Category Archives: Chemistry (relatively pure)

A scary paper: Cancer by proxy

Can a good kid growing up in a bad neighborhood turn bad? Most think so. What about a genetically normal cell growing up in a bad neighborhood? Can it turn cancerous if its neighbors have a mutation ? A recent paper [ Nature vol. 539 pp.304 – 308 ’16b] demonstrates how this can happen.

A gene called PTPN11 is mutated in myelomonocytic leukemia (MML)in humans and mice. Expressing the mutant in blood cells causes leukemia in mice (nothing spectacular there).

However, expressing the mutant in marrow supporting cells, not blood cells or blood stem cells for long enough gives MML in mice which can be transplanted into normal mice producing MML there.

Note that the blood stem cells don’t contain the mutant gene. One theory has it that mutant PTPN11 recruits monocytes, which then produce other stuff (CCL3 also known as MIP1alpha and interleukin1Beta), which then turns on blood stem cells to proliferate madly causing leukemia. Giving a CCL3 receptor antagonist reverses the myeloproliferation (but it isn’t clear to me if it reverses the leukemia once established)

As far as we know the cells developing into MML don’t contain mutant PTPN11. So it’s cancer by proxy. Obviously some changes (mutations, epigenetic changes) have have occurred in the leukemic cells, but at this point we don’t know what they are.

What is ICP27 trying to tell us? One of you could get a PhD if you figure it out !

It wouldn’t be the first time a viral protein led us to an important cellular mechanism. Consider what the polio virus taught us about the translation of mRNA into protein. It cleaves two components of eIF-4F (eukaryotic Initiation (of ribosome translation of mRNA into protein) Factor 4F totally shutting down synthesis of mRNAs with a cap on their 5′ end (which is most of them). Poliovirus proteins don’t have these caps so their proteins continue to be made.

Well this brings us to ICP27 (Infected Cell Protein 27) a product of the Herpes Simplex virus. You can read all about it in [ Proc. Natl. Acad. Sci. vol. 113 pp. 12256 – 12261 ’16 ]. ICP27 is essential for herpes virus infection. This work shows that it inhibits intron splicing (but in under 1% of cellular genes) and also promotes the use of alternative 5′ splice sites.

It also induces the expression of pre-mRNAS prematurely cleaved and polyAdenylated from cryptic polyAdenylation signals located in intron 1 or intron 2 of an amazing 1% of all cellular genes. These prematurely cleaved and polyAdenylated mRNA sometimes contain novel open reading frames (ORFs). They are typically intronless (they should be) and under 2 kiloBases long. They are expressed early during viral infection and efficiently exported to cytoplasm. The ICP27 targeted genes are GC rich (as are all Herpes simplex genes), contain cytosine rich sequences near the 5′ splice site.

The paper also showed that optimization of splice site sequences, or mutation of nearby cytosines eliminated ICP27 mediated splicing inhibition. Introduction of cytosine rich sequences to an ICP27 INsensitive splicing reporter conferred susceptibility to ICP27.

How is this going to help you get a PhD? Ask yourself. What are cryptic polyAdenylation signals doing in the first two introns in so many genes? It seems obvious (to me) that as well as the virus the cell is using them for some purpose. It isn’t hard to mutate something to the signal for polyadenylation AAUAAA. Interestingly cleavage doesn’t occur here, but 30 nucleotides or so downstream. The sequence occurs every 4^6 == 4096 nucleotides (if they’re random). I’m not sure what the total length of introns #1 and #2 are of our 20,000 or so protein coding genes, but someone should be able to find out and see if 200 occurrences of this sequence is more than would be expected by chance.

The plot thickens when the paper notes that “Over 200 genes are affected by ICP27. Over 30 (including PML, STING, TRAF6, PPP6C, MAP3K7, FBXw11, IFNAR2, NKFB1, RELA and CREBP are related to the immune pathway). Do you think the cell doesn’t use this pathway as well?

What about the existence of other viral (and cellular) proteins doing the same sort of thing (but on different introns perhaps). What are those novel open reading frames in the alternatively spliced mRNAs doing?

