Category Archives: Chemistry (relatively pure)

The chemical ingenuity of the lake Ontario midge

Well we’re freezing our butts off here in sunny New England, so it’s time to discourse upon the chemical ingenuity of antifreeze proteins. They’ve long been known, with most found in fish living in arctic waters. A very unusual structure is found in a 79 amino acid protein from an insect living near Lake Ontario. It contains 79 amino acids with a set of 10 amino acid tandem repeats making up most of the protein. Here is the the repeat.

X X Cys X Gly X Tyr Cys X Gly ; X = any amino acid.

Can you as a computational chemistry expert figure out what it forms?

The 10 amino acids form a complete circle with the peptide backbone looking nothing like an alpha helix, a beta sheet or anything else I’ve seen. It just sort of wanders around for 360 degrees. In cross section the ‘circle’ resembles the Greek letter theta with a disulfide bond between the two cysteines forming a crossbar inside the circle. This puts all 7 tyrosines from the 7 repeats in a row on one side of the circle, where they form the presumed ice binding site. The solenoid is reinforced by intrachain hydrogen bonds, and side chain salt bridges. You can read about it and see some pictures in Proc. Natl. Acad. Sci. vol. 112 pp. 737 – 742 ’15 ].

The chemical ingenuity of some of these proteins is remarkable. None of them (except one) appear to have been figured out before their structures were determined.

[ Proc. Natl. Acad. Sci. vol. 108 pp. 7281 – 7282 ’11 ] Even now, the structural differences between the surface of ice nuclei and liquid water are poorly characterized (we don’t even know how many hydrogen bonds are involved), yet antifreeze proteins somehow recognize it. Some 12 different structural motifs have been found in antifreeze proteins. 3 are given — one is a small globular protein (sea pout) another is an alpha helix (winter flounder), and the third is a stack of left handed PolyProtein-II helices (snow flea). The present work gives a fourth example — a right handed parallel beta helix from (Marinomonas primoyensis). It is a 34 kiloDalton domain — it is a calcium bound parallel beta helix, with an extensive array of icelike surface waters that are anchored via hydrogen bonds directly to the protein backbone and adjacent side chains. The bound waters make an excellent 3 dimensional match to the primary prism and basal planes of ice.

Probably the most counterintuitive antifreeze protein is the following. It stands a lot of what we thought we knew about protein structure on its head.

[ Science vol. 343 pp. 743 – 744, 795 – 798 ’14 ] Almost all globular proteins reported to date have a dry protein core (e.g. water free). An antifreeze protein called Maxi from the winter flounder (Pseudopleuronectes americanus) has been found with a water filled core. It is a 3 kiloDalton alanine rich 4 helix bundle 145 Angstroms long. The periodicity of the alpha helices is 11 amino acids. A single turn of an alpha helix is 5.4 Angstroms high and 11 Angstroms wide. So 11 amino acids fairly neatly comes out to 16 Angstroms in length (because each helical turn is 3.7 residues (vs. the normal 3.6 in the classic alpha helix). The ice binding residues are Threonine at position i, Alanine at position i+4 and Alanine at position i + 8 (putting them along one face of the helix). The protein is a dimer of monomers each containing two helices. The core is comprised of 400 (yes 400 !) highly organized water molecules. The water is interleaved as a roughly two molecule thick layer between both intra and intermonomer helix interfaces, extending to the ice binding surfaces. Maxi must bind ice nuclei and inhibit their growth. The water molecules inside the bundle form pentagons ! ! ! Amazingly, this was predicted 50 years ago by Scheraga . The 5 membered water rings form cages around individual amino acid side chains, illustrating their semi-clathrate structure — rather than ice. Most of the carbonyls are involved in hydrogen bonding interactions with water — helping to keep the protein soluble. The protein denatures at low temperatures (16 C)

Ordered water can be found in most high resolution Xray crystallograpy protein structures, but they are usually between the proteins. Maxi retains the very structure of water.

Removal of water has been proposed as a potential rate limiting step in protein folding. Maxi folds to the point where water not in direct contact with the protein chain is removed from its core. It then arrests further folding to retain a beautifully ordered core of water interleaved between the protein helices.

Amazing! No one would ever have predicted something like Maxi (except Sheraga).

An interesting way to study the hydrophobic effect between protein surfaces

Protein interaction domains haven’t been studied to nearly the extent they need to be, and we know far less about them than we should. All the large molecular machines of the cell (ribosome, mediator, spliceosome, mitochondrial respiratory chain) involve large numbers of proteins interacting with each other not by the covalent bonds beloved by organic chemists, but by much weaker forces (van der Waals,charge attraction, hydrophobic entropic forces etc. etc.).

