Category Archives: Chemistry (relatively pure)

Are Van der Waals interactions holding asteroids together?

A recent post of Derek’s concerned the very weak (high kD) but very important interactions of proteins within our cells. http://pipeline.corante.com/archives/2014/08/14/proteins_grazing_against_proteins.phpAr

Most of this interaction is due to Van der Waals forces — http://en.wikipedia.org/wiki/Van_der_Waals_force. Shape shape complementarity (e.g. steric factors) and dipole dipole interactions are also important.

Although important, Van der Waals interactions have always seemed like a lot of hand waving to me.

Well guess what, they are now hypothesized to be what is holding an asteroid together. Why are people interested in asteroids in the first place? [ Science vol. 338 p. 1521 '12 ] “Asteroids and comets .. reflect the original chemical makeup of the solar system when it formed roughly 4.5 billion years ago.”

[ Nature vol. 512 p. 118 '14 ] The Rosetta spacecraft reached the comet 67P/Churyumov-Gerasimenko after a 10 year journey becoming the first spacecraft to rendezvous with a comet. It will take a lap around the sun with the comet and will watch as the comet heats up and releases ice in a halo of gas and dust. It is now flying triangles in front of the comet, staying 100 kiloMeters away. In a few weeks it will settle into a 30 kiloMeter orbit around he comet. It will attempt to place a lander (Philae) the size of a washing machine on its surface in November. The comet is 4 kiloMeters long.

[ Nature vol. 512 pp. 139 - 140, 174 - 176 '14 ] A kiloMeter sized near Earth asteroid called (29075) 1950 DA (how did they get this name?) is covered with sandy regolith (heterogeneous material covering solid rock { on earth } it includes dust, soil, broken rock ). The asteroid rotates every 2+ hours, and it is so small that gravity alone can’t hold the regolith to its surface. An astronaut could scoop up a sample from its surface, but would have to hold on to the asteroid to avoid being flung off by the rotation. So the asteroid must have some degree of cohesive strength. The strength required is 64 pascals to hold the rubble together — about the pressure that a penny exerts on the palm of your hand. A Pascal is 1/101,325 of atmospheric pressure.

They think the strength comes from van der Waals interactions between small (1 – 10 micron) grains — making it fairy dust. It’s rather unsatisfying as no one has seen these particles.

The ultimate understanding of the large multi-protein and RNA machines (ribosome, spliceosome, RNA polymerase etc. etc. ) without which life would be impossible will involve the very weak interactions which hold them together. Along with permanent dipole dipole interactions, charge interactions and steric complementarity, the van der Waals interaction is high on anyone’s list.

Some include dipole dipole interactions as a type of van der Waals interaction. The really fascinating interaction is the London dispersion force. These are attractions seen between transient induced dipoles formed in the electron clouds surrounding each atomic nucleus.

It’s time to attempt the surmount the schizophrenia which comes from trying to see how quantum mechanics gives rise to the macroscopic interactions between molecules which our minds naturally bring to matters molecular (with a fair degree of success).

Steric interactions come to mind first — it’s clear that an electron cloud surrounding molecule 1 should repel another electron cloud surrounding molecule 2. Shape complementarity should allow two molecules to get closer to each other.

What about the London dispersion forces, which are where most of the van der Waals interaction is thought to be. We all know that quantum mechanical molecular orbitals are static distributions of electron probability. They don’t fluctuate (at least the ones I’ve read about). If something is ‘transiently inducing a dipole’ in a molecule, it must be changing the energy level of a molecule, somehow. All dipoles involve separation of charge, and this always requires energy. Where does it come from? The kinetic energy of the interacting molecules? Macroscopically it’s easy to see how a collision between two molecules could change the vibrational and/or rotation energy levels of a molecule. What does a collision between between molecules look like in terms of the wave functions of both. I’ve never seen this. It has to have been worked out for single particle physics in an accelerators, but that’s something I’ve never studied.

One molecule inducing a transient dipole in another, which then induces a complementary dipole in the first molecule, seems like a lot of handwaving to me. It also appears to be getting something for nothing contradicting the second law of thermodynamics.

Any thoughts from the physics mavens out there?

