Category Archives: Molecular Biology

Cultural appropriation, neuroscience division

If Deng Xiaoping can have Socialism with Chinese Characteristics, I can have a Chinese saying with neuroscientific characteristics — “The axon and the dendrite are long and the nucleus is far away” mimicking “The mountains are high and the Emperor is far away”. The professionally offended will react to the latest offense du jour — cultural appropriation  — of course.  But I’m entitled and I spoke to my Chinese daughter in law, and people over there found it flattering and admiring of Chinese culture that the girl in Utah wore a Chinese cheongsam dress to her prom.

Back to the quote.  “The axon and the dendrite are long and the nucleus is far away”.  Well, neuronal ends are far away from the cell body — the best example are axons from the sacral spinal cord which in an NBA player can be a yard long.  But forget that, lets talk about the ends of dendrites which are much closer to the cell body than that.

Presumably neurons have different types of dendrites so they can respond to different types of inputs. Why should dendrites respond identically if their inputs are different? They don’t.    A dendrite responding to acetyl choline will express neurotransmitter receptors distinct from another dendrite on the same neuron distinct from a dendrite responding to dopamine.  The protein cohorts of axons and dendrites are different.  How does this come about?  Because the untranslated part of mRNA on the 3′ end (3’UTR) contains a sequence called a zipcode which binds to specific proteins which then move the mRNA to a specific location in the neuron (axon or dendrite).  Presumably all dendrites initially had the same complement of mRNA.

So depending on what’s happening at a particular dendrite on a neuron, more or less of a given protein is made.   This is way too abstract.  Suppose you want to strengthen a synapse.  You’d make more of a neurotransmitter receptor or an ion channel for whatever transmitter that dendrite is getting.

It is well established that axons and dendrites store mRNAs and make proteins from them far from the nucleus (aka the emperor).  If you think about it, just how a receptor for dopamine gets to a dendrite receiving dopamine and not to a dendrite (on the same neuron) getting glutamic acid as a transmitter, is far from clear.  There are zipcodes distinguishing axons from dendrites, but I’m unaware that there are zipcodes for dopamine dendrites distinct from other types of dendrites.

If that weren’t enough consider [ Neuron vol. 98 pp. 495 – 511 ’18 ].  Even for an mRNA coding for the same protein (presumably transcribed from just one gene), there can be more than one type of 3’UTR (and this in the same cell).  Note also that 3’UTRs are longer in neurons than in other tissues.

So the authors looked at the mRNAs in dendrites — they did this by choosing a tissue (the hippocampus) where rows of cell bodies are well separated from their dendrites.  They found that for a given dendritic mRNA there was more than one 3’UTR, and that the mRNAs with longer 3’UTRs had longer halflives.  Even more exquisitly neuronal activity altered the proportion of the different 3’UTR isoforms. The phenomenon is quite general — over 50% of all genes and over 70% of genes enriched in neurons showed multiple 3′ UTRs.

So there is a whole control system built into the dendritic system, and it varies with what is happening locally.

The emperor emits directives (mRNAs) but what happens locally is anyone’s guess

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Sad

Very sad — Nature vol. 557 p. 144 ’18 (10 May) “PNAS resignation On 1 May, Inder Verma, a cancer researcher at the Salk Institute for Biological Sciences in La Jolla, California, resigned as editor-in-chief of the journal Proceedings of the National Academy of Sciences. The move comes after the publication of an investigation by Science, in which several female researchers who were either at the institute or had ties to it between 1976 and 2016 allege that Verma harassed them. Verma, who served on powerful committees at the institute, vehemently denied the allegations in a statement to Nature. The Salk Institute suspended him on 21 April while it investigates the claims.”

Why sad?  Because my late Princeton classmate and good friend Nick Cozzarelli edited PNAS for 10 years.  He died far too soon at 68 of Burkitt’s lymphoma after doing great work on DNA gyrase.  From the Wiki about him ” In 1995, Cozzarelli was invited to become the editor-in-chief of the Proceedings of the National Academy of Sciences. He took the position because felt that the journal had great unrealized potential as a scientific publication.[3] During his tenure, he expanded the editorial board from 26 to more than 140 and created a second track to allow scientists to submit manuscripts directly.”

