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.


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.



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).

The butterfly effect in embryology

How the snake lost its legs. No, this isn’t a Just So story a la Rudyard Kipling, but a fascinating paper in Cell (vol. 167 pp. 598 – 600, 633 – 642 ’16 ). All it takes is a 17 nucleotide deletion in ZRS (Zone of polarizing activity Regulatory Sequence), an enhancer of gene expression involved in limb development. The enhancer is at least 1,300 nucleotides long (but I can’t find out just how long ZRS is). The deletion removes a binding site for a transcription factor (ETS) which turns on some limb development genes.

ZRS has long been known to be involved in limb development, and mutations distributed over 700 nucleotides are associated with a variety of human limb malformations. So the authors sequenced the enhancer in a variety of species (including many snakes) and found that only snakes had the deletion.

Then they put the snake ZRS into genetically engineered transgenic mice and found markedly shortened limbs. That was all it took. Reintroducing the missing 17 nucleotides into the transgenics restores normal limb development. Staggering what genetic technology is capable of.

Where does the butterfly effect come in? Because the enhancer is 1,000,000 nucleotides away from some of the genes it controls. If you were studying sequences around the genes it controls, you’d never find the deletion (until you’d run through a large number of grad students). Human biology (with limb malformations) told the authors where to look.

Straightened out 1,000,000 nucleotides is 3,200,000 Angstroms,or 320 microns (32 times the size of the average 10 micron nucleus). Remarkable how it finds its target. You might be interested in a series of posts which try to imagine these goings on at human scale — blowing up the nucleus so it fits in a football stadium with our double stranded DNA blown up to the size of linguini with a total total length of 2840 miles. Start here –

Two disconcerting papers

We all know that mutations cause cancer and that MRI lesions cause disability in multiple sclerosis. We do, don’t we? Maybe we don’t, say two papers out this October.

First: cancer. The number of mutations in stem cells from 3 organs (liver, colon, small intestine) was determined in biopsy samples from 19 people ranging in age 3 to 87 [ Nature vol. 538 pp. 260 – 264 ’16 ].th How did they get stem cells? An in vitro system was sued to expand single stem cells into epithelial organoids, and then the whole genome was sequenced of each. Some 45 organoids were used. Some 79,790 heterozygous clonal mutations were found. They then plotted the number of mutations vs. the age of the patient. When you have a spread in patient ages (which they did) you can calculate a tissue mutation rate for its stem cells. What is remarkable, is that all 3 tissues had the same mutation rate — about 40 mutations per year. Not bad. That’s only 4,000 if you live to 100 in your 3.2 BILLION nucleotide genome.

This is so  remarkable because the incidence of cancer is wildly different in the 3 tissues, so if mutations occurring randomly cause cancer, all 3 tissues should have the same cancer incidence (and there is much less liver cancer than gut cancer).

Of course there’s a hooker. The numbers are quite small, only 9 organoids from liver with a relatively small age range spanning only 25 years. There were more organoids from colon and small and the age ranges was wider but, clearly, the work needs o be replicated with a lot more samples. However, a look at figure one shows that the slope of the plot of mutation number vs. age is quite similar.

Second: Multiple sclerosis. First, some ancient history. I started in neurology before there were CAT scans and MRIs. All we had to evaluate the MS patient was the neurologic exam. So we’d see if new neurologic signs had developed, or the old ones worsened. There were all sorts of clinical staging scores and indices. Not terribly objective, but at least they measured function which is what physician and patient cared about the most.

The MRI revolutionized both diagnosis and our understanding of MS. We quickly found that even when the exam remained constant, that new lesions appeared and disappeared on the MRI totally silent to both patient and physician. I used to say that prior to MRI neurologists managed patients the way a hematologist would manage leukemics without blood counts, by looking at them to see how pale they were.

In general the more lesions that remained fixed, the worse shape the patient was in. So new drugs against MS could easily be evaluated without waiting years for the clinical exam to change, if a given drug just stopped lesions from appearing — stability was assumed to ensue (or at least it was when I retired almost exactly 4 presidential elections ago).

