Category Archives: Neurology & Psychiatry

Do glia think? Take II

Do glia think Dr. Gonatas?  This was part of an exchange between G. Milton Shy, head of neurology at Penn, and Nick Gonatas a brilliant neuropathologist who worked with Shy as the two of them described new disease after new disease in the 60s ( myotubular (centronuclear) myopathy, nemaline myopathy, mitochondrial myopathy and oculopharyngeal muscular dystrophy).

Gonatas was claiming that a small glial tumor caused a marked behavioral disturbance, and Shy was demurring.  Just after I graduated, the Texas Tower shooting brought the question back up in force — https://en.wikipedia.org/wiki/University_of_Texas_tower_shooting.

Well that was 55 years ago, and we’ve learned a lot more about glia since.  

If glia don’t actually think, they may actually help neurons think better.  Since the brain is consuming 20% of your cardiac output as you sit there, it had better use the energy in the form of glucose  brought to it efficiently, and so it does, oxidizing it using oxygen (aerobic metabolism).  Glia on the other hand for reasons as yet unknown oxidize glucose anaerobically producing lactic acid (aerobic glycolysis). They transport the lactic acid to neurons and blocking transport impairs memory consolidation in experimental animals.  In fact aerobic glycolysis occurs in conditions of high synaptic plasticity and remodeling.  

The brain is 60% fat, some of which is cholesterol, which has to be made in the brain, as it doesn’t cross the blood brain barrier. Although neurons can synthesize cholesterol from scratch, most synthesis of cholesterol in the brain occurs in astrocytes.  It is than carried to neurons by apolipoprotein E.  As you are doubtless aware, apolipoprotein E (APOE) comes in three flavors 2, 3 and 4, and having two copies of APOE4 increases your risk of Alzheimer’s disease. 

But APOE does much more than schlep cholesterol to neurons according to a recent paper [ Neuron vol. 109 pp. 907 – 909, 957 – 970 ’21 ] Inside the particles are microRNAs.  You’ll recall that microRNAs decrease  the expression of proteins they target by binding to the messenger RNA (mRNA) for the targeted protein triggering its destruction. 

The microRNAs inside APOE suppress enzymes involved in de novo neuronal cholesterol biosynthesis (why work making cholesterol when the astrocyte is giving to you for free?).

This is unprecedented.  Passing metabolites (lactic acid, cholesterol) to neurons is one thing, but changing neuronal protein expression is quite another. 

Passing microRNAs in exosomes has been well worked out between cells (particularly cancer cells) outside the brain, but that’s for another time. 

More moonlighting

Well we used to think we understood what ion channels in the cell membrane did and how they worked. To a significant extent we do know how they conduct ions, permitting some and keeping others out in response to changes in membrane potential and neurotransmitters. It’s when they start doing other things that we begin to realize that we’re not in Kansas anymore.

Abnormal binding of one protein (filamin A) to one of the classic ion channels (the alpha7 nicotinic cholinergic receptor) may actually lead to a therapy for Alzheimer’s disease — for details please see — https://luysii.wordpress.com/2021/03/25/the-science-behind-cassava-sciences-sava/

The Kv3.3 voltage gating potassium channel is widely expressed in the brain.  Large amounts are found neurons concerned with sound, where firing rates are high.  Kv3.3 repolarizes them (and quickly) so they can fire again in response to high frequency stimuli (e.g. sound).  Kv3.3 is also found in the cerebellum and a mutation Glycine #529 –> Arginine is associated with a hereditary disease causing incoordination (type 13 spinocerebellar ataxia or SCA13 to be exact).

Amazingly the mutant conducts potassium ions quite normally.  The mutation (G529R) causes the channel not to bind to something called Arp2/3 with the result that actin (a muscle protein but found in just about every cell in the body) doesn’t form the network it usually does  at the synapse.  Synapses don’t work normally when this happens. 

Why abnormally functioning synapses isn’t lethal is anyone’s guess, as is why the mutation only affects the cerebellum.  So it’s another function of an ion channel, completely unrelated to its ability to conduct ions (e.g. moonlighting). 

The science behind Cassava Sciences (SAVA)

I certainly hope Cassava Sciences new drug Sumifilam for Alzheimer’s disease works for several reasons

l. It represents a new approach to Alzheimer’s not involving getting rid of the plaque which has failed miserably

2. The disease is terrible and I’ve watched it destroy patients, family members and friends

3. I’ve known one of the principals (Lindsay Burns) of Cassava since she was a teenager and success couldn’t happen to a nicer person. For details please see https://luysii.wordpress.com/2021/02/02/montana-girl-does-good-real-good/.

