Tag Archives: ribonuclease

Tubulin needs a lot of help from its friends

Our neurons (and us) would be the size of amoebas if weren’t for tubulin which forms the superhighways (microtubules) along which cargo is shipped to the end of axons.   Your average NBA player has axons over 3 feet long going from his sacral spinal cord to his calf muscles.   Split the difference and call it a meter.  Diffusion is way too slow to get anything that far. The trucks schlepping things back and forth on the microtubular highway are called Kinesin and dynein. 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.

How many jumps do Kinesin and Dynein have to make to go a meter? Just 10^9/80 — call it 10,000,000. Kinesin and Dynein 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 Kinesin and Dynein have to jump. That’s 10,000,000 jumps of 48 feet or 90,909 miles.  It’s amazing they get the job done.

Now that you’re sufficiently impressed with tubulin’s importance, it’s time to see why it needs help.  First a bit of history.  Christian Anfinsen was a Swarthmore football player who happened to win the Nobel prize 50 years ago for his work on the protein ribonuclease, an enzyme.  If you heat it, enzymatic activity is lost (the protein is said to be denatured).  This is because the exact 3 dimensional path of the protein backbone forming the catalytic site of ribonuclease was lost. However if you leave the denatured protein alone (under the proper conditions) it folds back up to the correct 3 dimensional shape.  His point was that the amino acid sequence of the protein was all that was needed to determine ‘the’ three dimensional shape of the protein.  This was at a time when we didn’t know that most proteins have a variety of shapes not just one.

Unfortunately tubulin does not fold up to the shape found in microtubules.  It needs significant help from two friends, prefoldin and TRiC.  TRiC is a monster conglomerate of 2 copies each of 8 different proteins with a molecular mass over 1,000,000 Daltons (e.g. a megaDalton).  What is one Dalton — it’s the mass of a hydrogen atom.   TRiC is made of two back to back rings (with built in lids) each ring consisting of 8 different but related proteins).  Each of the proteins has a domain which binds ATP and a domain which binds the protein to be folded.  There is a central cavity 90 x 90 x 50 Angstroms in size.  Since each hydrogen atom is about 1 Angstrom in diameter, it can fit 405,000 hydrogen atoms inside, or about 200,000 carbons, hydrogens, oxygens and nitrogens — enough room for most proteins.

Prefoldin is equally amazing.  It basically looks like a Portuguese man o’ war — https://en.wikipedia.org/wiki/Portuguese_man_o%27_war.  It is made of 2 copes of one protein and 4 of another.  The tentacles are long alpha helices projecting down from the body.

The tentacles interact with tubulin, carrying it in an unstructured form, thrusting one of its tentacles into the central chamber of TRiC carrying unstructured tubulin with it.   ATP addition leads to lid closure and tubulin encapsulation in the chamber.

A magnificent paper [ Cell vol. 185 pp. 4770 – 4787 ’22 ] describes what happens to tubulin in the TRiC chamber at near atomic resolution.  They are literally watching tubulin fold as it passes from one of the 8 different proteins making up the TRiC ring to another.  The disordered carboxy terminal chains of TRiC are postulated to function as a tethered solvent allowing the intially disordered amino acid sequence of tubulin, to slither into their correct positions more easily.

I’m sure it’s behind a paywall, but if you can look at the figures in the paper, you’ll be bound to be impressed.

So Anfinsen turned out to be wrong, and some 10%  of newly translated proteins turn our to need TRiC’s help.  And yet he wasn’t, because AlphaFold uses only the amino acid sequence of proteins to predict their three dimensional structure.

One further point.  The ancestral bacterial protein for tubulin is called FtsZ.  It happily folds to the correct structure by itself.  However tubulin developed new domains, some of which are for the motor proteins Dynein and Kinesin, and others are for microtubule associated proteins such as tau, the major component of the neurofibrillary tangle of Alzheimer’s disease. These domains are on the surface of the protein, making it harder to fold by itself.