Old dog does new(ly discovered) tricks

One of the evolutionarily oldest enzyme classes is aaRS (for amino acyl tRNA synthetase). Every cell has them including bacteria. Life as we know it wouldn’t exist without them. Briefly they load tRNA with the appropriate amino acid. If this Greek to you, look at the first 3 articles in https://luysii.wordpress.com/category/molecular-biology-survival-guide/.

Amino acyl tRNA syntheses are enzymes of exquisite specificity, having to correctly match up 20 amino acids to some 61 different types of tRNAs. Mistakes in the selection of the correct amino acid occurs every 1/10,000 to 1/100,000, and in the selection of the correct tRNA every 1/1,000,000. The lower tRNA error rate is due to the fact that tRNAs are much larger than amino acids, and so more contacts between enzyme and tRNA are possible.

As the tree of life was ascended from bacteria over billions of years, 13 new protein domains which have no obvious association with aminoacylation have been added to AARS genes. More importantly, the additions have been maintained over the course of evolution (with no change in the primary function of the synthetase). Some of the new domains are appended to each of several synthetases, while others are specific to a single synthetase. The fact that they’ve been retained implies they are doing something that natural selection wants (teleology inevitably raises its ugly head with any serious discussion of molecular biology or cellular physiology — it’s impossible to avoid).

[ Science vol.345 pp 328 - 332 '14 ] looked at what mRNAs some 37 different AARS genes were transcribed into. Six different human tissues were studied this way. Amazingly, 79% of the 66 in-frame splice variants removed or disrupted the aaRS catalytic domain. . The AARS for histidine had 8 inframe splice variants all of which removed the catalytic domain. 60/70 variants losing the catalytic domain (they call these catalytic nulls) retained at least one of the 13 added domains in higher eukaryotes. Some of the transcripts were tissue specific (e.g. present in some of the 6 tissues but not all).

Recent work has shown roles for specific AARSs in a variety of pathways — blood vessel formation, inflammation, immune response, apoptosis, tumor formation, p53 signaling. The process of producing a completely different function for a molecule is called exaptation — to contrast it with adaptation.

Up to now, when a given protein was found to have enzymatic activity, the book on what that protein did was closed (with the exception of the small GTPases). End of story. Yet here we have cells spending the metabolic energy to make an enzymatically dead protein (aaRSs are big — the one for alanine has nearly 1,000 amino acids). Teleology screams — what is it used for? It must be used for something! This is exactly where chemistry is silent. It can explain the incredible selectivity and sensitivity of the enzyme but not what it is ‘for’. We have crossed the Cartesian dualism between flesh and spirit.

Could this sort of thing be the tip of the iceberg? We know that splice variants of many proteins are common. Could other enzymes whose function was essentially settled once substrates were found, be doing the same thing? We may have only 20,000 or so protein coding genes, but 40,000, 60,000, . . . or more protein products of them, each with a different biological function.

So aaRSs are very old molecular biological dogs, who’ve been doing new tricks all along. We just weren’t smart enough to see them (’till now).

Novels may have only 7 basic plots, but molecular biology continues to surprise and enthrall.

Keep on truckin’ Dr. Schleyer

My undergraduate advisor (Paul Schleyer) has a new paper out in the 15 July ’14 PNAS pp. 10067 – 10072 at age 84+. Bravo ! He upends what we were always taught about electrophilic aromatic addition of halogens. The Arenium ion is out (at least in this example). Anyone with a smattering of physical organic chemistry can easily follow his mechanistic arguments for a different mechanism.

However, I wonder if any but the hardiest computational chemistry jock can understand the following (which is how he got his results) and decide if the conclusions follow.

Our Gaussian 09 (54) computations used the 6-311+G(2d,2p) basis set (55, 56) with the B3LYP hybrid functional (57⇓–59) and the Perdew–Burke–Ernzerhof (PBE) functional (60, 61) augmented with Grimme et al.’s (62) density functional theory with added Grimme’s D3 dispersion corrections (DFT-D3). Single-point energies of all optimized structures were obtained with the B2-PLYP [double-hybrid density functional of Grimme (63)] and applying the D3 dispersion corrections.

This may be similar to what happened with functional MRI in neuroscience, where you never saw the raw data, just the end product of the manipulations on the data (e.g. how the matrix was inverted and what manipulations of the inverted matrix was required to produce the pretty pictures shown). At least here, you have the tools used laid out explicitly.