Fascinating stuff. Time to get busy if you’re an enterprising grad student, or young faculty member.

The proteasome branches out

The surface of a protein is not at all like a ball of yarn, even though they are both one long string. This has profound implications for the immune system. Look at any solved protein structure. The backbone bobs and weaves taking water hating (hydrophobic) amino acids into the center of the protein, and putting water loving (hydrophilic) amino acids on the surface. So even though the peptide backbone is continuous, only discontinuous patches of it are displayed on the protein surface.

Which is a big problem for the immune system which wants to recognize the surface of the protein (which is all it first gets to see with an invading bug). Now we know that foreign proteins are ingested by the cell, chopped up by the proteasome, and fragments loaded on to immune molecules (class I Major Histocompatibility Complex antigens) and displayed on the cell surface so the immune system can learn what it looks like and react to it. The peptides aren’t very long — under 11 or so amino acids, but they are continuous.

What if the really distinct part of the protein surface (e.g. the immunogen)  is made of two distinct patches from the backbone? A fascinating paper shows how the immune system might still recognize it. Chop the protein up into fragments by the proteasome, and then have the fragments from adjacent patches put back together. You know that any enzyme can be run in reverse, so if the proteasome can split peptide bonds apart it can also join them together.

This is exactly what was found in a recent paper — Science vol. 354 pp. 354 – 358 ’16. The small peptides (containing at most 11 amino acids) finding their way to the cell surface were analyzed in a technical tour de force. In aggregate they go by the fancy name of immunopeptidome. They found that the proteasome IS actually splicing peptide fragments together. This is called Proteasome Catalyzed Peptide Splicing (PCPS). The present work shows that it accounts for 1/3 of the class I immunopeptidome in terms of diversity and 1/4 in terms of abundance. One-third of self antigens are represented on the cell surface of the immune cell line they studied (GR-LCL the GR-lymphoblastoid cell line) ONLY by spliced peptides. The ordering of the spliced peptide was the same as the parent protein in only half. There was no preference for the length of the protein skipped by the splice.

The work has huge implications for immunology, not least autoimmune disease.

So today I wrote the author the following

Dr. Mishto

Terrific paper ! Do you have any evidence for the spliced peptides being spatially contiguous on the surface of the parent protein. Have you looked?

This makes a lot of sense, because the immune system should ‘want’ to recognize protein conformations as they exist in the living cell, rather than stretches of amino acid sequence in the parent protein. Also, with few exceptions the surface of a given protein in vivo is a collection of discontinuous peptide sequences of the parent protein. I’ve always wondered how the immune system did this, and perhaps your paper explains things.

Luysii

and got this back almost immediately

Dear Luysii

Interesting idea. We shall have a look for few examples where the crystallography structure or the parental protein is disclosed already.

regards

Michele

It doesn’t get any better than this. Tomorrow I will be exactly 78 years and 6 months old. It shows I can still think (on occasion).

Addendum 17 Nov ’16;  It looks as though proteins are fed into the central cavity of the proteasome as a completely denatured single strand.  See figure 5 of PNAS 113 pp 12991 -m12996 ’16.  The channel to get in appears quite narrow.

The world’s longest allosteric effect

I think there is some very interesting protein physical chemistry to be discovered/worked out based on a recent report [ Nature vol. 537 pp. 107 – 111 ’16 ]. It involves a long (2,200 Angstrom) coiled coil protein called EEA1 (Early Endosome Antigen 1). It contains 1,400 amino acids 1,275 of which form a coiled coil.

If you are conversant with the alpha helix and how two of them form a coiled coil, jump to ****. Otherwise here is some background and links to pictures which should help.

The alpha helix is a type of protein secondary structure in which the protein backbone assumes the shape of a coiled spring. There are 3.64 amino acids per turn. A single turn is 5.4 Angstroms high and 11 Angstroms wide. The alpha helix is right handed. That is to say, that if you orient the chain so that your thumb points from the N terminal to C terminal amino acid, the chain will twist in the direction of the fingers of the right hand as it rises. For some reason I can’t provide a link to a very large number of images for you hit. However, when I go to Google and type images of alpha helices you see them immediately — you’ll have to do the same to get there.