Enter Laquinimod [ Proc. Natl. Acad. Sci. vol. 113 pp. E6145 – E6152 ’16 ] which has a much greater beneficial effect on disability progression (e.g. less) than it does on clinical relapse rate (also less) and lesion appearance rate on MRI (also less). So again there is a dissociation between the MRI findings and the patient’s clinical status. Here are references to relevant papers — which I’ve not read —
Comi G, et al.; ALLEGRO Study Group (2012) Placebo-controlled trial of oral laquini- mod for multiple sclerosis. N Engl J Med 366(11):1000–1009.

Filippi M, et al.; ALLEGRO Study Group (2014) Placebo-controlled trial of oral laqui- nimod in multiple sclerosis: MRI evidence of an effect on brain tissue damage. J Neurol Neurosurg Psychiatry 85(8):851–858.

Vollmer TL, et al.; BRAVO Study Group (2014) A randomized placebo-controlled phase III trial of oral laquinimod for multiple sclerosis. J Neurol 261(4):773–783.

It is well known that there are different kinds of lesions in MS (some destroying axons, others just stripping off their myelin). Since I’ve left the field, I don’t know if MRI can distinguish the two types, and whether this was looked at.

The disconcerting thing about this paper, is that we may have given up on drugs which would  clinically help patients (rather than a biological marker) because they didn’t help the MRI ! ! !

Book Review — The Kingdom of Speech — Part III

The last half of Wolfe’s book is concerned with Chomsky and Linguistics. Neurologists still think they have something to say about how the brain produces language, something roundly ignored by the professional linguistics field. Almost at the beginning of the specialty, various types of loss of speech (aphasias) were catalogued and correlated with where in the brain the problem was. Some people could understand but not speak (motor aphasia). Most turned out to have lesions in the left frontal lobe. Others could speak but not understand what was said to them (receptive aphasia). They usually had lesions in the left temporal lobe (e.g. just behind the ear amazingly enough).

Back in the day this approach was justifiably criticized as follows — yes you can turn off a lightbulb by flicking a switch, but the switch isn’t producing the light, but is just something necessary for its production. Nowadays not so much, because we see these areas lighting up with increased blood  flow (by functional MRI) when speech is produced or listened to.

I first met Chomsky’s ideas, not about linguistics, but when I was trying to understand how a compiler of a high level computer language worked. This was so long ago that Basic and Pascal were considered high level languages. Compilers worked with formal rules, and Chomsky categorized them into a hierarchy which you can read about here —

The book describes the rise of Chomsky as the enfant terrible, the adult terrible, then the eminence grise of linguistics. Wolfe has great fun skewering him, particularly for his left wing posturing (something he did at length in “Radical Chic”). I think most of the description is accurate, but if you have the time and the interest, there’s a much better book — “The Linguistics Wars” by Randy Allen Harris — although it’s old (1993), Chomsky and linguistics had enough history even then that the book contains 356 pages (including index).

Chomsky actually did use the term language organ meaning a facility of the human brain responsible for our production of language of speech. Neuroscience never uses such a term, and Chomsky never tried to localize it in the brain, but work on the aphasias made this at least plausible. If you’ve never heard of ‘universal grammar, language acquisition device, deep structure of language, the book is a reasonably accurate (and very snarky) introduction.

As the years passed, for everything that Chomsky claimed was a universal of all languages, a language was found that didn’t have it. The last universal left standing was recursion (e.g. the ability the pack phrase within phrase — the example given “He assumed that now that her bulbs had burned out, he could shine and achieve the celebrity he had always longed for” — thought within thought within thought.

Then a missionary turned linguist (Daniel Everett) found a tribe in the Amazon (the Piraha) with a language which not only lacked recursion, but tenses as well. It makes fascinating reading, including the linguist W. Tecumseh Fitch (yes Tecumseh) who travelled up the Amazon to prove that they did have recursion (especially as he had collaborated with Chomsky and the (now disgraced) Marc Hauser on an article in 2002 saying that recursion was the true essence of human language — how’s this horrible sentence for recursion ?

The book ends with a discussion of the quote Wolfe began the book with — “Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved. We show that, to date, (1) studies of nonhuman animals provide virtually no relevant parallels to human linguistic communication, and none to the underlying biological capacity; (2) the fossil and archaeological evidence does not inform our understanding of the computations and representations of our earliest ancestors, leaving details of origins and selective pressure unresolved; (3) our understanding of the genetics of language is so impoverished that there is little hope of connecting genes to linguistic processes any time soon; (4) all modeling attempts have made unfounded assumptions, and have provided no empirical tests, thus leaving any insights into language’s origins unverifiable. Based on the current state of evidence, we submit that the most fundamental questions about the origins and evolution of our linguistic capacity remain as mysterious as ever, with considerable uncertainty about the discovery of either relevant or conclusive evidence that can adjudicate among the many open hypotheses. We conclude by presenting some suggestions about possible paths forward.”