More chemical insanity from neuroscience

The current issue of PNAS contains a paper (vol. 111 pp. 8961 – 8966, 17 June ’14) which uncritically quotes some work done back in the 80’s and flatly states that synaptic vesicles http://en.wikipedia.org/wiki/Synaptic_vesicle have a pH of 5.2 – 5.7. Such a value is meaningless. Here’s why.

A pH of 5 means that there are 10^-5 Moles of H+ per liter or 6 x 10^18 actual ions/liter.

Synaptic vesicles have an ‘average diameter’ of 40 nanoMeters (400 Angstroms to the chemist). Most of them are nearly spherical. So each has a volume of

4/3 * pi * (20 * 10^-9)^3 = 33,510 * 10^-27 = 3.4 * 10^-23 liters. 20 rather than 40 because volume involves the radius.

So each vesicle contains 6 * 10^18 * 3.4 * 10^-23 = 20 * 10^-5 = .0002 ions.

This is similar to the chemical blunders on concentration in the nano domain committed by a Nobelist. For details please see — http://luysii.wordpress.com/2013/10/09/is-concentration-meaningful-in-a-nanodomain-a-nobel-is-no-guarantee-against-chemical-idiocy/

Didn’t these guys ever take Freshman Chemistry?

Addendum 24 June ’14

Didn’t I ever take it ? John wrote the following this AM

Please check the units in your volume calculation. With r = 10^-9 m, then V is in m^3, and m^3 is not equal to L. There’s 1000 L in a m^3.
Happy Anniversary by the way.

To which I responded

Ouch ! You’re correct of course. However even with the correction, the results come out to .2 free protons (or H30+) per vesicle, a result that still makes no chemical sense. There are many more protons in the vesicle, but they are buffered by the proteins and the transmitters contained within.

Why marihuana scares me

There’s an editorial in the current Science concerning how very little we know about the effects of marihuana on the developing adolescent brain [ Science vol. 344 p. 557 '14 ]. We know all sorts of wonderful neuropharmacology and neurophysiology about delta-9 tetrahydrocannabinol (d9-THC) — http://en.wikipedia.org/wiki/Tetrahydrocannabinol The point of the authors (the current head of the Amnerican Psychiatric Association, and the first director of the National (US) Institute of Drug Abuse), is that there are no significant studies of what happens to adolescent humans (as opposed to rodents) taking the stuff.

Marihuana would the first mind-alteraing substance NOT to have serious side effects in a subpopulation of people using the drug — or just about any drug in medical use for that matter.

Any organic chemist looking at the structure of d9-THC (see the link) has to be impressed with what a lipid it is — 21 carbons, only 1 hydroxyl group, and an ether moiety. Everything else is hydrogen. Like most neuroactive drugs produced by plants, it is quite potent. A joint has only 9 milliGrams, and smoking undoubtedly destroys some of it. Consider alcohol, another lipid soluble drug. A 12 ounce beer with 3.2% alcohol content has 12 * 28.3 *.032 10.8 grams of alcohol — molecular mass 62 grams — so the dose is 11/62 moles. To get drunk you need more than one beer. Compare that to a dose of .009/300 moles of d9-THC.

As we’ve found out — d9-THC is so potent because it binds to receptors for it. Unlike ethanol which can be a product of intermediary metabolism, there aren’t enzymes specifically devoted to breaking down d9-THC. In contrast, fatty acid amide hydrolase (FAAH) is devoted to breaking down anandamide, one of the endogenous compounds d9-THC is mimicking.

What really concerns me about this class of drugs, is how long they must hang around. Teaching neuropharmacology in the 70s and 80s was great fun. Every year a new receptor for neurotransmitters seemed to be found. In some cases mind benders bound to them (e.g. LSD and a serotonin receptor). In other cases the endogenous transmitters being mimicked by a plant substance were found (the endogenous opiates and their receptors). Years passed, but the receptor for d9-thc wasn’t found. The reason it wasn’t is exactly why I’m scared of the drug.

