A few Thanksgiving thankyou’s

The following was published 5 years ago, but with time and ever more research our organization seems even more miraculous (see last paragraph).  It’s amazing that it lasts as long as it does, and for that we should be thankful.   Call this prayer if you wish.

As CEO of a very large organization, it’s time to thank those unsung divisions that make it all possible.  Fellow CEOs should take note and act appropriately regardless of the year it’s been for them.

First: thanks to the guys in shipping and receiving.  Kinesin moves the stuff out and Dynein brings it back home.  Think of how far they have to go.  The head office sits in area 4 of the cerebral cortex and K & D have to travel about 3 feet down to the motorneurons in the first sacral segment of the spinal cord controlling the gastrocnemius and soleus, so the boss can press the pedal on his piano when he wants. Like all good truckers, they travel on the highway.  But instead of rolling they jump.  The highway is pretty lumpy being made of 13 rows of tubulin dimers.

Now chemists are very detail oriented and think in terms of Angstroms (10^-10 meters) about the size of a hydrogen atom. As CEO and typical of cell biologists, I have to think in terms of the big picture, so I think in terms of nanoMeters (10^-9 meters).  Each tubulin dimer is 80 nanoMeters long, and K & D essentially jump from one to the other in 80 nanoMeter steps.  Now the boss is shrinking as he gets older, but my brothers working for players in the NBA have to go more than a meter to contract the gastrocnemius and soleus (among other muscles) to help their bosses jump.  So split the distance and call the distance they have to go one Meter.  How many jumps do Kinesin and Dynein have to make to get there? Just 10^9/80 — call it 10,000,000. The boys also have to jump from one microtubule to another, as the longest microtubule in our division is at most 100 microns (.1 milliMeter).  So even in the best of cases they have to make at least 10,000 transfers between microtubules.  It’s a miracle they get the job done at all.

To put this in perspective, consider a tractor trailer (not a truck — the part with the motor is the tractor, and the part pulled is the trailer — the distinction can be important, just like the difference between rifle and gun as anyone who’s been through basic training knows quite well).  Say the trailer is 48 feet long, and let that be comparable to the 80 nanoMeters K and D have to jump. That’s 10,000,000 jumps of 48 feet or 90,909 miles.  It’s amazing they get the job done.

Second: Thanks to probably the smallest member of the team.  The electron.  Its brain has to be tiny, yet it has mastered quantum mechanics because it knows how to tunnel through a potential barrier.   In order to produce the fuel for K and D it has to tunnel some 20 Angstroms from the di-copper center (CuA) to heme a in cytochrome C oxidase (COX).  Is the electron conscious? Who knows?  I don’t tell it what to do.   Now COX is just a part of one of our larger divisions, the power plant (the mitochondrion).

Third: The power plant.  Amazing to think that it was once (a billion years or more ago) a free living bacterium.  Somehow back in the mists of time one of our predecessors captured it.  The power plant produces gas (ATP) for the motors to work.  It’s really rather remarkable when you think of it.   Instead of carrying a tank of ATP, kinesin and dynein literally swim in the stuff, picking it up from the surroundings as they move down the microtubule.  Amazingly the entire division doesn’t burn up, but just uses the ATP when and where needed.  No spontaneous combustion.

There are some other unsung divisions to talk about (I haven’t forgotten you ladies in the steno pool, and your incredible accuracy — 1 mistake per 100,000,000 letters [ Science vol. 328 pp. 636 – 639 ’10 ]).  But that’s for next time.

To think that our organization arose by chance, working by finding a slightly better solution to problems it face boggles this CEO’s mind (but that’s the current faith — so good to see such faith in an increasingly secular world).

Call the thankfulness of the CEO prayer if you wish.

Addendum 29 November ’22 — from a friend “We also have to thank all the tau molecules that stabilize the microtubules— until the misbehavior of ERK and JNK1 overdecorate them with holiday lighting (phosphates) and they fall apart. So after Thanksgiving, be careful not to overcommercialize the holiday season.”

The cryoEM work of the last 5 years has shown us the structure of large molecular machines made of multiple proteins, DNAs and RNAs which are even more impressive (to me) than single protein structure.   One example [ Nature vol. 609 pp. 630 – 639 ’22 ] shows the Holliday junction which allows strand migration between the strands of two DNA duplexes.   Pictured is the complex from bacteria which is confined in a rectangle with sides 220 and 120 Angstroms (not sure how thick it is).  The complex contains a molecular motor which slides the junction.  You could spend your life just studying this one structure.  It’s hard for me to see how it arose.

A few Thanksgiving thank you’s

As CEO of a very large organization, it’s time to thank those unsung divisions that make it all possible.  Fellow CEOs should take note and act appropriately regardless of the year it’s been for them.

First: thanks to the guys in shipping and receiving.  Kinesin moves the stuff out and Dynein brings it back home.  Think of how far they have to go.  The head office sits in area 4 of the cerebral cortex and K & D have to travel about 3 feet down to the motorneurons in the first sacral segment of the spinal cord controlling the gastrocnemius and soleus, so the boss can press the pedal on his piano when he wants. Like all good truckers, they travel on the highway.  But instead of rolling they jump.  The highway is pretty lumpy being made of 13 rows of tubulin dimers.