Nick was credited for strongly increasing the quality and influence of PNAS.  This was recognized by the journal in the form of the Cozzarelli prizes established a year after his death.  There are 6 chosen from the more than 3,200 research articles appearing in the journal each year, representing the six broadly defined classes under which the National Academy of Sciences is organized.

A social note:  Although Princeton University was the home of many bluebloods in the late 50s, this was not true of all.  Nick went through Princeton on scholarship (waiting on tables in commons etc. etc.).  He was the son of an immigrant shoemaker from Jersey City.  Hopefully Princeton is still doing this.

Addendum 10 May — a friend said  ”

Your blog post seems to be one big non sequitur.
I doubt that harassment victims are “sad” that their complaints are finally getting heard and acted on. The fact that Verma’s behavior was allowed to continue all these years reflects poorly on the Salk Institute, but I don’t see how it reflects poorly on PNAS, where he was simply an editor and has now resigned. Essentially, Verma received PNAS submissions while sitting at his desk (at the Salk Institute) and declared “yes” or “no.”  I don’t see how your late friend Nick’s PNAS legacy has been sullied by any of that. “
To which I replied

No it’s sad because of what Verma’s behavior (at Salk and likely as PNAS editor) would have meant to Nick (and how he loved PNAS), given the type of guy Nick was.  My late father (an attorney) and uncle (a judge) took things the same way when a lawyer got disbarred for some malfeasance or other, e.g. as a reflection on the institution of the legal profession.   They took it personally as a reflection on them.  Perhaps illogically, but that’s the way they and Nick were. “

How Badly are Thy Genomes, Oh Humanity — take II

With apologies to Numbers 24:5, “How goodly are thy tents, Oh Jacob” —  a recent paper shows how shockingly error ridden our genomes actually are [ Science vol. 360 pp. 327 – 331  ’18 ].  I’d written about this in 2012 (see the end), but technology has marched on.  Back then only the parts of the genome coding for protein (the exome) were sequenced.  The present work did whole genome sequencing (WGS) to a mean coverage of 40+ (e.g. they sequenced the other 98 percent of the genome).

The authors were studying families in which one or more children had autism spectrum disorder to find genome abnormalities which might have caused the ASD. They were looking for structural variants (SVs) by which they mean ” biallelic deletion, tandem duplications, inversions, four classes of complex SV, and four families of mobile element insertions”

Why?  Because studying proteins alone doesn’t tell you how they are controlled.  That’s in the DNA surrounding them.  Structural variants are more likely to affect control elements than the proteins themselves.

Showing how technology has marched on they determined the whole genomes of 9274 subjects from 2600 families affected by ASD.

The absolutely mindboggling point in the article is the following direct quote “An average of 3746 SVs were detected per individual”.  That’s simply incredible (assuming the above isn’t a misprint).

Here’s the older post

How Badly Are Thy Genomes, Oh Humanity

With apologies to Numbers 24:5, “How goodly are thy tents, Oh Jacob” —  a recent paper shows how shockingly error ridden our genomes actually are [ Science vol. 337 pp. 64 – 69 ’12 ].  The authors sequenced roughly three quarters of the genes coding for proteins in some 2,439 people — e.g. 15,585 protein coding genes.  This left 98% of the genome untouched, primarily because we really don’t know what it does or how it does it, despite the fact that it controls, when, where and how much of each protein is made.  So they basically looked at the bricks from which we are built (the proteins) and not the plans (the 98%).

The news is not very good.  The subjects came from two groups: 1,351 Europeans and 1,088 Africans (the latter, because genetic diversity is far higher among Africans as that’s where humanity arose, and where mutations have had the longest time to accumulate).

The news is not very good. First, some background.

Recall that each nucleotide is one of four possibilities (A, T, G, C), and that each 3 nucleotides therefore has 4^3 = 64 possibilities.  61/64 combinations code for amino acids which, since we have only 20 gives a certain redundancy of the famed genetic code.   The other 3 combinations code for no amino acid (usually) and tell the machinery making proteins to stop.  Although crucial to our existence, these are called nonsense codons.