Coiled coils have two alpha helices winding around each other. This means that for secure interactions, the same types of amino acids must repeat again and again. A 7 residue periodicity (abcdefg)n in the distribution of nonpolar and charged amino acid residues is a feature characteristic of proteins which form alpha helices coiled about each other (coiled coil molecules). The 7 amino acids are lettered a – g from amino to carboxy. Positions a and d are usually hydrophobic amino acids (Leu, Ile, Val, Ala), positions e and g are usually polar or charged. The nonpolar a and d side chains associate by means of complementary knobs into holes packing. Each individual alpha helix is right handed, but the two helices wind around each other with a left handed turn. There are 3.64 amino acids per turn of an alpha helix, so for a regular repeating structure an amino acid should appear at the same position in space on the alpha helix (which forms a rigid rod). To see all the pictures you want — go to Google and type “Images of the Alpha Helix”.

To get the number of amino acids down so there are 3.5 per/turn (so the structure can repeat exactly every 7 amino acids –e.g. after 2 alpha helical turns) left handed supercoiling of each helix occurs (it’s a chicken and the egg situation). The helices are at an angle of 18 degrees to each other, and every 3.5 amino acids still form a 5.4 Angstrom (when one helix is viewed in isolation), but due to the tilt, they take up 5.1 Angstroms. This means that the same type of amino acid is found at positions 1, 8, 15, 22 etc. All intermediate filament proteins (keratin, neurofilaments, vimentin, etc.) contain a coiled coil structure. So to see all the pictures you could want — go to Google and type “Images of coiled coil proteins”

****
So the 1,275 amino acids of EEA1 divided by 3.5 and multiplied by 5.1 give you a coiled coil of fairly enormous length for a protein (1,858 Angstroms) — average protein diameter (if there is such a thing) is under 50 Angstroms

Functionally, EEA1 seems to be used as a tether with one end free and the other end hooked to a target membrane which wants to ‘catch’ the early endosome. The target membrane isn’t specified in the paper. Apparently EEA1 when not binding the endosome, is in a fully extended state, at around 2,000 Angstroms.

A protein called Rab5 is found on the early endosome membrane, and when EEA1 contacts it, the long coiled coil helix collapses, dragging the endosome toward the target membrane.  This is entropy in action, there being far more configurations of a collapsed protein than a rigidly extended one. To feel entropy for yourself, just pull on a rubber band, entropic effects just like this one are what you feel pulling back.

The collapse of EEA1  is an allosteric effect and a very long one, although the authors note long range allosteric effects are “not uncommon among coiled coil proteins”.

EEA1 is more complicated than initialy described. It contains amino acids which disrupt the 7 amino acid periodicity of the coiled coil (making it a jointed structure). The authors then made an EEA1 protein without the joints (so it was a perfect very long coiled coil). Binding of this protein to Rab5 on an endosome doesn’t result in collapse. So clearly normal EEA1 collapses at the ‘joints’.

The authors talk about some hypotheses as to how this happens in the Supplementary material (but I was unable to find).

So here’s a good research proejct for an enterprising grad student: either find out why and how a protein with multiple joints should exist in a fully extended configuration, or figure out how binding of Rab5 at one end of EEA1 produces such profound allosteric changes through this long linear protein. Happy hunting and thinking.

I must say it’s a pleasure to get back to chemistry after writing about the neurologic and medical issues of the presidential candidates.

Addendum 29 September — I wrote one the following to one of the authors (Dr. Grill) sending him the post above

Dr. Grill

Greatly enjoyed the paper.  I could never find the discussion of possible mechanism in the supplementary material.  You might enjoy the following post written about the paper

Luysii
He replied as follows:

“Dear Luysii thank you very much for the kind words, and I really like your title!

With the supplementary discussion, besides the method part there is an additional supplement file on the Nature website that is easy to miss…I attach it here for you. We discuss this a bit more, but I must admit that this is not very satisfactory at the moment. We just don’t know how this works, and much of our efforts at the moment are dedicated to understand”
So for other readers of the original paper who also can’t find the supplement with the authors’ speculations as to what is going on– here  is what he sent.