How were the various receptors for mind benders found? You throw a radioactively labelled drug (say morphine) at a brain homogenate, and purify what it is binding to. That’s how the opiate receptors etc. etc. were found. Why did it take so long to find the cannabinoid receptors? Because they bind strongly to all the fats in the brain being so incredibly lipid soluble. So the vast majority of stuff bound wasn’t protein at all, but fat. The brain has the highest percentage of fat of any organ in the body — 60%, unless you considered dispersed fatty tissue an organ (which it actually is from an endocrine point of view).

This has to mean that the stuff hangs around for a long time, without any specific enzymes to clear it.

It’s obvious to all that cognitive capacity changes from childhood to adult life. All sorts of studies with large numbers of people have done serial MRIs children and adolescents as the develop and age. Here are a few references to get you started [ Neuron vol. 72 pp. 873 - 884, 11, Proc. Natl. Acad. Sci. vol. 107 pp. 16988 - 16993 '10, vol. 111 pp. 6774 -= 6779 '14 ]. If you don’t know the answer, think about the change thickness of the cerebral cortex from age 9 to 20. Surprisingly, it get thinner, not thicker. The effect happens later in the association areas thought to be important in higher cognitive function, than the primary motor or sensory areas. Paradoxical isn’t it? Based on animal work this is thought to be due pruning of synapses.

So throw a long-lasting retrograde neurotransmitter mimic like d9-THC at the dynamically changing adolescent brain and hope for the best. That’s what the cited editorialists are concerned about. We simply don’t know and we should.

Having been in Cambridge when Leary was just getting started in the early 60’s, I must say that the idea of tune in turn on and drop out never appealed to me. Most of the heavy marihuana users I’ve known (and treated for other things) were happy, but rather vague and frankly rather dull.

Unfortunately as a neurologist, I had to evaluate physician colleagues who got in trouble with drugs (mostly with alcohol). One very intelligent polydrug user MD, put it to me this way — “The problem is that you like reality, and I don’t”.

Further (physical) chemical elegance

If the chemical name phosphatidyl serine (PS) draws a blank, read the verbatim copy of a previous post under the *** to find out why it is so important to our existence. It is an ‘eat me’ signal when there is lots of it around, telling professional scavenger cells to engulf the cell showing lots of PS on its surface.

Life, as usual, is more complicated. There are a variety of proteins exposed on cell surfaces which bind to phosphoserine. Not only that, but exposing just a little PS on the surface of a cell can trigger a protective immune response. Immune cells binding to just a little PS on the surface of another cell proliferate rather than eat the cell expressing the PS. This brings us to Proc. Natl. Acad. Sci. vol. 111 pp 5526 – 5531 ’14 that explains how a given PS receptor (called TIM4) acts differently depending how much PS is present.

Some PS receptors such as Annexin V have essentially an all or none response to PS, if they bind at all, they trigger a response in the cell carrying them. Not so for TIM4 which only reacts if there is a lot of PS around, leaving cells which express less PS alone. This allows these cells to function in the protective immune response.

So how does TIM4 do this? See if you can think of a mechanism before reading the rest.

In addition to the PS binding pocket TIM4 has 4 peripheral basic residues in separate places. The basic residues are positively charged at physiologic pH and bind to the negatively charged phosphate group of phosphatidyl serene or to the carboxylate anion of phosphatidyl serine. The paper doesn’t explain how these basic residues don’t bind to the other phospholipids of the cell surface (such as phosphatidyl choline or sphingomyelin). It is conceivable that the basic side chains (arginine, lysine etc.) are so set up that they only bind to carboxylate anions and not phosphate anions (but this is a stretch). That would at least give them specificity for phosphatidyl serene as opposed the other phospholipids present in both leaflets of the cell membrane. In any even TIM4 will be triggered only if these groups also bind PS, leaving cells which show relatively little PS alone. Clever no?

For the cognoscenti, the Hill coefficient of TIM4 is 2 while that of Annexin V is 8 (describing more than explaining the all or none character of Annexin V binding).

****
Flippase. Eat me signals. Dragging their tails behind them. Have cellular biologists and structural biochemists gone over to the dark side? It’s all quite innocuous as the old nursery rhyme will show

Little Bo Peep has lost her sheep
and doesn’t know where to find them
Leave them alone, and they’ll come home
wagging their tails behind them.