The genetic code is therefore 3fold degenerate (on average).  However, some amino acids are coded for by just 1 combination of 3 nucleotides while others are coded by as many as 6.  So some single nucleotide variants (SNVs) leave the amino acid coded for the same (these are the synonymous SNVs), while others change the amino acid (nonSynonymous SNVs), and possibly protein function.

Ask some one with sickle cell anemia how much trouble just one nonSynonymous SNV can cause — it’s only 1 amino acid out of 147.  Even worse, ask someone with cystic fibrosis where just one of 1,480 amino acids is missing.

Here’s the bad news.  In the population as a whole, they found 500,000 single nucleotide variants (SNVs).  If you’re still not sure what is meant by this, the 5 articles in https://luysii.wordpress.com/category/molecular-biology-survival-guide/ should be all the background you need.

More than 400,000 of the variants were previously unknown.  Also more than 400,000 of them were found either in Africans or Europeans but not both.  If you divide 500,000 by 2,439 you get 205 variants per person.  However, SNVs are far more common than that, and each individual contains an average of 14,000.

Well, how many of the 500,000 or so SNVs they found are nonSynonymous? One would think about 1/3 statistically.  However, They found more than half 292,125/500,000 — nearly 60% — were nonSynonymous.

It get’s worse: 6,165 of the nonSynonymous variants are nonSense codons.  This means that the protein coded for by such a gene, terminates prematurely, meaning that it can terminate anywhere.  On average one would expect that half of these nonsense codons result in a protein of less than half the normal length.   This would very likely obliterate whatever function the protein had.

Obviously, they couldn’t test all 500,000 SNVs to see how they affected protein function (and we really only have a decent idea of what half our 20,000 or so proteins are doing).  They had to guess.  They came up with a figure of 2 – 4% of the 14,000 SNVs being functionally significant — That’s 280 – 560 significant mutations per individual.

Clearly, despite the horrible examples of cystic fibrosis and sickle cell anemia above, most of these can’t be doing very much, because these were normal people being studied.

There are all sorts of implications of this work.  One is the subject of a future post — how hard this diversity makes drug discovery.  Another reiterates the Tolstoy theme mentioned earlier about the genetic defects causing schizophrenia and autism — ““Happy families are all alike; every unhappy family is unhappy in its own way”.  Thus beginneth Anna Karenina.

For details please see https://luysii.wordpress.com/2010/04/25/tolstoy-was-right-about-hereditary-diseases-imagine-that/  and  https://luysii.wordpress.com/2010/07/29/tolstoy-rides-again-autism-spectrum-disorder/

A third is that this shows that the 1000 fold expansion of the human population has pretty much obviated much natural selection eliminating these variants.  I’ll leave it to the geneticists to figure out what this means for the eventual survival of the species, as these mutants continue to accumulate.

The paper is fascinating, and sure to change our conception of what a ‘normal’ genome actually is.  Nonetheless, all they did was follow Yogi Berra’s dictum — “You can observe a lot by watching.”   It certainly wasn’t creative or ingenious in any sense.  Sometimes grunt work like this wins the day.

In which we find the new tricks an old dog can do

We all know that the carboxy terminal glycine of ubiquitin forms an amide with with the epsilon amino group of lysine.  Like a double play in baseball, 3 enzymes are involved, which move ubiquitin to E1 (the shortstop) to E2 (the second baseman) to E3 (the first baseman).  We have over 600 E3 enzymes, 40 E2s and 9 E1s.

A new paper [ Nature vol. 556 pp. 381 – 385 ’18 ] describes an E3 enzyme (called MYCBP2 aka PHR1) with a different specificity — it forms esters between the carboxy terminal glycine of ubiquitin and the hydroxyl group of serine or threonine.  The authors speculate a bit, noting that there are a lot of hydroxyl groups around in the cell that aren’t on proteins — sugars and lipids come to mind.   Just how widespread this is and whether any of the other 600 E3’s have similar activity isn’t known.

So now we have yet another new (to us) player in the metabolic life of the cell. It is yet another post-translational protein modification.   The enzyme is found in neurons, making understanding the workings of the brain even harder.

Consensus isn’t what it used to be.