All this information would have been impossible to get 10 years ago, and it’s all due to the sharpening of our technological tools.

Chemistry and Biochemistry can’t answer the important questions but without them we are lost

The last two posts — one concerning the histone code and cerebral embryogenesis https://luysii.wordpress.com/2018/06/07/omar-khayyam-and-the-embryology-of-the-cerebral-cortex/ and the other concerning PVT1 enhancers promoters and cancer https://luysii.wordpress.com/2018/06/04/marshall-mcluhan-rides-again/ — would be impossible without chemical and biochemical knowledge and technology, but the results they produce and the answers they seek and lie totally outside both disciplines.

In fact they belong outside the physical realm in the space of logic, ideas, function — e.g. in the other half of the Cartesian dichotomy — the realm of ideas and spirit.  Certainly the biological issues are instantiated physically in molecules, just as computer memory used to be instantiated in magnetic cores, rather than transistors.

Back when I was starting out as a grad student in Chemistry in the early 60s, people were actually discovering the genetic code, poly U coded for phenylalanine etc. etc.  Our view was that all we had to do was determine the structure of things and understanding would follow.  The first xray structures of proteins (myoglobin) and Anfinsen’s result on ribonuclease showing that it could fold into its final compact form all by itself reinforced this. It also led us to think that all proteins had ‘a’ structure.

This led to people thinking that the only difference between us and a chimpanzee were a few amino acid differences in our proteins (remember the slogan that we were 98% chimpanzee).

So without chemistry and biochemistry we’d be lost, but the days of crude reductionism of the 60s and 70s are gone forever.  Here’s another example of chemical and biochemical impotence from an earlier post.

The limits of chemical reductionism

“Everything in chemistry turns blue or explodes”, so sayeth a philosophy major roommate years ago.  Chemists are used to being crapped on, because it starts so early and never lets up.  However, knowing a lot of organic chemistry and molecular biology allows you to see very clearly one answer to a serious philosophical question — when and where does scientific reductionism fail?

Early on, physicists said that quantum mechanics explains all of chemistry.  Well it does explain why atoms have orbitals, and it does give a few hints as to the nature of the chemical bond between simple atoms, but no one can solve the equations exactly for systems of chemical interest.  Approximate the solution, yes, but this his hardly a pure reduction of chemistry to physics.  So we’ve failed to reduce chemistry to physics because the equations of quantum mechanics are so hard to solve, but this is hardly a failure of reductionism.

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.  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.

Cellular and organismal molecular biology is full of questions like that, but gamma and beta actin are the closest chemists have come to explaining the disparity in the abundance of two closely related proteins on a purely chemical basis.

So there you have it.  Physicality has gone as far as it can go in explaining the mechanism of the effect, but has nothing to say whatsoever about why the effect is present.  It’s the Cartesian dualism between physicality and the realm of ideas, and you’ve just seen the junction between the two live and in color, happening right now in just about every cell inside you.  So the effect is not some trivial toy model someone made up.

Whether philosophers have the intellectual cojones to master all this chemistry and molecular biology is unclear.  Probably no one has tried (please correct me if I’m wrong).  They are certainly capable of mounting intellectual effort — they write book after book about Godel’s proof and the mathematical logic behind it. My guess is that they are attracted to such things because logic and math are so definitive, general and nonparticular.

Chemistry and molecular biology aren’t general this way.  We study a very arbitrary collection of molecules, which must simply be learned and dealt with. Amino acids are of one chirality. The alpha helix turns one way and not the other.  Our bodies use 20 particular amino acids not any of the zillions of possible amino acids chemists can make.  This sort of thing may turn off the philosophical mind which has a taste for the abstract and general (at least my roommates majoring in it were this way).

If you’re interested in how far reductionism can take us  have a look at http://wavefunction.fieldofscience.com/2011/04/dirac-bernstein-weinberg-and.html

Were my two philosopher roommates still alive, they might come up with something like “That’s how it works in practice, but how does it work in theory?