Category Archives: Neurology & Psychiatry

A possible new way to attack Parkinson’s disease

Alpha-synuclein is the main component of the Lewy body of Parkinson’s disease.  It contains 140 amino acids, and is ‘natively unfolded’ in that it has no apparent ordered secondary structure (alpha helices, beta pleated sheets) detectable by a variety of methods — far ultraviolet circular dichroism, Fourier transform infrared spectroscopy or NMR spectroscopy. When the protein binds to artificial membranes half of it forms alpha helices.   Amazingly, after a huge amount of work we don’t know what alpha-Synuclein actually does.  Knockouts have only minor CNS abnormalities.

However, alpha synuclein forms fibrils which bind to cell surface receptors with internalization and transmission to other cells, just like prions.   Two such receptors for alpha-synuclein fibrils are Lymphocyte Activation Gene E (LAG3) and Amyloid PrecursorLike Protein 1 (ALPL1).

LAG3 has 4 immunoglobulin like domains (D1 – D4).  It uses D1 to capture the carboxy terminus which is exposed and concentrated on the surface of the alpha-synuclein fibrils.

Interestingly the monomers are said to adopt a self-shielded conformation which impedes the exposure of the carboxy terminus.  Phosphorylation of serine #129 enhances the binding of alpha-synuclein preformed fibrils to LAG3 and APLP1.  So the carboxy terminus of alpha-synuclein is a promising traget to block Parkinson’s disease progression.

Nightmare on Wall Street

I’ve written several posts about Cassava Biosciences (symbol SAVA) and their potential drug for Alzheimer’s (see the end). The recent approval of Biogen’s ineffective (but highly lucrative) therapy Aducanumab for the disease brings forth the following nightmare. At a cost of > $50,000/year and millions of desperate famililes, Biogen will soon be rolling in money. The Cassava drug is orally available and should cost a fraction of that. Even better — it may actually work, although I think serious side effects are likely. Given the sketchy data getting Aducanumab through the FDA, Cassava’s drug represents a real threat to Biogen.

It will be perfectly legal for Biogen to outright buy Cassava and stop development. They will have the money. They won’t be able to do it on the sly, as any position of one company (or individual) in another greater than 5% of the value of the company must be reported to the SEC where it becomes public knowledge.

This from a cousin who is a stock market guru. His wife wasn’t available when I called being next door taking care of a woman with early Alzheimer’s, whose husband had to leave as his father suddenly passed away. She can’t be left alone. Such is the market for Aducanumab.

So will my friend Lindsay and her husband have the moral strength to resist Biogen?

Back in the day when I was in the service in Denver, a very wealthy stockbroker (who had brought the waterPik public) bought up many of beautiful old mansions on the west side of Cheeseman park. He then sold them to people he trusted (such as ourselves), so they wouldn’t be broken up into apartments (which was quite lucrative). I asked why the other people living on Humboldt street didn’t do the same. He said they had so much money they didn’t need character. The folks at Cassava don’t have a hell of a lot of money but hopefully they do have character.

Other posts on Cassava should you be interested are

The science behind Cassava Sciences (SAVA)

Book Review: Hawking Hawking

To this neurologist, Stephen Hawking’s greatest contribution wasn’t in physics. I ran a muscular dystrophy clinic for 15 years in the 70s and 80s. Few of my ALS patients had heard of Hawking back then. I made sure they did. Hawking did something for them, that I could never do as a physician — he gave them hope.

Which brings me to an excellent biography of Hawking by Charles Seife “Hawking Hawking” which tries to strip away the aura and myths that Hawking assiduously constructed and show the man underneath.

Even better, Seife is an excellent writer and has the mathematical and scientific  chops (Princeton math major, Yale masters in math) to explain the problems Hawking was wrestling with.

Hawking was smart.  One story tells it all (p. 328).  Apparently there were only 3 other physics majors at Oxford that year.  They were all given a set of 13 problems on electromagnetism and a week to do them.    One of the others (Derek Powney) tells the tale. “I discovered very rapidly that I couldn’t do any of them”.  So he teamed up with one of the others, and by the end of the week they’d done 1.5 problems.  The thrd student (working alone) solved one. 

At the end of the week “Stephen as always hadn’t even started”. He went to his room and came out 3 hours later. “Well, I’ve only had the time to do the first ten.”  “I think at that point we realized that it’s not just that we weren’t on the same street, we weren’t on the same planet.”

Have you ever had an experience like that?  I’ve had two.  The first occurred in grade school. I was a pretty good piano player, better than the rest of Dr, Rudnytsky’s students.  Then, someone told me that at age 3 his son would tell him what notes passing trains were whistling on, and that later on he’d sit behind a door listening to his father give lessons, and then come in afterwards and play by ear what the students had been playing.  The second occurred a within day or so of starting my freshman year in college. My roommate told me about a guy who thought he ought to know everybody in our class of 700+.  So he got out the freshman herald which had our pictures and names and a day later knew everyone in the class by name. 