First, some cellular biochemistry. The lipid bilayer encasing all our cells is made of two leaflets, inner and outer. The composition of the two is different (unlike the soap bubble). On the inside we find phosphatidylethanolamine (PE), phosphatidylserine (PS). The outer leaflet contains phosphatidylcholine (PC) and sphingomyelin (SM) and almost no PE or PS. This is clearly a low entropy situation compared to having all 4 randomly dispersed between the 2 leaflets.

What is the possible use of this (notice how teleology invariably creeps into cellular biology)? Chemistry is powerless to explain such things. Much as I love chemistry, such truths must be faced.

It takes energy to maintain this peculiar distribution. The enzyme moving PE and PS back inside the cell is the flippase. It requires energy in the form of ATP to operate. When a cell is dying ATP drops, and entropy takes its course moving PE and PS to the cell surface. Specialized cells (macrophages) exist to scoop up the dying or dead cells, without causing inflammation. They recognize PE and PS by a variety of receptors and munch up cells exposing them on the surface. So PE and PS are eat me signals which appear when there isn’t enough ATP around for flippase to use to haul PE and PS back inside. Clever no?

No for some juicy chemistry (assuming that you consider transport of a molecule across a lipid bilayer actual chemistry — no covalent bonds to the transferred molecule are formed or removed, although they are to the transporter). Well it certainly is physical chemistry isn’t it?

Here are the structures of PE, PS, PC, SM http://www.google.com/search?q=phosphatidylserine&client=safari&rls=en&tbm=isch&tbo=u&source=univ&sa=X&ei=bDRLU5yfHOPLsQSOnoG4BA&ved=0CPABEIke&biw=1540&bih=887#facrc=_&imgdii=_&imgrc=qrLByG2vmhWdwM%253A%3BwAtgsTPwCxeZXM%3Bhttp%253A%252F%252Fscience.csumb.edu%252F~hkibak%252F241_web%252Fimg%252Fpng%252FCommon_Phospholipids.png%3Bhttp%253A%252F%252Fscience.csumb.edu%252F~hkibak%252F241_web%252Fcoursework_pages%252F2012_02_2.html%3B1297%3B934.

There are a few things to notice. Like just about every lipid found in our membranes, they are amphipathic — they have a very lipid soluble part (look at the long hydrocarbon changes hanging below them) and a very water soluble part — the head groups containing the phosphate.

This brings us to [ Proc. Natl. Acad. Sci. vol. 111 pp. E1334 - E1343 '14 ] Which describes ATP8A2 (aka the flippase). Interestingly, the protein, with at least 10 alpha helices spanning the membrane, and 3 cytoplasmic domains closely resembles the classic sodium pump beloved of neurophysioloogists everywhere, which pumps sodium ions out of neurons and pumps potassium ions inside, producing the equally beloved membrane potential of neurons.

Look at those structures again. While there are charges on PE, PS (on the phosphate group), these molecules are far larger than the sodium or the potassium ion (easily by a factor of 10). This has long been recognized and is called the ‘giant substrate problem’.

The paper solved the structure of ATP8A2 and used molecular dynamics stimulations to try to understand how it works. What they found is that transmembrane alpha helices 1, 2, 4 and 6 (out of 10) form a water filled cavity, which dissolves the negatively charged phosphate of the head group. What happens to those long hydrocarbon tails? The are left outside the helices in the lipid core of the membrane. It is the charged head groups that are dragged through by the flippase, with the tails wagging along behind them, just like little Bo Peep.

There’s a lot more great chemistry in the paper, particularly how Isoleucine #364 directs the sequential formation and annihilation of the water filled cavities between alpha helices 1, 2, 4 and 6, and how a particular aspartic acid is phosphorylated (by ATP, explaining why the enzyme no longer works in energetically dying cells) changing conformation of all 10 transmembrane helices, so that only one half of the channel is open at a time (either to the inside or the outside).

Go read and enjoy. It’s sad that people who don’t know organic chemistry are cut off from appreciating such elegance. There is more to esthetics than esthetics.

Little Bo Peep meets cellular biology and biochemistry.

Flippase. Eat me signals. Dragging their tails behind them. Have cellular biologists and structural biochemists gone over to the dark side? It’s all quite innocuous as the old nursery rhyme will show

Little Bo Peep has lost her sheep
and doesn’t know where to find them
Leave them alone, and they’ll come home
wagging their tails behind them.