Technology marches on.  The influence of all 2^20 = 1,048,576 variants of 5 nucleotides on either side of two consensus sequences for transcription factor binding were (1) synthesized (2) had their dissociation constants (Kd’s) measured.  The consensus sequences were for two yeast transcription factors (Pho4 and Cbf1).  [ Proc.  Natl. Acad. Sci. vol. 115 pp. E3692 – E3702 ’18 ] .  The technique is called BET-seq (Binding Energy Topography by sequencing).

What do you think they found?

A ‘large fraction’ of the flanking mutations changed overall binding energies by as much as consensus site mutations.  The numbers aren’t huge (only 2.6 kiloCalories/mole).  However at 298 Kelvin 25 Centigrade 77 Fahrenheit (where RT = .6) every 1.36 kiloCalories/mole is worth a factor of 10 in the equilibrium constant.  So binding can vary by 100 fold even in this range.

The work may explain some ChIP data in which some strips of DNA are occupied despite the lack of a consensus site, with other regions containing consensus sites remaining unoccupied.  The authors make the interesting point that submaximal binding sites might be preferred to maximal ones because they’d be easier for the cell to control (notice the anthropomorphism of endowing the cell with consciousness, or natural selection with consciousness).  It is very easy to slide into teleological thinking in these matters.  Whether or not you like it is a matter of philosophical and/or theological taste.

Pity the poor computational chemist, trying to figure out binding energy to such accuracy with huge molecules like a transcriptional factors and long segments of DNA.

It is also interesting to think what “Molar” means with these monsters.  How much does a mole of hemoglobin weigh?  64 kiloGrams more or less.  It simply can’t be put into 1000 milliliters of water (which weighs 1 kiloGram).  A liter of water contains 1000/18 moles (55.6) moles of water.  So solubilizing 1 molecule of hemoglobin would certainly use more than 55 molecules of water.  Reality must intrude, but we blithely talk about concentration this way.  Does anyone out there know what the maximum achievable concentration of hemoglobin actually is?

A research idea yours for the taking

Why would the gene for a protein contain a part which could form amyloid (the major component of the senile plaque of Alzheimer’s disease) and another part to prevent its formation. Therein lies a research idea, requiring no grant money, and free for you to pursue since I’ll be 80 this month and have no academic affiliation.

Bri2 (aka Integral TransMembrane protein 2B — ITM2B) is such a protein.  It is described in [ Proc. Natl. Acad. Sci. vol. 115 pp. E2752 – E2761 ’18 ] http://www.pnas.org/content/pnas/115/12/E2752.full.pdf.

As a former neurologist I was interested in the paper because two different mutations in the stop codon for Bri2 cause 2 familial forms of Alzheimer’s disease  Familial British Dementia (FBD) and Familial Danish Dementia (FDD).   So the mutated protein is longer at the carboxy terminal end.  And it is the extra amino acids which form the amyloid.

Lots of our proteins form amyloid when mutated, mutations in transthyretin cause familial amyloidotic polyneuropathy.  Amylin (Islet Amyloid Polypeptide — IAPP) is one of the most proficient amyloid formers.  Yet amylin is a protein found in the beta cell of the pancreas which releases insulin (actually in the same secretory granule containing insulin).

This is where Bri2 is thought to come in. It is also found in the pancreas.   Bri2 contains a 100 amino acid motif called BRICHOS  in its 266 amino acids which acts as a chaperone to prevent IAPP from forming amyloid (as it does in the pancreas of 90% of type II diabetics).

Even more interesting is the fact that the BRICHOS domain is found in 300 human genes, grouped into 12 distinct protein families.

Do these proteins also have segments which can form amyloid?  Are they like the amyloid in Bri2, in segments of the gene which can only be expressed if a stop codon is read through.  Nothing in the cell is perfect and how often readthrough occurs at stop codons isn’t known completely, but work is being done — Nucleic Acids Res. 2014 Aug 18; 42(14): 8928–8938.

I find it remarkable that the cause and the cure of a disease is found in the same protein.

Here’s the research proposal for you.  Look at the other 300 human genes containing the BRICHOS motif (itself just a beta sheet with alpha helices on either side) and see how many have sequences which can form amyloid.  There should be programs which predict the likelihood of an amino acid sequence forming amyloid.