Unfortunately even if Sumifilam works I doubt that it will be widely used because of the side effects (unknown at present) it is very likely to cause.  I certainly hope I’m wrong.

Here is the science behind the drug.  We’ll start with the protein the drug is supposed to affect — filamin A, a very large protein (2,603 amino acids to be exact).  I’ve known about it for years because it crosslinks actin in muscle, and I read everything I could about it, starting back in the day when I ran a muscular dystrophy clinic in Montana.  

Filamin binds actin by its amino terminal domain.  It forms a dimerization domain at its carboxy terminal end.  In between are 23 repeats of 96 amino acids which resemble immunoglobulin — forming a rod 800 Angstroms long.  The dimer forms a V with the actin binding domain at the two tips of the V, making it clear how it could link actin filaments together. 

Immunoglobulins are good at binding things and Lindsay knows of 90 different proteins filamin A binds to.  This is an enormous potential source of trouble.  

As one might imagine, filamin A could have a lot of conformations in addition to the V, and the pictures shown in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099194/.

One such altered (from the V) conformation binds to the alpha7 nicotinic cholinergic receptor on the surface of neurons and Toll-Like Receptor 4 (TLR4) inside the cell.

Abeta42, the toxic peptide, has been known for years to bind tightly to the alpha7 nicotinic receptor — they say in the femtoMolar (10^-15 Molar) range, although I have my doubts as to whether such tiny concentration values are meaningful.  Let’s just say the binding is tight. 

The altered conformation of filamin A makes the binding of Abeta to alpha7even tighter. 

In some way, the tight binding causes signaling inside the cell (mechanism unspecified) to hyperphosphorylate the tau protein, which is more directly correlated with dementia in Alzheimer’s disease than the number of senile plaques. 

So what does Sumifilam actually do — it changes the ‘altered’ conformation of filamin A back to normal, decreasing Abeta signaling inside the cell.  

How do they know the conformation of filamin A has changed?  They haven’t done cryoEM or Xray crystallography on the protein.  The only evidence for a change in conformation, is a change in the electrophoretic mobility (which is pretty good evidence, but I’d like to know what conformation is changed to what).

Notice just how radical this proposed mechanism of action actually is.  The nicotinic cholinergic receptor is an ion channel, yet somehow the effect of Sumifilam is on how the channel binds to another protein, rather than how it conducts ions. 

However they have obtained some decent results with the drug in a very carefully done (though small — 13 patients) study in J. Prev Alz. Dis. 2020 (http://dx.doi.org/10.14283/ipad2020.6) and the FDA this year has given the company the go ahead for a larger phase III trial.

Addendum 26 March: The above link didn’t work.  This one should — it’s from Lindsay herself

https://link.springer.com/article/10.14283/jpad.2020.6

Why, despite rooting for the company and Lindsay am I doubtful that the drug will find wide use.  We are altering the conformation of a protein which interacts with at least 90 other proteins (Lindsay Burns, Personal Communication).  It seems inconceivable that there won’t be other effects in the neuron (or elsewhere in the body) due to changes in the interaction with the other 89 proteins filaminA interacts with.  Some of them are likely to be toxic. 

To understand anything in the cell you need to understand nearly everything in the cell

Understanding how variants in one protein can either increase or decrease the risk of Parkinson’s disease requires understanding of the following: the lysosome, TMEM175, Protein kinase B, protein moonlighting, ion channel lysoK_GF, dopamine neurons among other things. So get ready for a deep dive into molecular and cellular biology.

It is now 50 years and 6 months since L-DOPA was released in the USA for Parkinson’s disease, and I was tasked as a resident by the chief with running the first L-DOPA clinic at the University of Colorado.  We are still learning about the disease as the following paper Nature vol. 591 pp. 431 – 437 ’21 will show. 

The paper describes an potassium conducting ion channel in the lysosomal membrane called LysoK_GF.  The channel is made from two proteins TMEM175 and protein kinase B (also known as AKT).

TMEM175 is an ion channel conducting potassium.  It is unlike any of the 80 or so known potassium channels.  It  contains two repeats of 6 transmembrane helices (rather than 4) and no pore loop containing the GYG potassium channel signature sequence. Lysosomes lacking it aren’t as acidic as they should be (enzymes inside the lysosome work best at acid pH).  Why loss of a potassium channel show affect lysosomal pH is a mystery (to me at least).