First, some cellular biochemistry. The lipid bilayer encasing all our cells is made of two leaflets, inner and outer. The composition of the two is different (unlike the soap bubble). On the inside we find phosphatidylethanolamine (PE), phosphatidylserine (PS). The outer leaflet contains phosphatidylcholine (PC) and sphingomyelin (SM) and almost no PE or PS. This is clearly a low entropy situation compared to having all 4 randomly dispersed between the 2 leaflets.

What is the possible use of this (notice how teleology invariably creeps into cellular biology)? Chemistry is powerless to explain such things. Much as I love chemistry, such truths must be faced.

It takes energy to maintain this peculiar distribution. The enzyme moving PE and PS back inside the cell is the flippase. It requires energy in the form of ATP to operate. When a cell is dying ATP drops, and entropy takes its course moving PE and PS to the cell surface. Specialized cells (macrophages) exist to scoop up the dying or dead cells, without causing inflammation. They recognize PE and PS by a variety of receptors and munch up cells exposing them on the surface. So PE and PS are eat me signals which appear when there isn’t enough ATP around for flippase to use to haul PE and PS back inside. Clever no?

No for some juicy chemistry (assuming that you consider transport of a molecule across a lipid bilayer actual chemistry — no covalent bonds to the transferred molecule are formed or removed, although they are to the transporter). Well it certainly is physical chemistry isn’t it?

Here are the structures of PE, PS, PC, SM http://www.google.com/search?q=phosphatidylserine&client=safari&rls=en&tbm=isch&tbo=u&source=univ&sa=X&ei=bDRLU5yfHOPLsQSOnoG4BA&ved=0CPABEIke&biw=1540&bih=887#facrc=_&imgdii=_&imgrc=qrLByG2vmhWdwM%253A%3BwAtgsTPwCxeZXM%3Bhttp%253A%252F%252Fscience.csumb.edu%252F~hkibak%252F241_web%252Fimg%252Fpng%252FCommon_Phospholipids.png%3Bhttp%253A%252F%252Fscience.csumb.edu%252F~hkibak%252F241_web%252Fcoursework_pages%252F2012_02_2.html%3B1297%3B934.

There are a few things to notice. Like just about every lipid found in our membranes, they are amphipathic — they have a very lipid soluble part (look at the long hydrocarbon changes hanging below them) and a very water soluble part — the head groups containing the phosphate.

This brings us to [ Proc. Natl. Acad. Sci. vol. 111 pp. E1334 - E1343 '14 ] Which describes ATP8A2 (aka the flippase). Interestingly, the protein, with at least 10 alpha helices spanning the membrane, and 3 cytoplasmic domains closely resembles the classic sodium pump beloved of neurophysioloogists everywhere, which pumps sodium ions out of neurons and pumps potassium ions inside, producing the equally beloved membrane potential of neurons.

Look at those structures again. While there are charges on PE, PS (on the phosphate group), these molecules are far larger than the sodium or the potassium ion (easily by a factor of 10). This has long been recognized and is called the ‘giant substrate problem’.

The paper solved the structure of ATP8A2 and used molecular dynamics stimulations to try to understand how it works. What they found is that transmembrane alpha helices 1, 2, 4 and 6 (out of 10) form a water filled cavity, which dissolves the negatively charged phosphate of the head group. What happens to those long hydrocarbon tails? The are left outside the helices in the lipid core of the membrane. It is the charged head groups that are dragged through by the flippase, with the tails wagging along behind them, just like little Bo Peep.

There’s a lot more great chemistry in the paper, particularly how Isoleucine #364 directs the sequential formation and annihilation of the water filled cavities between alpha helices 1, 2, 4 and 6, and how a particular aspartic acid is phosphorylated (by ATP, explaining why the enzyme no longer works in energetically dying cells) changing conformation of all 10 transmembrane helices, so that only one half of the channel is open at a time (either to the inside or the outside).

Go read and enjoy. It’s sad that people who don’t know organic chemistry are cut off from appreciating such elegance. There is more to esthetics than esthetics.