The reason people of a scientific bent should read the book, is not the sociology, or the complicated sexuality of Hawking and his two wives, and god knows what else.  It is the excellent explanations of the problems in math and physics that Hawking faced and solved.  Even better, Seife puts them in context of the work done before Hawking was born.  

Two  examples

1. pp. 14 – 18 — a superb explanation of what Einstein did to create special relativity. 

2. pp. 240 – 245 an excellent description of the horizon problem, the flatness problem and how inflation solved it. 

Any really good book will teach you something.  People in physics, math and biology are consumed with the idea of information.  The book (pp. 131 – 134) explains why Hawking was so focused on the black hole information paradox.  It always seemed pretty arcane and superficial to me (on the order of how many angels could dance on the head of a pin).  

Wrong ! Wrong !

The black hole information paradox is at the coalface of ignorance in modern physics.  Why?  Because the two great theories we have in  (quantum mechanics and general relativity) disagree with what happens to the information contained in an object (such as an astronaut) swallowed by a black hole.  Relativity says it’s destroyed, while quantum mechanics says that’s impossible. 

So reconciling the two descriptions would lead to a deeper theory, and showing that one was wrong, would discredit a powerful theory. 

So even if you’re not interested in the sociology of the circles Hawking moved in or his sex life, there is a lot of well-explained physics and math to be learned for the general reader.  

The black hole information paradox resembles a similarly unresolved pair of phenomena in the world we live in, the Cartesian dualism between flesh and spirit.  It is writ large in biology.

Chemistry is great and can provide mechanistic explanations what we see, such as the example from the following old post, produced after the ***

It’s quite technical, but is an elegant explanation of how different cells make different amounts of two different forms of a muscle protein (beta actin and gamma actin ).  I never thought we’d have an explanation this good, but we do.  Well that’s the flesh and the physicality of the explanation.  Asking why different cells would want this, or what the function of all is puts you immediately in the world of spirit (ideas, which are inherently noncorporeal).  Physical chemistry and biochemistry are silent, and all the abstract explanations science gives us (the function, the why, the reason) is essentially teleological. 

*****

The last post “The death of the synonymous codon – II” puts you exactly at the nidus of the failure of chemical reductionism to bag the biggest prey of all, an understanding of the living cell and with it of life itself.  We know the chemistry of nucleotides, Watson-Crick base pairing, and enzyme kinetics quite well.  We understand why less transfer RNA for a particular codon would mean slower protein synthesis.  Chemists understand what a protein conformation is, although we can’t predict it 100% of the time from the amino acid sequence.  

Addendum 30 April ’21:  Called to task on the above  by a reader.  This statement is no longer true.  The material below the *** was bodily lifted from something I wrote 10 years ago.  Time and AI have marched on since then.

So we do understand exactly why the same amino acid sequence using different codons would result in slower synthesis of gamma actin than beta actin, and why the slower synthesis would allow a more leisurely exploration of conformational space allowing gamma actin to find a conformation which would be modified by linking it to another protein (ubiquitin) leading to its destruction.  Not bad.  Not bad at all.

Now ask yourself, why the cell would want to have less gamma actin around than beta actin.  There is no conceivable explanation for this in terms of chemistry.  A better understanding of protein structure won’t give it to you.  Certainly, beta and gamma actin differ slightly in amino acid sequence (4/375) so their structure won’t be exactly the same.  Studying this till the cows come home won’t answer the question, as it’s on an entirely different level than chemistry.

 

The wiring diagram of the brain takes another hit

Is there anything duller than wire? It conducts electricity. That’s about it. Copper wires conduct better than Aluminum wires. So what.  End of story. 

That’s pretty much the way we thought of axons, the wires of the nervous system. Thicker axons conduct faster than thin ones, and insulated axons conduct faster than non-insulated ones. The insulation is made out of fat and called myelin.  Just as fat in meat looks white, a bunch of axons sheathed by myelin looks white, which is how white matter got its name. 

Those of you old enough to remember vinyl records, know just how different a record sounds when played at the wrong speed.  That’s what an MS patient has to deal with.  The disease attacks white matter mostly, which means that when myelin is lost or damaged, nerve impulses slow down.  Information gets through, but it’s garbled. 

So we knew that losing myelin causes trouble, but other than that, it was assumed that myelin, once laid down by the cell producing it (the oligodendrocyte) was stable unless trauma or disease damaged it. 

That was until adaptive myelination came along roughly 10 years ago.  There is an excellent review [ Neuron vol. 109 pp. 1258 – 1273 ’21 ] which is irritating to read if you are looking for solid experimental facts.  This is not the fault of the authors.  They are trying to picture the frontier of a fast moving field.  By nature there is a lot of speculation in such an article, which would be a lot shorter (and duller) without it.  

However the following words occur frequently — could (43), has been understood (3), suggested (6), would (12), may (39) and is thought to (2).