” A key question is how Rab5 can induce such a long-range global molecular transition in flexibility of EEA1. Indeed, long-range allosteric effects have been observed for other coiled-coil proteins. In the case of myosin, the presence of discontinuities in the coiled-coil heptads drive structural changes to flexibility. Other tethering factors may bend through large breaks in coiled-coil structure acting as joints, although it remains to be shown whether and how conformational changes are triggered by Rab binding, as shown for EEA1.

Furthermore, a dynamically flexible coiled-coil is mostly extended, provided its ends are free60. However, when the ends of this coiled coil are tethered, bent, or when torsion is locally applied, compensatory structural changes are propagated and even amplified through the length of the structure. Our results suggest that a change in intrinsic static curvature may contribute but is not the major cause for the reduction in end-to-end distance. However, a more rigorous assessment would require visualizing the thermal fluctuations of the bound and unbound EEA1 very rapidly and in three dimensions.

Force generation due to entropic effects plays a key role in many processes in biology ranging from DNA cytoskeletal filaments to motor proteins. Switching a molecule from stiff to flexible could be an effective and general mechanism of many coiled-coil proteins for generating an attractive force, thereby pulling two objects together or allowing reactions otherwise hindered by polymer rigidity. Future experiments will test to what extent the entropic collapse is a general mechanism used not only by membrane tethers but also in other biological processes.”

 

Baudelaire comes to Chemistry

Could an evil molecule be beautiful? In Les Fleurs du Mal, a collection of poems, Baudelaire argued that there was a certain beauty in evil. Well, if there ever was an evil molecule, it’s the Abeta42 peptide, the main component of the senile plaque of Alzheimer’s disease, a molecule whose effects I spent my entire professional career as a neurologist ineffectually fighting. And yet, in a recent paper on the way it forms the fibrils constituting the plaque I found the structure compellingly beautiful.

The papers are Proc. Natl. Acad. Sci. vol. 113 pp. 9398 – 9400, E4976 – E4984 ’16. People have been working on the structure of the amyloid fibril of Alzheimer’s for decades, consistently stymied by its insolubility. The authors solved it not by Xray crystallography, not by cryoEM, but by solid state NMR. They basically looked at the distance constraints between pairs of isotopically labeled atoms, and built their model that way. Actually they built a bouquet of models using computer aided energy minimization of the peptide backbone. Another independent study produced nearly the same set.

The root mean square deviation of backbone atoms of the 10 lowest energy models of the bouquets in the two studies was small (.89 and .71 Angstroms). Even better the model bouquets of the two papers resemble each other.

There are two chains of Abeta42, EACH shaped like a double horseshoe (similar to the letter S). The two S’s meet around a twofold axis. The interface between the two S’s is form by two noncontiguous areas on each monomer (#15 – #17) and (#34 – #37).

The hydrophilic amino terminal residues (#1 – #14) are poorly ordered, but amino acids #15 – #42 are arranged into 4 short beta strands (I only see 3 obvious ones) that stack up and down the fibril into parallel in register beta-sheets. Each stack of double horseshoes forms a thread and the two threads twist around each other to form a two stranded protofilament.

Glycines allow sharp turns at the corners of the horseshoes. Hydrogen bonds between amides link the two layers of the fibrils. Asparagine side chains form ladders of hydrogen bonds up and down the fibrils. Water isn’t present between the layers because the beta sheets are so close together (counterintuitively this decreases the entropy, because water molecules don’t have to align themselves just so to solvate the side chains).

Each of the horseshoes is stabilized by hydrophobic interactions among the hydrophobic side chains buried in the core. Charged residues are solvent exposed. The interface between the two horsehoes is a hydrophobic interface.

Many of the famlial mutations are on the outer edges of double S structure — they are K16N, A21G, D23N, E22A, E22K, E22G, E22Q.

The surface hydrophobic patch formed by V40 and A42 may explain the greater rate of secondary nucleation by Abeta42 vs. Abeta40.

The cryoEM structures we have of Abeta42 are different showing the phenomenon of amyloid polymorphism.