The prions within us

Head for the hills. All of us have prions within us sayeth [ Cell vol. 156 pp. 1127 - 1129, 1193 - 1206, 1206 - 1222 '14 ]. They are part of the innate immune system and help us fight infection. But aren’t all sorts of horrible disease (Bovine Spongiform Encephalopathy aka BSE, Jakob Creutzfeldt disease aka JC disease, Familial Fatal Insomnia etc. etc.) due to prions? Yes they are.

If you’re a bit shaky on just what a prion is see the previous post which should get you up to speed — https://luysii.wordpress.com/2014/03/30/a-primer-on-prions/.

Initially there was an enormous amount of contention when Stanley Prusiner proposed that Jakob Creutzfeldt disease was due to a protein forming an unusual conformation, which made other copies of the same protein adopt it. It was heredity without DNA or RNA (although this was hotly contended at the time), but the evidence accumulating over the years has convinced pretty much everyone except Laura Manuelidis (about whom more later). It convinced the Nobel Prize committee at any rate.

JC disease is a rapidly progressive dementia which kills people within a year. Fortunately rare (attack rate 1 per million per year) it is due to misfolded protein called PrP (unfortunately initially called ‘the’ prion protein although we now know of many more). Trust me, the few cases I saw over the years were horrible. Despite decades of study, we have no idea what PrP does, and mice totally lacking a functional Prp gene are normal. It is found on the surface of neurons. Bovine Spongiform Encephalopathy was a real scare for a time, because it was feared that you could get it from eating meat from a cow which had it. Fortunately there have been under 200 cases, and none recently.

If you cut your teeth on the immune system being made of antibodies and white cells and little else, you’re seriously out of date. The innate immune system is really the front line against infection by viruses and bacteria, long before antibodies against them can be made. There are all sorts of receptors inside and outside the cell for chemicals found in bacteria and viruses but not in us. Once the receptors have found something suspicious inside the cell, a large protein aggregate forms which activates an enzyme called caspase1 which cleaves the precursor of a protein called interleukin 1Beta, which is then released from some immune cells (no one ever thought the immune system would be simple given all that it has to do). Interleukin1beta acts on all sorts of cells to cause inflammation.

There are different types of inflammasomes and the nomenclature of their components is maddening. Two of the sensors for bacterial products (AIM, NLRP2) induce a polymerization of an inflammasome adaptor protein called ASC producing a platform for the rest of the inflammasome, which contains other proteins bound to it, along with caspase1 whose binding to the other proteins activates it. (Terrible sentence, but things really are that complicated).

ASC, like most platform proteins (scaffold proteins), is made of many different modules. One module in particular is called pyrin (because one of the cardinal signs of inflammation is fever). Here’s where it gets really interesting — the human pyrin domain in ASC can replace the prion domain of the first yeast prion to be discovered (Sup35 aka [ PSI+ ] — see the above link if you don’t know what these are) and still have it function as a prion in yeast. Even more amazing, is the fact that the yeast prion domain can functionally replace ASC modules in our inflammasomes and have them work (read the references above if you don’t believe this — I agree that it’s paradigm destroying). Evidence for human prions just doesn’t get any better than this. Fortunately, our inflammasome prions are totally unrelated to PrP which can cause such havoc with the nervous system.

Historical note: Stanley Prusiner was a year behind me at Penn Med graduating in ’67. Even worse, he was a member of my med school fraternity (which was more a place to get a decent meal than a social organization). Although I doubtless ate lunch and dinner with him before marrying in my Junior year, I have absolutely no recollection of him. I do remember our class’s medical Nobel — Mike Brown. Had I gone to Yale med instead of Penn, Laura Manuelidis would have been my classmate. Small world

A primer on prions

Actually Kurt Vonnegut came up with the basic idea behind prions in his 1963 Novel “Cat’s Cradle”. Instead of proteins, it involved a form of water (Ice-9) which had never been seen before, but one which was solid at room temperature. Unfortunately, it also solidified all liquid water it came in contact with effectively ending life on earth.

Now for some history.

The first Xray crystallographic structures of proteins were incredibly seductive intellectually, much as false color functional magnetic resonance (fMRI) images are today. It was hard not to think of them as the structure of the protein.