It’s very hard to avoid teleology when thinking about cellular biochemistry and physiology.  It’s back to Aristotle where everything has a purpose and a design.  Clearly BRICHOS is being used for something or evolution/nature/natural selection/the creator would have long ago gotten rid of it.  Things that aren’t used tend to disappear in evolutionary time — witness the blind fish living in caves in Mexico that have essentially lost their eyes. The BRICHOS domain clearly hasn’t disappeared being present in over 1% of our proteins.

Suppose that many of the BRICHOS containing proteins have potential amyloid segments.  That would imply (to me at least) that the amyloid isn’t just junk that causes disease, but something with a cellular function. Finding out just what the function is would occupy several research groups for a long time.   This is also where you come in.  It may not pan out, but pathbreaking research is always a gamble when it isn’t stamp collecting.

 

Homework assignment and answer

A few days ago I gave the following homework assignment for the ace protein chemist, and promised an answer.

Here’s the assignment

Homework assignment for the protein chemist

As an ace protein chemist you are asked to design two proteins, both intrinsically disordered which form a tight complex with a picoMolar dissociation constant.  To make the problem ‘easier’ there is no need for specific amino acid interactions between the proteins.  To make the problem harder, even in the tight complex formed, the two proteins remain intrinsically disordered.

Hint: ‘nature’, ‘evolution’, ‘God’ —  whatever you chose to call it, has solved the problem.

Here’s the answer

The structure of an unstructured protein

Protein structure without structure.  No I haven’t fallen under the spell of a Zen master.  As Bill Clinton would say, it depends on what you mean by structure.

If you mean a segment of the protein chain which doesn’t settle down into one structure, you are talking about intrinsically disordered proteins. It is estimated that 40% of all human proteins contain at least one intrinsically disordered segment of 30 amino acids or more ( Nature vol. 471 pp. 151 – 153 ’11 ).   The same paper ‘estimates’ that 25% of all human proteins are likely to be disordered from beginning to end.

Frankly, I’ve always been amazed that any protein settles down into one shape — for details please see — https://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/. But that’s ‘old news’ as another Clinton would say.

Two fascinating papers in the current Nature (vol. 555 pp. 37 – 38, 61 – 66 ’18 1 March) describe the interaction of two very unstructured proteins.  One is prothymosin-alpha with 111 amino acids and a net negative charge of -44.  The other is Histone H1 with at least 189 amino acids and a net positive charge of + 53.  With such a charge imbalance it’s unlikely that they can coalesce into a compact single form.  So they are both intrinsically disordered proteins.

However the two proteins bind to each other quite tightly (dissociation constant is in the picoMolar range).  Even when they form a complex, a variety of techniques (NMR, single molecule fluorescent techniques, computation) show that neither settles down into a single form and are still unstructured.

So where’s the structure?  It isn’t in the amino acid sequence.  It isn’t the conformations adopted in space.  The structure is  in the net charge.  Many intrinsically disordered proteins have levels of net charge similar to those of prothymosin alpha and histone H1.  In the human proteome alone, several hundred proteins that are predicted to be intrinsically disordered contain contiguous stretches of at least 50 residues with a fractional net charge similar to that of H1 or proThymosin alpha (Bioinformatics 21, 3433–3434 2005) — hopefully there’s something newer.

The amino-acid sequences of disordered regions in proteins evolve rapidly, yet (Proc. Natl. Acad. Sci vol. 114 pp. E1450–E1459 2017) showed that the net charge is conserved despite a high degree of sequence diversity .  This should be a current enough reference.

Why in the world would the cell have something like this?  Most readers probably know what histones are.  If so, stop and think how the binding of the two proteins could be used by the cell before reading what the authors say about it.

“The interaction mechanism of proThymosin alpha and Histone H1 probably aids their biological function.  proThymosin alpha assists with the assembly and disassembly of chromatin, the material in which DNA is packaged with histone proteins (such as H1) in cells. To perform its function, proThymosin alpha must recognize its histone substrates rapidly and with sufficient affinity to compete with the high affinity of histone–DNA interactions (a similar high positive charge high negative charge interaction). The high binding affinity of Pro-Tα for H1 and the association rate of the two pro-teins imply that the dissociation of proThymosin alpha–H1 complexes is slow enough to allow functional outcomes, but fast enough not to slow down biological turnover.”