Now chemists are very detail oriented and think in terms of Angstroms (10^-10 meters) about the size of a hydrogen atom. As CEO and typical of cell biologists, I have to think in terms of the big picture, so I think in terms of nanoMeters (10^-9 meters).  Each tubulin dimer is 80 nanoMeters long, and K & D essentially jump from one to the other in 80 nanoMeter steps.  Now the boss is shrinking as he gets older, but my brothers working for players in the NBA have to go more than a meter to contract the gastrocnemius and soleus (among other muscles) to help their bosses jump.  So split the distance and call the distance they have to go one Meter.  How many jumps do Kinesin and Dynein have to make to get there? Just 10^9/80 — call it 10,000,000. The boys also have to jump from one microtubule to another, as the longest microtubule in our division is at most 100 microns (.1 milliMeter).  So even in the best of cases they have to make at least 10,000 transfers between microtubules.  It’s a miracle they get the job done at all.

To put this in perspective, consider a tractor trailer (not a truck — the part with the motor is the tractor, and the part pulled is the trailer — the distinction can be important, just like the difference between rifle and gun as anyone who’s been through basic training knows quite well).  Say the trailer is 48 feet long, and let that be comparable to the 80 nanoMeters K and D have to jump. That’s 10,000,000 jumps of 48 feet or 90,909 miles.  It’s amazing they get the job done.

Second: Thanks to probably the smallest member of the team.  The electron.  Its brain has to be tiny, yet it has mastered quantum mechanics because it knows how to tunnel through a potential barrier.   In order to produce the fuel for K and D it has to tunnel some 20 Angstroms from the di-copper center (CuA) to heme a in cytochrome C oxidase (COX).  Is the electron conscious? Who knows?  I don’t tell it what to do.   Now COX is just a part of one of our larger divisions, the power plant (the mitochondrion).

Third: The power plant.  Amazing to think that it was once (a billion years or more ago) a free living bacterium.  Somehow back in the mists of time one of our predecessors captured it.  The power plant produces gas (ATP) for the motors to work.  It’s really rather remarkable when you think of it.   Instead of carrying a tank of ATP, kinesin and dynein literally swim in the stuff, picking it up from the surroundings as they move down the microtubule.  Amazingly the entire division doesn’t burn up, but just uses the ATP when and where needed.  No spontaneous combustion.

There are some other unsung divisions to talk about (I haven’t forgotten you ladies in the steno pool, and your incredible accuracy — 1 mistake per 100,000,000 letters [ Science vol. 328 pp. 636 – 639 ’10 ]).  But that’s for next time.

To think that our organization arose by chance, working by finding a slightly better solution to problems it face boggles this CEO’s mind (but that’s the current faith — so good to see such faith in an increasingly secular world).

How little we know

Who would have thought that a random mutagenesis experiment throwing Ethyl Nitroso Urea (ENU) at unsuspecting mice looking for genes using a mutagenesis strategy to identify novel immune regulatory genes would point to a possible treatment for muscular dystrophy? When the experimenters looked at the mutated offspring, they found that the muscles appeared unusually red.

What happened?

You need to know a bit more about muscles. On a very simplistic level there are only two types of muscle fibers, red and white. Carnivores eating chicken know about dark meat and white meat. The dark meat is composed of red fibers, which have that appearance because of large numbers of mitochondria (which are full of iron) giving them the same red appearance as blood (which is also full of iron). In both cases the iron is bound by porphyrin rings. As one might expect, these muscles consume a lot of energy, being postural for the most part. The white meat made of white fibers has muscle which can contract very quickly and strongly, for flight and fight. They don’t have nearly the endurance of red muscle, because they can’t produce energy for the long term.

Humans have the two types of muscle fibers mixed up in each of our muscles.

The ENU had produced a mutation in something called fnip1 (Folliculin INteracting Protein 1). What’s folliculin? It prevents a gene transcription factor (TFE3) from getting into the nucleus. Folliculin prevents an embryonic stem cell from differentiating. It is mutated in the Birt Hogg Dube syndrome which is characterized by many benign hair follicle tumors. What in the world does this have to do with muscular dystrophy? It’s not something someone would start investigating looking for a cure is it? Knock out both copies of folliculin and the embryo dies in utero.

It gets deeper.

What does Fnip1 do to folliculin? It, and its cousin fnip2 form complexes with folliculin. The complex binds an enzyme called AMPK (which is turned on by energy depletion in the cell. AMPK phosphorylates both fnip1 and folliculin. Folliculin binds and inhibits AMPK.

So animals lacking fnip1 have a more activated AMPK. So what? Well AMPK activates a transcriptional coactivator called PGC1alpha (you don’t want to know what the acronym stands for). This ultimately results in production of more mitochondria (recall that AMPK is an energy sensor, and one of the main functions of mitochondria is to produce energy, lots of it).

This ultimately means more red muscle fibers. There is a mouse model of Duchenne dystrophy called the mdx mouse (which has a premature termination codon in the dystrophin protein, resulting in a protein only 27% as long as it should be. That still leaves a lot, as normal dystrophin contains 3,685 amino acids. Knocking out fnip1 in the mdx mice improved muscle function. Impressive !!

I’m quite interested in this sort of work, as I ran a muscular dystrophy clinic from ’72 to ’87 and watched a lot of kids die. The major advance during that time wasn’t anything medical. It came from engineering — lighter braces using newer materials allowed the kids to stay out of wheelchairs longer.

You can read all about it in Proc. Natl. Acad. Sci. vol. 112 pp. 424 – 429 ’15 ] Clearly we know a lot (AMPK, dystrophin, PGC1alpha, fnip1, fnip2, folliculin, TFE3), but what we didn’t know was how in the world they function together in the cell. We’re sure to learn a lot more, but this whole affair was uncovered when looking for something else (immune regulators) using the bluntest instrument possible (throw a mutagen at an animal and see what happens). No one applying for a muscular dystrophy grant would dare to offer the original work as a rationale, yet here we are.

So directed research isn’t always the way to go. Although we know a lot, we still know very little.