The cells making the myelin are just that: cells.  Since the myelin they make is confined within them, a myelinated axon looks like a string of hot dogs, each dog the province of one oligo.  The space between the hot dogs is called the node (of Ranvier), and this is why myelinated axons conduct faster.  The impulse jumps between the nodes (saltatory conduction). 

Adaptive myelination comes in when you stimulate an axon — the myelin gets thicker, meaning that it conducts faster.   Also neuronal activity is held to alter myelin (the space between nodes gets longer meaning they conduct faster). 

Not all axons are myelinated, and activity ‘is thought to’ increase myelination of them. 

This has extremely profound consequences for how we think the brain works.  At the end of the post you’ll find an older one arguing that a wiring diagram of the brain (how the neurons are connected to each other) is far from enough to understand the brain.  But the article assumes that the wires are pretty much fixed in how they act. The Neuron article shows that this is wrong.  

Imagine if the connections between transistors on a computer chip, grew and shrunk depending on how much current flowed through them.   That appears to be the case for the brain.

Here’s the old post

Would a wiring diagram of the brain help you understand it?

Every budding chemist sits through a statistical mechanics course, in which the insanity and inutility of knowing the position and velocity of each and every of the 10^23 molecules of a mole or so of gas in a container is brought home.  Instead we need to know the average energy of the molecules and the volume they are confined in, to get the pressure and the temperature.

However, people are taking the first approach in an attempt to understand the brain.  They want a ‘wiring diagram’ of the brain. e. g. a list of every neuron and for each neuron a list of the other neurons connected to it, and a third list for each neuron of the neurons it is connected to.  For the non-neuroscientist — the connections are called synapses, and they essentially communicate in one direction only (true to a first approximation but no further as there is strong evidence that communication goes both ways, with one of the ‘other way’ transmitters being endogenous marihuana).  This is why you need the second and third lists.

Clearly a monumental undertaking and one which grows more monumental with the passage of time.  Starting out in the 60s, it was estimated that we had about a billion neurons (no one could possibly count each of them).  This is where the neurological urban myth of the loss of 10,000 neurons each day came from.  For details see https://luysii.wordpress.com/2011/03/13/neurological-urban-legends/.

The latest estimate [ Science vol. 331 p. 708 ’11 ] is that we have 80 billion neurons connected to each other by 150 trillion synapses.  Well, that’s not a mole of synapses but it is a nanoMole of them. People are nonetheless trying to see which areas of the brain are connected to each other to at least get a schematic diagram.

Even if you had the complete wiring diagram, nobody’s brain is strong enough to comprehend it.  I strongly recommend looking at the pictures found in Nature vol. 471 pp. 177 – 182 ’11 to get a sense of the  complexity of the interconnection between neurons and just how many there are.  Figure 2 (p. 179) is particularly revealing showing a 3 dimensional reconstruction using the high resolutions obtainable by the electron microscope.  Stare at figure 2.f. a while and try to figure out what’s going on.  It’s both amazing and humbling.

But even assuming that someone or something could, you still wouldn’t have enough information to figure out how the brain is doing what it clearly is doing.  There are at least 3 reasons.

l. Synapses, to a first approximation, are excitatory (turn on the neuron to which they are attached, making it fire an impulse) or inhibitory (preventing the neuron to which they are attached from firing in response to impulses from other synapses).  A wiring diagram alone won’t tell you this.

2. When I was starting out, the following statement would have seemed impossible.  It is now possible to watch synapses in the living brain of awake animal for extended periods of time.  But we now know that synapses come and go in the brain.  The various papers don’t all agree on just what fraction of synapses last more than a few months, but it’s early times.  Here are a few references [ Neuron vol. 69 pp. 1039 – 1041 ’11, ibid vol. 49 pp. 780 – 783, 877 – 887 ’06 ].  So the wiring diagram would have to be updated constantly.

3. Not all communication between neurons occurs at synapses.  Certain neurotransmitters are generally released into the higher brain elements (cerebral cortex) where they bathe neurons and affecting their activity without any synapses for them (it’s called volume neurotransmission)  Their importance in psychiatry and drug addiction is unparalleled.  Examples of such volume transmitters include serotonin, dopamine and norepinephrine.  Drugs of abuse affecting their action include cocaine, amphetamine.  Drugs treating psychiatric disease affecting them include the antipsychotics, the antidepressants and probably the antimanics.

Statistical mechanics works because one molecule is pretty much like another. This certainly isn’t true for neurons. Have a look at http://faculties.sbu.ac.ir/~rajabi/Histo-labo-photos_files/kora-b-p-03-l.jpg.  This is of the cerebral cortex — neurons are fairly creepy looking things, and no two shown are carbon copies.

The mere existence of 80 billion neurons and their 150 trillion connections (if the numbers are in fact correct) poses a series of puzzles.  There is simply no way that the 3.2 billion nucleotides of out genome can code for each and every neuron, each and every synapse.  The construction of the brain from the fertilized egg must be in some sense statistical.  Remarkable that it happens at all.  Embryologists are intensively working on how this happens — thousands of papers on the subject appear each year.

 

 

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.