Designing drugs to interfere (or promote) such interactions will be tricky, yet they should have profound effects on cellular and organismal physiology. Off target effects are almost certain to occur (particularly since we know so little about the partners of a given motif). Showing how potentially useful such a drug can be, a small molecule inhibitor of the interaction of the AIDs virus capsid protein with two cellular proteins (CPSF6, TNPO3) the capsid protein must interact with to get into the nucleus has been developed. (Unfortunately I’ve lost the reference). For more about the host of new protein interaction domains (and potential durable targets) just discovered please see https://luysii.wordpress.com/2015/01/04/microexons-great-new-drugable-targets/

Hydrophobic ‘forces’ are certain to be important in protein protein interactions. A very interesting paper figured out a way to measure them using atomic force microscopy (AFM). [ Nature vol. 517 pp. 277 – 279, 347 – 350 ’15 ]. This is particularly interesting to me because entropy has nothing to do with the force as measured. I’ve always assumed that the the hydrophobic force was entropic, similar to the force exerted by rubber when you stretch it. It’s what pushes hydrophobic side chains into the interior of proteins (e.g water doesn’t have to decrease its entropy by organizing itself to solvate hydrophobic side chains). Not so in this case.

The authors prepared self-assembled monolayers using dodecyl thiol (CH3 (CH2) 10 CH2 SH) bound to gold. Every now and then an amino group or a guanido group was placed at the other end of the thiol. This allowed them to produce a mixture of hydrophobic groups (60%) and ionic species (NH4+ or guanidinium ions) within nanoMeters of the hydrophobic regions. The amine and the guanidino groups were the same distance as the hydrocarbon ends from the gold surface. A gold atomic force microscope (AFM) with a hydrophobic tip (the same C(12) moiety), was then used to measure the adhesive force between the tip and the surface in aqueous solution.

This is important because it is a measurement not a theoretical calculation (apologies Ashutosh). This is particularly useful since water is so complex that we don’t have a good understanding (potential function) for it.

Methanol was added (which eliminated most of the hydrophobic interactions). Sensitivity to methanol was taken as a signature of the hydrophobic component of the force. The pH could be manipulated, so the R – NH2 could be charged to R -NH3+, ditto for guanidinium to the uncharged species.

So guess what the effect of amino and guanidine groups were on the hydrophobic interaction. I was rather surprised.

The strength of hydrophobic interactions between the mixed monolayers and the tip doubled when neutral amino groups found within nanoMeters of hydrophobic regions are charged to form R -NH3+ ions by lowering the pH. A similarly placed guanidinium ion eliminates the hydrophobic interactions at all pHs. So the effect of the two side chains (NH2 for lysine, guanidinium for arginine) is opposite.

They note that the ammonium ion is well hydrated, but guanidinium is hydrated only at the edges of the plane (where the electrons are) but not above it. This allows guanidinium an amphipathic behavior, which is why it can be a denaturant (did you know this? I didn’t).

I’m sure that the effect of negative ions (e.g. carboxyl groups) and every other conceivable side chain will be studied in the future.

Thus hydrophobicity is not an intrinsic property of any given nonPolar domain. It can be changed by functional groups within 10 Angstroms.. So placing a charged group near a hydrophobic domain, should allow tuning of the hydrophobic driving force. I’d be amazed if this isn’t found to be the case evolutionarily.

They also studied some wierd looking stuff resembling proteins (beta peptides { e.g. the amino and carboxyl groups on adjacent carbons rather than the same one as with alpha amino acids) with weird side chains which are known to adopt an amphipathic helical conformation. THe nonpolar side chains were trans 2 aminocyclohexanecarboxylic acid (ACHC), and the cationic side chains were beta3 homolysine. Why didn’t they use something more natural. The peptide forms an ACHC rich nonPolar square domain 10 Angstroms on a side with a polar patch on the other side of the helix.

So it’s a fascinating piece of work with large implications for the design of drugs attacking protein protein interfaces.

Do enzymes chase their prey?

Do enzymes chase their prey? At first thought, this seems ridiculous. However people have been measuring diffusion of substances in water for over a century. Even Einstein worked on it (his paper on Brownian motion). So it’s fairly easy to measure the diffusion of an enzyme in water. Several enzymes (catalase — one of the most efficient enzymes known, and urease) diffuse faster when their substrate is present. [ Nature vol. 517 pp. 149 – 150, 227 – 230 ’15 ] The hydrolysis of urea by urease and the conversion of H2O2 to O2 and water by catalase enhances the molecular diffusion of the enzymes (this is called anomlous diffusion).If you inhibit catalase enzymatic activity using azide the anomalous diffusion disappears (even though there’s still plenty of H2O2 around). This work also showed that the rate of diffusion of catalase, urease and 2 more ezymes correlates with the heat produced by the reaction catalyzed.

Heating the catalytic center of catalase (using a short laser pulse) produces the same anomalous diffusion. Proteins exist in a world in which Brownian motion is governed by viscous forces rather than by inertia, so coasting (a la Galileo and Newton’s law of inertia) isn’t an option — continuous force generation is required.

