely come from chemistry. Think DNA and protein structure, enzyme analysis. However, cell biology is now beginning to return the favor and instruct chemistry by giving it new objects to study. Think phase transitions in the cell, liquid liquid phase separation, liquid droplets, and many other names (the field is in flux) as chemists begin to explore them. Unlike most chemical objects, they are big, or they wouldn’t have been visible microscopically, so they contain many, many more molecules than chemists are used to dealing with.
These objects do not have any sort of definite stiochiometry and are made of RNA and the proteins which bind them (and sometimes DNA). They go by any number of names (processing bodies, stress granules, nuclear speckles, Cajal bodies, Promyelocytic leukemia bodies, germline P granules. Recent work has shown that DNA may be compacted similarly using the linker histone [ PNAS vol. 115 pp.11964 – 11969 ’18 ]
The objects are defined essentially by looking at them. By golly they look like liquid drops, and they fuse and separate just like drops of water. Once this is done they are analyzed chemically to see what’s in them. I don’t think theory can predict them now, and they were never predicted a priori as far as I know.
No chemist in their right mind would have made them to study. For one thing they contain tens to hundreds of different molecules. Imagine trying to get a grant to see what would happen if you threw that many different RNAs and proteins together in varying concentrations. Physicists have worked for years on phase transitions (but usually with a single molecule — think water). So have chemists — think crystallization.
Proteins move in and out of these bodies in seconds. Proteins found in them do have low complexity of amino acids (mostly made of only a few of the 20), and unlike enzymes, their sequences are intrinsically disordered, so forget the key and lock and induced fit concepts for enzymes.
Are they a new form of matter? Is there any limit to how big they can be? Are the pathologic precipitates of neurologic disease (neurofibrillary tangles, senile plaques, Lewy bodies) similar. There certainly are plenty of distinct proteins in the senile plaque, but they don’t look like liquid droplets.
It’s a fascinating field to study. Although made of organic molecules, there seems to be little for the organic chemist to say, since the interactions aren’t covalent. Time for physical chemists and polymer chemists to step up to the plate.
Chemiotics II 