One of the authors is Chomsky himself.

You can read the whole article at

I think, that Wolfe is right — language is just a tool (like the wheel or the axe) which humans developed to help them. That our brain size is at least 3 times the size of our nearest evolutionary cousin (the Chimpanzee) probably had something to do with it. If language is a tool, then, like the axe, it didn’t have to evolve from anything.

All in all a fascinating and enjoyable book. There’s much more in it than I’ve had time to cover.  The prose will pick you up and carry you along.

Book Review — The Kingdom of Speech — Part II

Although Darwin held off writing up his ideas for 20 years, fearing the reaction he knew would come from the church, the criticisms that really bothered him the most were those of fellow intellectuals about the evolution of language. They began immediately after the Origin of Species came out in 1859, by linguists and later by Wallace himself. Even worse, one critic mocked him. The idea that language evolved from animal sounds was called the bow wow theory, or language arose from sounds that things made (the ding dong theory).

This is all detailed in pp. 54 – 87 of The Kingdom of Speech, about which I knew very little. If any real experts on the early history of evolutionary theory are out there and reading this and disagree, please post a comment. I am assuming that the facts as given by Wolfe are correct (I’ve already disagreed with him about his interpretation of some of them —

The real attack on Darwin’s ideas is that man’s mental capacities were so far above those of animals, that there was no missing link (particularly since there were lots or primates still around). By this critique man was so special, that a special act of creation (not evolution) was called for.  It’s theology getting in the back door, but of course this is essentially the claim of all theologies — special creation by a superior being(s).

In his later book “The Origin of Species and the Descent of Man” – 1871 (which I’ve not read), according to Wolfe Darwin made up all stories (many involving his beloved dog) to show the antecedents of all sorts of things in animal behavior — Darwin actually said that language originated with the songs birds sang during mating. Female protolanguage persists today in mothers cooing to their babies. Darwin spent a lot of time discussing his dog — how it recognized other dogs as a sign of intelligence. Religion came from the love of a dog for his master (Wolfe claims that Darwin said this in the book– I haven’t read the Descent of Man).

Darwin’s second book didn’t get much response. Postive reviews avoided his reasoning, and negative reviews said it was thin. In 1872 the Philological Society of London gave up on trying to find out the origin of language, and wouldn’t accept patpers about it. The Linguistic Society of Paris did this even earlier (1866).

Evolutionists basically stopped talking about language from 1872 to 1949.

As soon as Mendel’s work on genetics was discovered, evolution went into scientific eclipse. Here was something that wasn’t just armchair speculation about things happening in the remote past, something on which experiments could be done.
Mendel’s experiments with green peas took 9 years and involved 28,000 plants.

In a fascinating aside, Wolfe notes that Mendel actually sent his work to Darwin. Tragically it was found unread with its pages uncut in Darwin’s papers after his death. In all fairness to Darwin, he and his peers had no idea how heredity worked and there are parts in The Origin of Species in which Darwin appears to accept the inheritance of acquired characteristics (the blacksmith’s large muscles passed on to his son etc. etc.). I don’t think you can read the Origin without being impressed by the tremendous power of Darwin’s mind, and how much work he put in and how far he got with how little he had to go on.

Wolfe says Darwin’s ideas about the origin or language were mocked by Gould  one hundred years later (1972) as “Just So Stories”, fantastic bizarre explanations for why animals are the way they are — see I’m not so sure, the citation for this gives an article  Sociobiology which Gould and Lewontin (see later) relentlessly attacked. Gould himself saw what he wanted to see in his book “The Mismeasure of Man” — for details see —

As you can see,The Kingdom of Speech is full of all sorts of interesting stuff, and I’m not even halfway through talking about it.

Next up, linguistics, to include Noam  Chomsky and his admission that he doesn’t understand language or where it came from.

The energy of the future

Almost 60 years ago to the day, a group of Princeton freshman (including yours truly) were dazzled by a talk by Professor Lyman Spitzer, as he described the “Stellarator”, a machine designed to mimic the thermonuclear reaction of the sun. He said it would produce all the energy one could want using nothing more complicated than water (once it was broken down into hydrogen and oxygen). He described it as the ‘energy of the future’.