The PNAS paper used reombinant Abeta and prepared homogenous fibrils by repeated seeding of dissolved Abeta42 with preformed fibrils. The other study used chemically synthesized Abeta and got fibrils without seeding. Details of pH, peptide concentration, salt concentration differed, and yet the results are the same, making both structures more secure.

The new structure doesn’t immediately suggest the toxic mechanism of Abeta.

To indulge in a bit of teleology — the structure is so beautiful and so intricately designed, that the aBeta42 peptide has probably been evolutionarily optimized to perform an (as yet unknown) function in our bodies. Animals lacking Abeta42’s parent (the amyloid precursor protein) don’t form neuromuscular synapses correctly, but they are viable.

What is a hormone? What is an endocrine organ?

We all knew what hormones were back in the day. They were chemicals released by an endocrine gland into the blood where they went everywhere and affected distant organs. The classic example were the sex hormones (estrogen, progesterone, testosterone) eleased by the gonads affecting the reproductive organs, and not least the brain.

Things have changed mightily, and just about every tissue in the body does this now. There are at least 20 adipokines released by fat — examples are adiponectin, adipsin, and of course leptin. Muscle may be also getting into the act with irisin (although that is controversial). Other muscle produced hormones (myokines)  include atrial natriuretic peptide released by the heart and skeletal muscle releases at least 8 more.

There is even more stuff released into local tissue fluids which don’t get into the blood so they aren’t hormones. You can regard all neurotransmission this way. Paracrines are compounds which act only on cells close to them (because they don’t get into the blood). Examples include the huge class of prostaglandins and polypeptide growth factors such as the 22 member fibroblast growth factor family.

What to make of [ Cell vol. 166 pp. 424 – 435 ’16 ] which describes PM20D1 (Peptidase M20 Domain containing 1) which is secreted by fat cells. It’s an enzyme which builds compounds from substances already in the blood. The chemistry is simplicity itself — it takes a long chain fatty acid and an amino acid and forms the fatty acid amide — or an N-acyl amino acid.

What does the product do? It causes uncoupling of oxidative phosphorylation by mitochondria, so it just produces heat (something useful to an animal in the cold). Administration of N-acyl amino acids to mice increases energy expenditure and improves glucose metabolism. It’s possible that they could be used therapeutically.

Another example of how little we knew about what is going on inside us.

You are alive because the lipid bilayer of your plasma membrane is asymmetric

You are an organism with trillions of cells. A mosquito bit you depositing millions of viruses in your tissues. The virus can reproduce only within one of your cells and it has exploited all sorts of protein protein chemistry to get in. Antibodies (if you are fortunate enough to have them) can get rid of the extracellular critters. However, 500,000 have made into the same number of your cells, and are merrily trying to reproduce.

How does the asymmetry of the lipid bilayer of your plasma membrane help you survive. If each virus infected cell killed itself before the virus reproduced, you’d survive. Although 500,000 is a large number is is less than 1 millionth of your cell total.

Well you do have intracellular defenses against viruses, called the innate immune system. One of them is a protein with the ugly name of gasdermin D. The activated innate immune system (in the form of inflammatory caspases) cleaves gasdermin. This breaks up the inhibition of the amino terminal part of gasdermin by the carboxy terminal part giving a fragment which binds to one particular membrane component (phosphatidyl serine) which makes up 20% of the inner leaflet of the cell membrane. It then forms a large diameter (to a cell 140 Angstroms is quite large) pore in the cell membrane. No cell can survive this, so it dies, releasing cellular contents (probably some viral components but not fully formed one). For details see [ Nature vol. 535 pp 111 – 116, 153 – 158 ’16 ]

Wait a minute. The toxic gasdermin fragment is also released. So how come it doesn’t kill everything in sight? Because our cellular membranes keep phosphatidyl serine confined to the inner membrane, normal cells don’t show it on their exterior, so they can be bathed in gasdermin with no ill effect. What is responsible for this asymmetry — believe it or not an ATP consuming enzyme called flippase (about this more later) which takes any phosphatidyl serine it finds on the outer leaflet and schleps it back inside the cell.