Why don’t they form a coacervate — a bunch of molecules held together by hydrophobic forces? Why don’t they show liquid liquid phase separations? The authors speculate that it might be due to the complementarity of the two proteins in terms of effective length and opposite net charge. Also they don’t have hydrophobic and aromatic side chains and cation pi interations which are said to favor phase separation mediated by proteins.

Addendum 20 March’18 — from my comment and a response on Derek’s blog

Luysii:

Another way to look at these very charge imbalanced proteins, is that they are being strongly (and positively) selected for. They are incredibly improbable on a purely statistical basis. Prothymosin alpha has 111 amino acids of which 44 are negatively charged. There are 20 amino acids of which only 2 (glutamic acid and aspartic acid) have negative charges at physiologic pH — cysteine and tyrosine can form anions but under much more basic conditions. So, assuming a random assortment of amino acids, the idea that 10% of the amino acids could fight for space with 90% of the rest and win around 40% of the time in 111 battles is extremely improbable. You’d have to use Stirling’s approximation for factorials to figure out exactly how improbable this is. Any takers?

Reply
DCRogers says:
March 20, 2018 at 2:35 pm
CDF(N=111, X=44, p=0.1) = 1.87 * 10^-16

Homework assignment for the protein chemist

As an ace protein chemist you are asked to design two proteins, both intrinsically disordered which form a tight complex with a picoMolar dissociation constant.  To make the problem ‘easier’ there is no need for specific amino acid interactions between the proteins.  To make the problem harder, even in the tight complex formed, the two proteins remain intrinsically disordered.

Hint: ‘nature’, ‘evolution’, ‘God’ —  whatever you chose to call it, has solved the problem.

Answer in a few days.

The structure of an unstructured protein

Protein structure without structure.  No I haven’t fallen under the spell of a Zen master.  As Bill Clinton would say, it depends on what you mean by structure.

If you mean a segment of the protein chain which doesn’t settle down into one structure, you are talking about intrinsically disordered proteins. It is estimated that 40% of all human proteins contain at least one intrinsically disordered segment of 30 amino acids or more ( Nature vol. 471 pp. 151 – 153 ’11 ).   The same paper ‘estimates’ that 25% of all human proteins are likely to be disordered from beginning to end.

Frankly, I’ve always been amazed that any protein settles down into one shape — for details please see — https://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/. But that’s ‘old news’ as another Clinton would say.

Two fascinating papers in the current Nature (vol. 555 pp. 37 – 38, 61 – 66 ’18 1 March) describe the interaction of two very unstructured proteins.  One is prothymosin-alpha with 111 amino acids and a net negative charge of -44.  The other is Histone H1 with at least 189 amino acids and a net positive charge of + 53.  With such a charge imbalance it’s unlikely that they can coalesce into a compact single form.  So they are both intrinsically disordered proteins.

However the two proteins bind to each other quite tightly (dissociation constant is in the picoMolar range).  Even when they form a complex, a variety of techniques (NMR, single molecule fluorescent techniques, computation) show that neither settles down into a single form and are still unstructured.

So where’s the structure?  It isn’t in the amino acid sequence.  It isn’t the conformations adopted in space.  The structure is  in the net charge.  Many intrinsically disordered proteins have levels of net charge similar to those of prothymosin alpha and histone H1.  In the human proteome alone, several hundred proteins that are predicted to be intrinsically disordered contain contiguous stretches of at least 50 residues with a fractional net charge similar to that of H1 or proThymosin alpha (Bioinformatics 21, 3433–3434 2005) — hopefully there’s something newer.

The amino-acid sequences of disordered regions in proteins evolve rapidly, yet (Proc. Natl. Acad. Sci vol. 114 pp. E1450–E1459 2017) showed that the net charge is conserved despite a high degree of sequence diversity .  This should be a current enough reference.

Why in the world would the cell have something like this?  Most readers probably know what histones are.  If so, stop and think how the binding of the two proteins could be used by the cell before reading what the authors say about it.