Genome Wide Association Studies (GWAS) have pointed to the genomic region containing TMEM175 as having risk factors for Parkinsonism.  Some variants in TMEM175 are associated with increased risk of the disease and others are associated with decreased risk — something fascinating as knowledge here should certainly tell us something about Parkinsonism.  

The other protein making up LysoK_GF is protein kinase B (also known as AKT). It is found inside the cell, sometimes associated with membranes, sometimes free in the cytoplasm. It is big containing 481 amino acids. Control of its activity is important, and Cell vol. 169 pp. 381 – 405 ’17 lists 21 separate amino acids which can be modified by such things as acetylation, phosphorylation, sumoylation, Nacetyl glucosamine, proline hydroxylation.  Well 2^21 is 2,097,152, so this should keep cell biologists busy for some time. Not only that some 100 different proteins AKT phosphorylates were known as 2017.  

TMEM175 is opened by conformational changes in AKT.  Normally the enzyme is inactive because the pleckstrin homology domain binds to the catalytic domain inhibiting enzyme activity as the substrate can’t get in.

Remarkably you can make a catalytically dead AKT, and it still works as a controller of TMEM175 activity — this is an example of a moonlighting molecule — for more please see — https://luysii.wordpress.com/2021/01/11/moonlighting-molecules/.

Normally the activity and conformation of AKT is controlled by the metabolic state of the cell (with 21 different molecular knob sites on the protein this shouldn’t be hard).  So the fact that AKT conformation controls TMEM175 conductivity which controls lysosome activity gives the metabolic state of the cell a way to control lysosomal function.  

Notice how to understand anything in the cell you must ask ‘what’s it for’, thinking that is inherently teleological. 

Now on to the two risk factors for Parkinsonism in TMEM175.  The methionine –> threonine mutation at amino acid #393 reduces the lysoK_GF current and is associated with an increased risk of parkinsonism, while the glutamine –> proline mutation at amino acid position #65 gives a channel which remains functional under conditions of nutrient starvation. 

The authors cultured dopamine neurons and found out that the full blooded channel LysoK_GF (TMEM175 + AKT) protected neurons against a variety of insults (MPTP — a known dopamine neuron toxin, hydrogen peroxide, nutrient starvation). 

TMEM175 knockout neurons accumulate more alpha-synuclein — the main constituent of the Lewy body of Parkinsonism.

So it’s all one glorious tangle, but it isn’t just molecular biological navel gazing, because it is getting close to one cause (and hopefully a treatment) of Parkinson’s disease.  

TDP43 and the anisosome

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.

 

The pericyte controls local cerebral blood flow

Actively firing neurons get all the blood flow they need. More in fact. And this is the entire basis of functional magnetic resonance imaging (fMRI). At long, long last we may be close to understanding exactly how this happens.

Almost 100 years ago Wilder Penfield operating on unanesthetized patients with epilepsy to find the epileptic focus and remove it, noted that when a patient had a seizure on the table, veins became red, because so much blood flowed to the active area that it couldn’t absorb all the oxygen contained in the hemoglobin of the red cells, so they stayed red. Penfield was not a sadist, the brain contains no pain fibers, and so the skull could be opened using just local anesthetics. 

Exactly the same thing happens locally when neurons become active firing lots of action potentials. The functional MRI signal is due to the difference in magnetic susceptibility of the iron atom in hemoglobin when it is binding oxygen and when it isn’t.

So how does a firing neuron tell blood vessels it needs more flow?  A superb paper [ Proc. Natl. Acad. Sci. vol. 117 pp. 27022 – 27033 ’20 ]–https://www.pnas.org/content/pnas/117/43/27022.full.pdf probably explains exactly how this happens.  

The pericyte is a cell which is found outside cerebral capillaries and very small arteries.  It isn’t like a rubber band around the vessel (that’s for smooth muscle).  It’s like our bony spine with ribs coming from it, so the spine lies on the long axis of the vessel with the ribs coming down and wrapping (partially) around the vessel.

Pericytes in the brain and the retina are found primarily where two capillaries join each other according to the paper (which provides a convincing picture).