There is all sorts of elegant chemistry which explains just how gasdermin binds to phosphatidyl serine and none of the many other phospholipids found on the inner leaflet. There is more elegant chemistry explaining how flippase works (see later).

What chemistry cannot explain, is why organisms would ‘want’ an asymmetric membrane. As soon as you get into the function of a particular compound in an organism, chemistry is powerless to tell you why. Nothing else can explain how a given molecule does what it does on the molecular level but that is not enough for a satisfying explanation.

One further explanation before some hard core cellular biochemistry follows (after ***). Our cells are dying all the time. The lining of your gut is replaced every 5 days. Even the longest lasting element of your blood is gone after half a year, and most other elements are turned over at least once a month. When these cells die, they must be cleaned up, without undue fuss (such as inflammation). The cleaners are cells called macrophages. A dying cell releases chemical signals, actually called ‘eat me’, one of which is phosphatidyl serine found on the membrane fragments of a dead cell. The fact that flippases keep it on the inner leaflet means that macrophages won’t attack a normal cell.

Slick isn’t it?

***

Flippase is a MgATPdependent aminophospholipid translocase. It localizes phosphatidylserine and phosphatidylethanolamine to the inner membrane leaflet by rapidly translocating them from the outer to the inner leaflet against an electrochemical gradient. The stoichiometry between amino phospholipid translocation and ATP hydrolysis is close to one (how will the cell have enough ATP to do anything else?). The flippase is inhibited by high calcium, and by pseudosubstrates such as vanadate, acetylphosphate and para-nitrophenyl phosphate, and by SH reactive reagents such as N-ethylmaleimide and pyridyldithioethylamine (PDA) a specific inhibitor of phospholipid translocation

[ Proc. Natl. Acad. Sci. vol. 109 pp. 1449 – 1454 ’12 ] P4-ATPases are a subfamily of P-type ATPases. They transport aminophospholipids from the exoplasmic to the cytoplasmic leaflet (and are known as flippases). Man has 14 P4-ATPases, expressed in various cell types. They are thought to be similar to the catalytic subunits of the Ca++ ATPase, and the Na, K ATPase, consisting of cytoplasmic, N, P and A domains and a membrane domain made of 10 transmembrane helices (M1 – M10).

[ Proc. Natl. Acad. Sci. vol. 111 pp. E1334 – E1343 ’14 ] The P4-ATPases are thought to resemble the classic P-type ATPase cation pumps — a transmembrane domain of 10 helices and 3 cytoplasmic domains (P for phosphorylation, N for nucleotide binding and A for actuator). ATP8A2 forms an intermediate phosphorylated on aspartic acid (E2P)and undergoes a catalytic cycle similar to the sodium pump (Na+, K+ ATPase). Dephosphorylation of E2P is activated by the transported substrates phosphatidyl serine (PS) and phosphatidyl ethanolamine (PE), similar to the K+ activation of dephosphorylation in the sodium pump.

PE and PS are 10x as large as the cations transported by the sodium pump. This is known as the giant substrate problem. This work shows that isoleucine #364 (mutated in — patients with the ataxia, retardation and dysequilibrium syndrome Eur. J. Hum. Genet. vol. 21 pp. 281 – 285 ’13 aka CAMRQ syndrome ) forms a hydrophobic gate separating the entry and exit sites of PS. I364 likely directs the sequential formation and annihilation of water filled cavities (as shown by molecular dynamics simulations) allowing transport of the hydrophilic phospholipid head group, in a groove outlined by TMs 1, 2, 4 and 6, with the hydrocarbon chains following passively, still in the membrane lipid phase (and presumably outside the channel) — this must disrupt the hell out of the protein as it passes. They call this the credit card model — only the interaction with part of the molecule is important — just as the magnetic stripe is the only important thing about the credit card.

Another fail safe mechanism used by the cell — readthrough

Nothing is perfect in this world, not even the translation of mRNA into protein. The error rate is one amino acid misincorporated into a protein for every 10,000 or so done correctly — but these results are for one celled organisms (E. Coli, yeast). I can’t find a number for mammals, primates etc. etc.