“The interaction mechanism of proThymosin alpha and Histone H1 probably aids their biological function.  proThymosin alpha assists with the assembly and disassembly of chromatin, the material in which DNA is packaged with histone proteins (such as H1) in cells. To perform its function, proThymosin alpha must recognize its histone substrates rapidly and with sufficient affinity to compete with the high affinity of histone–DNA interactions (a similar high positive charge high negative charge interaction). The high binding affinity of Pro-Tα for H1 and the association rate of the two pro-teins imply that the dissociation of proThymosin alpha–H1 complexes is slow enough to allow functional outcomes, but fast enough not to slow down biological turnover.”

Why don’t they form a coacervate — a bunch of molecules held together by hydrophobic forces? Why don’t they show liquid liquid phase separations? The authors speculate that it might be due to the complementarity of the two proteins in terms of effective length and opposite net charge. Also they don’t have hydrophobic and aromatic side chains and cation pi interations which are said to favor phase separation mediated by proteins.

Old paradigms die hard

A statement in a recent Nature editorial [ vol. 554 pp. 308 – 309 ’18 ] had me thinking that a real paradigm shift in our understanding of cancer was under way, but in fact it was an out of date paradigm that tripped up the editorialist.  Since breast cancer is likely to affect us individually or someone we know, it’s worth looking at this paper.

Ductal Carcinoma In Situ (DCIS) of the breast, is breast cancer confined to one of the ducts in the breast bringing milk to the nipple.  If it stayed there forever it would be harmless, like a benign mole on the skin. Unfortunately ‘up to’ 40% of DCIS invades the lining of the duct and the soft tissue of the breast becoming Invasive Ductal Carcinoma (IDC) where it is not harmless at all.  There is currently no way to tell which DCIS will stay quiet so everyone gets treated.

A heroic paper in cell (vol. 172 pp, 205 – 217 ’18 ) used the highest of high technology to study the question.  First they used Laser Capture Microdissection to separate a selected cell from its neighbors by tracing a laser beam around the cell.  Then they used laser catapulting in which energy from an ultraviolet laser propels the microdissected cell into a collection tube.  Then they performed exon sequencing on the collected cells (e.g. they sequenced the parts of the gene coding for protein), comparing cells which were DCIS from IDCs.  Some 1,293 cells from 10 patients were studied.

There was an average of 23 mutations/patient.  “The transition from DCIS to IDC was not associated with a notable increase in the number of mutations.”  “The authors’ main finding is the remarkable genetic similarity of a patient’s tumor cells in these two distinct states”

Hello.

I thought mutations caused cancer and that the more you had the worse the cancer.  Not so in this paper. A paradigm shift indeed.

What’s wrong with this thinking?  Think a bit before reading further.

If you are old enough, you may remember statements that we were 98% chimps based on our genome (or at least what was known of it at the time).  This is because the sequence of the amino acids in our 20,000 or so proteins varies only by 2% from that of the chimp.

That proves it.  Except that it doesn’t.  Amazingly enough, the amount of all 3,200,000,000 positions of our genome coding for protein is under 2%.  So 98% of or genome does NOT code for protein.  It contains the code to determine when, for how long, and where each gene is made into messenger RNA which is then made into protein.

An analogy may help.

This is like saying Monticello and Independence Hall are just the same because they’re both made out of bricks. One could chemically identify Monticello bricks as coming from the Virginia piedmont, and Independence Hall bricks coming from the red clay of New Jersey, but the real difference between the buildings is the plan.

It’s not the proteins, but where and when and how much of them are made. The control for this (plan if you will) lies outside the genes for the proteins themselves, in the rest of the genome (remember only 2% of the genome codes for the amino acids making up our 20,000 or so protein genes). The control elements have as much right to be called genes, as the parts of the genome coding for amino acids. Granted, it’s easier to study genes coding for proteins, because we’ve identified them and know so much about them. It’s like the drunk looking for his keys under the lamppost because that’s where the light is.

On this point it would be very worthwhile to look beyond the genes mutated in both sets of tumors, sequencing their promotors and enhancers.  I think it would likely show profound differences.

No further posts for a while.  We’re going to visit a new grandson, 3 days old, whose parents apparently lack the creativity to name him.