Neurons firing impulses release potassium into the extracellular space.  The endothelial cells of brain capillaries sense this and open up the inwardly rectifying potassium channel KIR2.1, exposing the outside to the resting potential of potassium which is quite negative (e. g the endothelial cell hyperpolarizes in response to neuronal activity.  The signal propagates upstream THROUGH the endothelial cells (because they are coupled together by gap junctions). 

Enter the pericytes which are electrically coupled to the underlying capillary endothelium by gap junctions, so they can receive the endothelial hyperpolarizing signal directly.  This causes the pericyte process receiving the signal to relax opening up the capillary or small artery increasing blood flow.  The authors followed this by watching intracellular calcium changes in pericytes, and noted that individual processes (ribs in the analogy above) could respond individually.  This is how a pericyte straddling the junction of two capillaries will open just the one which is hyperpolarized by neural activity.  

An incredibly elegant mechanism.  Of course with something so dramatic the work needs to be repeated. 

It is a pleasure to write something not involving the pandemic virus and our response to it. 

The Grandmother cell comes to the neural net

We really don’t know how concepts are stored in the brain (or where) despite a lot of work.  Sure, if you destroy an area of the brain, you have a neurologic deficit, but if you pull out the plug of a lamp it does dark, but that the plug isn’t making the light. There has been a huge amount of human experimentation on subjects awaiting resection of an epileptic focus (to find and remove it).  Patients can be awake while all this is going on as the brain has no pain endings.

Is the concept of grandmother stored diffusely among many different neurons (or even glial cells) or is there a single cell storing it, so that if you lose that cell you lose the concept of grandmother.  Certainly the epilepsy work has found some very specific cells. In one fantastic (unreplicatable) paper, a neuron was found that responded to 7 different images of Jennifer Aniston, but not to other pictures of actresses (Julia Roberts) or even pictures of Aniston with another actor. [ Nature vol. 435 pp. 1102 – 1107, 2005 ].  Another neuron would respond only to another actress (Halle Berry).  The direction of presentation of the actress didn’t matter — face on, side view, etc. etc.

Nearly the same thing has been found with neural nets [ Proc. Natl. Acad. Sci. vol. 117 pp. 30071 – 30078 ’20 ].  A trained network contains units responding to high level visual concepts which aren’t explicitly labeled in the training data.  This paper was able to activate and deactivate any unit in the net to see where things were stored.

In a network with 512 output units, removing the 20 most important units for each class to be identified reduced accuracy to chance (53%).  Removing the 492 least important units only reduces class accuracy by 4%.

Not quite a grandmother cell, but getting close.

Moonlighting molecules

Just when you thought you knew what your protein did, it goes off and does something completely different (and unexpected). This is called moonlighting, and is yet another reason drug discovery is hard. You can never be sure that your target is doing only what you think it’s doing.

Today’s example is PACAP, a neuromodulator/neurotransmitter made by neurons. Who knew that PACAP can and does act as an antibiotic when the brain is infected. [ Proc. Natl. Acad. Sci. vol. 118 e1917623117 ’21 ] does (PNAS no longer pages its journals, as last year’s total was over 33,000 !).   PACAP is a member of the vasoactive intestinal polypeptide, secretin, glucagon family of neuropeptides (mammals have over 100 neuropeptides according to the paper).

PACAP stands for Pituitary Adenylate Cyclase Activating Polypeptide. It comes in two forms containing 27 or 38 amino acids, both cleaved from a 176 amino acid precursor. There are 3 receptors for PACAP, all G Protein Coupled Receptors (GPCRs). A zillion functions have been ascribed to it, setting the circadian clock, protecting granule cells of the cerebellum. Outside the nervous system it is produced by immune cells in response to inflammatory conditions and antigenic stimulation. It is one of the most conserved neuropeptides throughout the course of evolution. Now we probably know why.

Showing how hard protein chemistry really is, PACAP is structurally similar to cathelicidin LL-37 an antimicrobial peptide, despite having less than 5% amino acid sequences in common. PACAP is cationic. Different sides of the protein have different characteristics, with one side being highly positively charged, and the other being hydrophobic (e.g. the protein is amphipathic). This is typical of antimicrobial peptides, and perturbation of microbial membranes by inducing negative Gaussian curvature probably explains its antibacterial activity.

In mouse models of Staph Aureus or Candida infections, PACAP is induced ‘up to’ 50 fold in the brain (or spleen or kidney) where it kills the bugs. Yet another reason drug discovery is so hard. We are mucking about in a system we barely understand.