This means that occasionally one of the 3 codons which tell the ribosome to quit (stop codons), will be misread as an amino acid. This is called readthrough, and means that the ribosome will merrily march on producing a much larger protein than coded for by the mRNA until one of two things happens. l. the ribosome reaches the end of the mRNA and stops. 2. the mRNA contains another stop codon (there are 3). The probability of this is 3/64 per codon. If stop codons are randomly distributed (which they are most certainly not in the protein coding segment of an mRNA) the chances of 100 codons in a row not containing a stop codon is under 1% (.822 % to be exact). So any protein containing more than 100 amino acids is a statistical freak in this sense. Since the 3′ untranslated region (3’UTR) of mRNA doesn’t code for protein, they should have stop codons randomly distributed (there being no selective pressure to keep them away).

Enter Nature vol. 534 pp. 719 – 723 ’16 — if you attach a 3′ UTR section of an mRNA to a normal protein sequence (mimicking readthrough) you get much less protein. The authors think the 3’UTRs code for peptide sequences destabilizing the attached protein. They don’t know what this might be, so it’s terra incognita for researchers, and a worthwhile PhD project to figure it out. Another example of ‘coding’ by a presumably nonCoding sequence in the genome. It may also tell us something about protein structure.

You gotta love this structure

Science vol. 352 pp. 1555 – 1559 has a structure you have to love. It is a molecular knot containing a mere 30 pyridines and 10 benzenes all tied together in a knot which looks like a five pointed star. The tying was done by metathesis of benzenes with CH2 CH2 CH = CH2 dangling from them. To think of what needed to be tied to what was extremely clever.

Surprisingly with all this going on the knot coordinates just a single halogen atom. This shows why you must build a model of a complicated organic compound to see what it really looks like, something I learned with adamantane years ago — you can draw all the chairs you want, making it look rather spiky, but the damn thing is actually spherical. Well, no model was built, but the structure was determined using Xray crystallography (figure 3) Anyone playing with tinkertoys back in the day (or Legos now) and loving it will have a natural affinity for organic chemistry

Why you do and don’t need chemistry to understand why we have big brains

You need some serious molecular biological chops to understand why primates such as ourselves have large brains. For this you need organic chemistry. Or do you? Yes and no. Yes to understand how the players are built and how they interact. No because it can be explained without any chemistry at all. In fact, the mechanism is even clearer that way.

It’s an exercise in pure logic. David Hilbert, one of the major mathematicians at the dawn of the 20th century famously said about geometry — “One must be able to say at all times–instead of points, straight lines, and planes–tables, chairs, and beer mugs”. The relationships between the objects of geometry were far more crucial to him than the objects themselves. We’ll take the same tack here.

So instead of the nucleotides Uridine (U), Adenine (A), Guanine (G), Cytosine (C), we’re going to talk about lock and key and hook and eye.

We’re going to talk about long chains of these four items. The order is crucial Two long chains of them can pair up only only if there are segments on each where the locks on one pair with the keys on the other and the hooks with the eyes. How many possible combinations of the four are there on a chain of 20 — just 4^20 or 2^40 = 1,099,511,621,776. So to get two randomly chosen chains to pair up exactly is pretty unlikely, unless in some way you or the blind Watchmaker chose them to do so.

Now you need a Turing machine to take a long string of these 4 items and turn it into a protein. In the case of the crucial Notch protein the string of locks, keys, hooks and eyes contains at least 5,000 of them, and their order is important, just as the order of letters in a word is crucial for its meaning (consider united and untied).

The cell has tons of such Turing machines (called ribosomes) and lots of copies of strings coding for Notch (called Notch mRNAs).

The more Notch protein around in the developing brain, the more the proliferating precursors to neurons proliferate before differentiating into neurons, resulting in a bigger brain.

The Notch string doesn’t all code for protein, at one end is a stretch of locks, keys, hooks and eyes which bind other strings, which when bound cause the Notch string to be degraded, mean less Notch and a smaller brain. The other strings are about 20 long and are called microRNAs.