60 years later it still is.

An article in today’s Nature (vol. 537 pp. 14 – 15 ’16) describes the malfunction of the National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) founded by Spitzer himself. Apparently some component failed, and the machine will be taken offline for repairs. The machine was being upgraded to produce higher magnetic fields using new coils, and one of them failed.

Since a machine at MIT is being permanently shut down, this leaves US fusion physicists with just one functional machine for experiments.

Book Review — The Kingdom of Speech — Part I

If you’re interested in evolution, its history, English social and intellectual history, language, Chomsky and the origins of the journal Nature then Tom Wolfe’s “The Kingdom of Language” is the book for you. Fellow blogistas will be awed by the clarity and elegance of his writing, and how he easily carries the reader easily along. It’s very funny and sardonic as well. The review will be split into several parts because there’s so much in the book.

One caveat: I’ve made no attempt to check any of the historical statements in the book. Hopefully they are all true. If you think any of it is incorrect, please post a comment.

Although the book has a lot to say about language, it doesn’t get into this until nearly 1/3 of the way through. It starts with Alfred Russell Wallace in 1858 lying in a sickbed with Malaria in the Malay peninsula coming up with the idea of natural selection, survival of the fittest (his term) and the origin of species. He writes an essay of 20+ pages and sends it off to Darwin, in the hopes that Darwin will pass it to Sir Charles Lyell (who Wallace didn’t know) who might find it worthy enough to publish.

Darwin gets it in June and is floored. The ideas that he’s been working on since 1838 (in silence for fear of what the religious establishment will say) are all laid out by what was called a ‘flycatcher’, someone making their living by going off to the colonies and sending back exotica for British Gentleman back home.

Tom Wolfe has always been fascinated by social class and distinctions between them (about this much more in part II).

British Gentlemen were landed gentry, who inherited land and wealth (if not noble titles). Darwin’s history went back to Erasmus Earle who was an attorney for Cromwell in the mid 1600’s. He made so much money, that no one in the succeeding EIGHT generations had to work. Robert Darwin, Charles’s father) nonetheless did — he was an M. D. but was more a businessman. He also attained even more money by marrying Wedgewood’s daughter.

Fortunately Robert had lots of money, as Charles was something of a slacker. He started by studying medicine at Edinburgh, but dropped out. He then went to Christ’s College Cambridge to become a clergyman — he dropped this as well, graduating eventually from Cambridge without an honor to his man. So Robert paid to have Charles to on a 5 year voyage of exploration on the Beagle. On return, Robert bought Charles a amLL pied a terre in the country (Down House) with 8 – 9 servants. (Did you know any of this).

The idea of species change was not new. Erasmus Darwin (Darwin’s grandfather) in 1794 and Lamarck in 1800 thought present day species had evolved from earlier ones.

Lamarck’s rather blasphemous thinking was saved by his heroics in battle at age 17 (as a private). His unit was decimated, all officers killed, Lamarck took command somehow and held their position until reinforcements arrived.

There’s a lot in the book about how Darwin Lyell and Hooker screwed out of the priority of thinking of evolution and natural selection first. Here Wolfe gets things seriously wrong, while Wallace was first into print, his thinking lagged Darwin’s by 20 years. However, Darwin, not wishing to be attacked by the clergy kept things to himself, only telling Lyell about is in 1856.

Most of the readership is probably fully engaged with work, family career and doesn’t have time to actually read “The Origin of Species”. In retirement, I did,and the power of Darwin’s mind is simply staggering. He did so much with what little information he had. There was no clear idea of how heredity worked and at several points he’s a Lamarckian — inheritance of acquired characteristics. If you do have the time I suggest that you read the 1859 book chapter by chapter along with a very interesting book — Darwin’s Ghost by Steve Jones (published in 1999) which update’s Darwin’s book to contemporary thinking chapter by chapter.

Wolfe also gets evolution wrong, saying there is no evidence for it. E.g. no one has seen a species change, etc. etc.  Perhaps, but the biochemical evidence is incontrovertible for descent with modification, otherwise you couldn’t replace a vital yeast protein gene with the human homolog and have it work.

Do you know what the X club is? It was a group of 9 naturalists (including Thomas Huxley and Hooker) who met monthly to defend Darwin’s ideas. They also created the journal we know today as Nature.