There are many other examples of moonlighting proteins. Probably the best known is cytochrome c which is is a heme protein localized in the compartment between the inner and outer mitochondrial membranes where it functions to transfer electrons between complex III and complex IV of the respiratory chain. Oxidation and reduction of the iron atom in the heme along with movement along the mitochondrial intermembrane space allows it to schlep electrons between complexes of the respiratory chain.

All well and good. But cytochrome c also can tell a cell to commit suicide (apoptosis) when mitochondria are sufficiently damaged that cytochrome c can escape the intermembrane space. Who’d a thunk it?

How many more players are there in the cell (whose function we think we know) that are sneaking around — doing more things in heaven and Earth, Horatio, than are dreamt of in your philosophy?

Feeling mentally soggy? It could be that your brain has shrunk what with it being winter and all

I wouldn’t have believed that part of the brain can shrink by 40% and then regrow, but exactly that happens to the Etruscan Shrew in the winter. So maybe it’s not you or even COVID19.

It’s a fascinating critter — the world’s smallest mammal, tipping the scales at 1.8 grams (about 6 aspirins). It has a very rapid metabolic rate, eating twice its weight daily. Things get tight in the winter so it shrinks its brain. Remember that even in big and sluggish us, as we sit there reading (or writing) this, our brain is receiving 20% of our cardiac output, despite being 3% or so of our body weight. For more about the Shrew see https://en.wikipedia.org/wiki/Etruscan_shrew

For more detail see https://www.pnas.org/content/pnas/117/50/32136.full.pdf.

What’s really exciting is that the number of neurons increases in the shrew’s brain come summer. Since it’s a mammal, we’re not talking about lizards regrowing limbs, but something evolutionarily close to us. For more detail see https://www.pnas.org/content/pnas/117/50/32136.full.pdf.

There are actually some conditions with reversible cerebral atrophy, and as a neurologist I made sure to look for them.

Here they are

l. Alcoholism

2. Adrenal corticosteroids (exogenous or endogenous)

3. Malnutrition in kids

4. Depakene (valproic acid)

5. Anorexia nervosa.

 

Neuroscience can no longer ignore phase separation

As a budding organic chemist, I always found physical chemistry rather dull, particularly phase diagrams. Organic reactions give you a very clear and intuitive picture of energy and entropy without the math.

In past few years cell biology has been finding phase changes everywhere. Now it comes to neuroscience as the synaptic active zone (where vesicles are released) is an example of a phase change (macromolecular condensation, liquid liquid phase separation, biomolecular condensates — it goes by a lot of names as the field is new). If you are new to the field, have a look at an excerpt from an earlier post before proceeding further — it is to be found after the ****

Although the work [ Nature vol. 588 pp. 454 – 458 ’20 ] was done in C. elegans with proteins SYD2 (aka liprinAlpha) and ELKS1, humans have similar proteins.

Phase separation accounts for a variety of cellular organelles not surrounded by membranes. The best known example is the nucleolus, but others include Cajal bodies, ProMyelocytic Leukemia Bodies (PML bodies), gemline P granules, processing bodies, stress granules.

These nonmembranous organelles have 3 properties in common

l. They arise as a phase separation from the surrounding milieu

2. They remain in a liquid state, but with properties distinct from those in the surrounding cellular material

3. They are dynamic. Proteins move in and out of them in seconds (rather than minutes, hours or longer as is typical for stable complexes.

They are usually made of proteins and RNA, and proteins in them usually have low complexity sequences (one example contains 60 amino acids of which 45 are one of alanine, serine, proline and arginine)

Back to the synaptic active zone. The ELKS1 and SYD2 both have phase separation regions (which aren’t of low complexity but they both have lots of amino acids capable of making pi pi contacts). They undergo phase separation during an early stage of synapse development. Later they solidify and bind other proteins found in the active presynaptic zone. You can make mutant ELKS1 and SYD2 lacking the low complexity regions, but the synapses they form are abnormal.

The liquid phase scaffold formed by SYD2 and ELK1 can be reconstituted in vitro. It binds and incorporates downstream synaptic components. Both proteins are large (SYD2 has 1,139 amino acids, ELKS1 has 836).

What is remarkable is that you can take a phase separation motif from human proteins (FUS which when mutated can cause ALS, or from hnRNPA2) put them into SYD2 and ELK1 mutants lacking their low complexity region and have the proteins form a normal presynaptic active zone.

This is remarkable and exciting stuff

*****

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.