Nowaday we know that lots of proteins have at least one intrinsically disordered (trans. unstructured) segment of 30 amino acids ore more. [ Nature vol. 411 pp. 151 - 153 '11 ] says 40%, and also that 25% of all human proteins are likely to be disordered (translation; unstructured) from end to end — basic on a bioinformatics program.

I’ve always been amazed that any protein has only a few shapes, purely on the basis of the chemistry — read this if you have the time — http://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/. Clearly the proteins making us up do have a relatively limited number of shapes (or we’d all be dead).

The possible universe of proteins from which our proteins are selected is enormously large. In fact the whole earth doesn’t have enough mass (even if it were made entirely of hydrogen, carbon, nitrogen, oxygen and sulfur) to make just one copy of the 20^100 possible proteins of length 100. For the calculation please see — http://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/ — if you have the time.

So, even though it is meaningful question philosophically, just how common proteins with a few shapes are in this universe, we’ll never be able to carry out the experiment. Popper would say it’s a scientifically meaningless question, because it can’t be experimentally decided. Bertrand Russell would not.

Again, if you have time, take a look at http://luysii.wordpress.com/2010/08/08/a-chemical-gedanken-experiment/

Which, at long last, brings us to prions.

They were first discovered in yeast, and were extremely hard to figure out as they represented something in the cytoplasm which contained no DNA and yet which was heritable. The first prion was discovered nearly 50 years ago. It was called [PSI+] and it produced a lot of new proteins in yeast containing it (which is how its effects were measured) Mating [ PSI+ ] with [ psi-] (e.g. yeast cells without [ PSI+ ] converted the [ psi-] to [ PSI+ ]. It couldn’t be mapped to any known genetic element. Also [ PSI+ ] was lost at a higher rate than would be expected for a DNA mutation. The first clue that [ PSI+ ] was a protein was that it was lost faster when yeast were grown in the presence of protein denaturants (such as guanidine).

It turned out that [ PSI + ] was an aggregated form of the Sup35 protein, which basically functioned to suppress the ribosome from reading through the stop codon. If you need background on what was just said please see — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ and the subsequent 4 posts. This is why [ PSI+ ] yeast produced longer proteins.Things began to get exciting when Sup35 was dissected so domains could be found which induced [ PSI+ ] formation. Amazingly these domains spontaneously formed visible fibers in vitro resembling amyloid in some respects (binding the dye Congo Red for one). Then they found that preformed fibers, greatly accelerated fiber formation by unpolymerized Sup35 — beginning to sound a bit lice Ice 9 doesn’t it. Yeasts have many other prions, but the best studied and most informative is the one formed from Sup35.

So that’s how prions were found (in yeast) and what they are — an aggregated form of a given protein in a slightly different shape, which can cause another molecule of the same protein to adopt the prion proteins new shape. Amazingly, we have prions within us. But that’s the subject of the next post.

Was I the last to find out?

Quick ! Can you form a hydrogen bond from a carbon hybridized sp3 to an oxygen atom?

I didn’t think so, but you can. This, in spite of reading about proteins for over half a century. [ Proc. Natl. Acad. Sci. vol. 111 pp. E888 - E895 '14 ] describes this (along with lots of references backing up the statements which follow) to such bonds forming between the transmembrane segments of membrane proteins (estimated to be 30% of all our proteins).

Whether or not they contribute to membrane stability isn’t known. Consider the alpha carbon of an amino acid. It is adjacent to a carbonyl group of an amide (electron hungry, but less so than a pure carbonyl because of resonance) and the nitrogen atom of an amide (slightly more electronegative than carbon, and probably more electron hungry because it loses part of its lone pair to resonance).

They are usually found from the alpha carbon of glycine on one helix to the carbonyl of an adjacent transmembrane helix. Glycine zippers (e.g. the G X X X G motif) have long been known in transmembrane helices. Since glycine is the smallest amino acid, having them on the same side of the helix was thought to be a way to pack adjacent helices together.

What would you consider good evidence for such a bond? Spectroscopy of model compounds with deuterium for the alpha hydrogen would be one way (it’s been done). The best evidence would be a shortened distance between the hydrogen and the carbonyl and this has been found as well.

Humbling ! !

Follow

Get every new post delivered to your Inbox.

Join 66 other followers