This actually explains a lot of stuff there that I’ve read over the years — the correct interpretation of evolutionary doctrine receives a great deal of space — punctuated evolution, group selection, kin selection, what is the proper unit of selection etc. etc.

The attacks that bothered Darwin the most, were those about language. That’s the subject of the next part of the review.

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

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.”


Hillary’s health — you can see a lot by looking

Last night’s debates should put two suggestions about Hillary’s health to rest and gives some evidence for two others. First, she does not have Parkinson’s disease. Second, she does not have epilepsy. Third, her eye movements still show some residua from the stroke of December 2012. Fourth, she may have a mild proximal myopathy.

Now to elaborate.

Parkinson’s disease: Two great things happened in September 1970 — I finished my two years in the Air Force and L – DOPA was released for use in the USA. American neurologists had been reading about the great things it was doing for the disease in Europe for almost 10 years. So when I went back to complete the last two years of my residency, the chief put me in charge of the L – DOPA clinic he’d just set up. So until retirement in 2000, I treated lots of people with it.

As the chief said — Parkinson’s disease is a Yellow Cab disease. If you see a Yellow Cab on the street, you don’t write down the license number, go down to city hall and find that it was registered as a Yellow Cab. You look at it and say “that’s a Yellow Cab”.

Parkinsonians have a rather immobile face (masklike) — Hillary’s face is quite mobile. Their speech lacks the normal musicality of speech (prosody), Hillary’s speech has normal inflection. Parkinsonians have a slow, stiff gait with difficulty initiating it. Hillary has none of this. Finally there is no sign of any tremor.

Epilepsy: Videos of purported seizures are out and about on the internet, particularly one during an interview. I thought that the ones I saw looked rather edited, as though some individual frames had been deleted from the videos. Fortunately last night we had an opportunity to see for ourselves. Toward the end of the debate, she had another episode, during which she shook her head and her shoulders for a few seconds. This happened in real time, so we could run the video recording backwards and forwards. At no time did she appear to be out of contact, and she then continued on with what she was saying without pause. So it’s just something she voluntarily does. It isn’t epilepsy.

Eye movements: Recall that after the stroke in December 2012, Hillary had double vision and had to wear Fresnel lenses to correct it for a few weeks afterwards — pictures of her testifying in congress January 2013 show this. So last night there was a 90 minute opportunity to watch the way her eyes move. They aren’t quite normal – on looking to her left the right eye lags and doesn’t bury the white. Even though Trump was to her right, she turned her head rather than her eyes to look at him, so I only saw her look to her right on a few occasions, but when she did her eyes appeared to move together. No other residua of a brainstem stroke were present such as slurred speech (dysarthria), facial weakness, facial asymmetry.

Proximal muscle weakness: The internist referred to in a previous post noted the following:

“There were shots a month or so ago of her needing help to get up outdoor stairs and also needing a small step-stool to get up into a Secret Service Suburban. My wife and I hop in and out of a Yukon and do not need any step device (they are of comparable age). After a photo of her doing that was published, she started getting in and out of vehicles on the side away from cameras and was also switched to a taller van with a step mounted on the vehicle. In February, press was forbidden by her staff from filming her climbing the stairs to board her private jet.”

He wondered if she could have something like limb girdle dystrophy.

Well, such a dystrophy is certainly possible. Although Hillary  had no difficulty standing for 90 minutes, at the end, she appeared to waddle as she walked toward the moderator.. There wasn’t really enough time to definitely say that she waddled.  It’s worth carefully watching the way she walks in the future.

Why is waddling a sign of mild weakness of the muscles of the pelvic girdle? Believe it or not the buttocks are not a secondary sexual characteristic. The main buttock muscle (gluteus maximus) is so big because it has so much work to do.

Think about what you do when you take a step forward with your right foot. To remain stable, your entire upper body weight must  be strongly plastered to your left hip. You need a strong, large muscle to do this (the gluteus maximus). What happens if the muscle is weak? Your upper body would fall to the right. How would you prevent this? By throwing your upper body to the left, putting its center of gravity there, so it presses on the left hip with greater force. A similar thing happens when stepping forward with the left foot. The net effect is that you waddle, which is what Hillary appeared to do.

It’s worth watching her walk in the future.

Stamina: she was under 90 minutes of stress, and showed no sign of fatigue.