So to get more Notch and a bigger brain, you need to decrease the number of microRNAs specifically binding to the Notch string. One particular microRNA (called miR-143-3p) has it in for the Notch string. So how did primates get rid of miR-143-3p they have an insert (unique to them) in another string which contains 16 binding sites for miR-143-3p. So this string called lincND essentially acts as a sponge for miR-143-3p meaning it can’t get to the Notch string, meaning that neuronal precursor cells proliferate more, and primate brains get bigger.

So can you forget organic chemistry if you want to understand why we have big brains? In the above sense you can. Your understanding won’t be particularly rich, but it will be at a level where chemical explanation is powerless.

No amount of understanding of polyribonucleotide double helices will tell you why a particular choice out of the 1,099,511,621,776 possible strings of 20 will be important. Literally we have moved from physicality to the realm of pure ideas, crossing the Cartesian dichotomy in the process.

Here’s a copy of the original post with lots of chemistry in it and all the references you need to get the molecular biological chops you’ll need.

Why our brains are large: the elegance of its molecular biology

Primates have much larger brains in proportion to their body size than other mammals. Here’s why. The mechanism is incredibly elegant. Unfortunately, you must put a sizable chunk of recent molecular biology under your belt before you can comprehend it. Anyone can listen to Mozart without knowing how to read or write music. Not so here.

I doubt that anyone can start from ground zero and climb all the way up, but here is all the background you need to comprehend what follows. Start here — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/
and follow the links (there are 5 more articles).

Also you should be conversant with competitive endogenous RNA (ceRNA) — here’s a link — https://luysii.wordpress.com/2014/01/20/why-drug-discovery-is-so-hard-reason-24-is-the-3-untranslated-region-of-every-protein-a-cerna/

Also you should understand what microRNAs are — we’re still discovering all the things they do — here’s the background you need — https://luysii.wordpress.com/2015/03/22/why-drug-discovery-is-so-hard-reason-26-were-discovering-new-players-all-the-time/weith.

Still game?

Now we must delve into the embryology of the brain, something few chemists or nonbiological type scientists have dealt with.

You’ve probably heard of the term ‘water on the brain’. This refers to enlargement of the ventricular system, a series of cavities in all our brains. In the fetus, all nearly all our neurons are formed from cells called neuronal precursor cells (NPCs) lining the fetal ventricle. Once formed they migrate to their final positions.

Each NPC has two choices — Choice #1 –divide into two NPCs, or Choice #2 — divide into an NPC and a daughter cell which will divide no further, but which will mature, migrate and become an adult neuron. So to get a big brain make NPCs adopt choice #1.

This is essentially a choice between proliferation and maturation. It doesn’t take many doublings of a NPC to eventually make a lot of neurons. Naturally cancer biologists are very interested in the mechanism of this choice.

Well to make a long story short, there is a protein called NOTCH — vitally important in embryology and in cancer biology which, when present, causes NPCs to make choice #1. So to make a big brain keep Notch around.

Well we know that some microRNAs bind to the mRNA for NOTCH which helps speed its degradation, meaning less NOTCH protein. One such microRNA is called miR-143-3p.

We also know that the brain contains a lncRNA called lncND (ND for Neural Development). The incredible elegance is that there is a primate specific insert in lncND which contains 16 (yes 16) binding sites for miR-143-3p. So lncND acts as a sponge for miR-143-3p meaning it can’t bind to the mRNA for NOTCH, meaning that there is more NOTCH around. Is this elegant or what. Let’s hear it for the Blind Watchmaker, assuming you have the faith to believe in such things.

Fortunately lncND is confined to the brain, otherwise we’d all be dead of cancer.

Should you want to read about this, here’s the reference [ Neuron vol. 90 pp. 1141 – 1143, 1255 – 1262 ’16 ] where there’s a lot more.

Historically, this was one of the criticisms of the Star Wars Missile Defense — the Russians wouldn’t send over a few missles, they’d send hundreds which would act as sponges to our defense. Whether or not attempting to put Star Wars in place led to Russia’s demise is debatable, but a society where it was a crime to own a copying machine, could never compete technically to produce such a thing.