Now, hopefully, back to the science, with a very long (over 1,000 Angstroms) allosteric effect.

Trump’s health

Here is a link to an article containing the full text of the letter by Trump’s personal physician Harold Bornstein M. D. -=-

Trump’s lipids could be better (total 232) and he is currently taking a lipid lowering agent (a statin). Aside from this, his labs are good (perfect in fact). He does take care of himself, and has annual physicals.

It isn’t clear why he had a transthoracic echocardiogram 2 years ago. Otherwise aside from that every test performed is pretty standard for a man his age.

Despite being overweight his blood pressure is excellent (particularly for man his size).

The indications for low dose aspirin aren’t stated, but yours truly has taken much more for decades based on a reading of the literature while in practice showing that doses of two adult aspirin a day reduced the recurrence rate of stroke by 33%.

So his main health problem is weight and mildly elevated lipids (even on medication).

His BMI (Body Mass Index) is stated to be 29.5. So it’s time for you to calculate your own — don’t worry that BMI is usually based on weight in kilograms and height in meters — the following site lets you put in your weight in pounds, and your height in inches — To get started, calculate your own BMI– A 6 footer would have to weigh 222 pounds to be obese (BMI over 30).

So is Trump’s BMI of 29.5 bad? Overweight is defined as a BMI over 25. So is a BMI over 25 bad? Not if you’re interested in mortality (death) as opposed to morbidity (things like heart attack and stroke). It turns out that the BMI with the lowest mortality at 70 is over 25 — e.g. 26. e.g. in the overweight range as currently defined. I don’t think there are good statistics on overall morbidity vs. BMI (there probably is for heart attack and stroke separately).

Now it gets interesting. That statistic cited above is based on the following data on 3 million people in 97 different studies [ J. Am. Med. Assoc. vol. 309 pp. 71 – 82 ’13 ].

At 6 feet 1+ (which I used to be) a weight of 190 puts me at 24.69. To be obese (BMI over 30) I’d need to weigh 228 (which I almost did 54 years ago).

When you plot BMI vs. probability of death you get a U shaped cure, with the very thin and the very fat showing increased risk of dying (mortality). The paper is interesting as it shows 6 curves for people at ages 20, 30, 40, 50, 60, 70. As one might expect, the curves for each age lie below the next oldest. All of them rise with BMIs under 20 and over 30, so there’s no argument about whether obesity (BMI over 30) is bad for longevity.

Well, if the curve is U shaped, it has a minimum. The excitement comes in because the healthiest weight (the minimum) is a BMI of just over 25 for those in their 60s and around 26 for those in their 70s. Also in ALL 6 age groups the curve is pretty flat between 25 and 30, rising on either side of the range.

Naturally people who’ve invested their research careers in telling everyone to diet and that weight is bad, don’t like this, and a symposium involving 200 unhappy people convened 20 February at the Harvard School of Public Health is described, along with a lot of the back and forth between the authoress of the study (Flegel) and Willett of Harvard who didn’t like it one bit. The best comment IMHO is from Robert Eckel “We’re scientists. We pay attention to data, we don’t try to unexplain them.” Read the article, it’s well written and there’s a lot more.

One final point, which might explain why the minima of the curves shift to higher BMIs at older age — which the article didn’t contain. People lose height as they age, yet the BMI is quite sensitive to it (remember the denominator has height squared). The great thing about BMI is that it’s easily measured, and doesn’t rely on what people remember about their weight or their height. Well as a high school basketball player my height was 6′ 1”+, now (at age 78) it’s 6’0″. So even with constant weight my BMI goes up.

Well it’s time to do the calculation to see what a fairly common shrinkage from 73.5 inches to 72 would to to the BMI (at a constant weight). Surprisingly it is not trivial — (72/73.5) * (72/73.5) = .9596. So the divisor is 4% less meaning the BMI is 4% more, which is almost exactly what the low point on the curve does with each passing decade after 50 ! ! ! This might even be an original observation, and it would explain a lot.

Well, that’s the take of this neurologist on Trump’s health —’s pretty good. I’m going to pass this post on to the very smart internist (whose comments about Hillary you can read in — for his take, as there really isn’t anything in the history suggest a neurologic problem. Unlike Hillary, he hasn’t fainted twice in the past 4 years, and hasn’t had a neurologic deficit persisting for a month.