Heat generated from each catalytic cycle could be transmitted through the enzyme as a pressure wave. For this to happen the catalytic center must be NOT at the center of mass of the enzyme, so the pressure wave will create differential stress at the enzyme solvent interface (which should propel the enzyme). They call this the chemoacoustic effect.

Molecular dynamics simulations suggest that the transmission of energy through a protein can be quite fast (5 Angstroms/picoSecond) and nonuniformly distributed.

Some enzymes have a near perfect catalytic efficiency. Every time a substrate hits them, the substrate is converted to product. Examples include catalase, acetyl cholinesterase, fumarase, and carbonic anhydrase. There are 100 million to a billion collisions per mole per second in solution.

Could this be a product of evolution (to make enzymes actively search out substrates?). Note, this won’t work if the catalytic center of the enzyme is in the center of mass.

I doubt that much catalytic efficiency is gained by having a huge protein molecule sluggishly move through the cytoplasm. Why? The molecular mass of H2O2 is 19 Daltons (vs. 18 for water), so it moves slightly more slowly but water moves at 20C in water at 590 meters/second. Of course it doesn’t get very far before it bumps into another water molecule and gets deflected.

Is there an ace physical chemist out there who can put numbers on this. I couldn’t believe that I couldn’t find a simple expression for the relation between the diffusion coefficient and the mass of the diffuser, ditto for the atomic volume of a water molecule, although I’m guessing that it’s pretty close to the length of the H – O bond (.95 Angstroms) giving a mass of 3.6 cubic Angstroms. I wanted this so I could see how much room to roam a water molecule has.

Paul Schleyer 1930 – 2014, A remembrance

Thanks Peter for your stories and thoughts about Dr. Schleyer (I never had the temerity to even think of him as Paul). Hopefully budding chemists will read it, so they realize that even department chairs and full profs were once cowed undergraduates.

He was a marvelous undergraduate advisor, only 7 years out from his own Princeton degree when we first came in contact with him and a formidable physical and intellectual presence even then. His favorite opera recording, which he somehow found a way to get into the lab, was don Giovanni’s scream as he realized he was to descend into Hell. I never had the courage to ask him if the scars on his face were from dueling.

We’d work late in the lab, then go out for pizza. In later years, I ran into a few Merck chemists who found him a marvelous consultant. However, back in the 50’s, we’d be working late, and he’d make some crack about industrial chemists being at home while we were working, the high point of their day being mowing their lawn.

I particularly enjoyed reading his papers when they came out in Science. To my mind he finally settled things about the nonclassical nature of the norbornyl cation — here it is, with the crusher being the very long C – C bond lengths

Science vol. 341 pp. 62 – 64 ’13 contains a truly definitive answer (hopefully) along with a lot of historical background should you be interested. An Xray crystallographic structure of a norbornyl cation (complexed with a Al2Br7- anion) at 40 Kelvin shows symmetrical disposition of the 3 carbons of the nonclassical cation. It was tricky, because the cation is so symmetric that it rotates within crystals at higher temperatures. The bond lengths between the 3 carbons are 1.78 to 1.83 Angstroms — far longer than the classic length of 1.54 Angstroms of a C – C single bond.

I earlier wrote a post on why I don’t read novels, the coincidences being so extreme that if you put them in a novel, no one would believe them and throw away the book — it involves the Princeton chemistry department and my later field of neurology — here’s the link https://luysii.wordpress.com/2014/11/13/its-why-i-dont-read-novels/

Here’s yet another. Who would have thought, that years later I’d be using a molecule Paul had synthesized to treat Parkinson’s disease as a neurologist. He did an incredibly elegant synthesis of adamantane using only the product of a Diels Alder reaction, hydrogenating it with a palladium catalyst and adding AlCl3. An amazing synthesis and an amazing coincidence.

As Peter noted, he was an extremely productive chemist and theoretician. He should have been elected to the National Academy of Sciences, but never was. It has been speculated that his wars with H. C. Brown made him some powerful enemies. I’ve heard through the grapevine that it rankled him greatly. But virtue is its own reward, and he had plenty of that.

R. I. P. Dr. Schleyer

Paul Schleyer (1930 – 2014) R. I. P.

This is a guest post by Peter J. Reilly, Anson Marston Distinguished Professor Emeritus, Department of Chemical and Biological Engineering, Iowa State University, fellow Schleyer undergraduate advisee Princeton 1958 – 1960, friend, and all around good guy.

I’ll follow with my own reminiscences in another post. Obits tend to be polished and bland, ‘speak no evil of the dead’ and all that, but Peter captures the flavor of what it was actually like to be Paul’s advisee and exposed to his formidable presence.

“Following are my thoughts on our undergraduate chemistry advisor at Princeton, Paul von Ragué Schleyer, who died on November 21 of this year at 84.

Paul was an amazingly prolific chemist. He started publishing in 1956, soon after he arrived at Princeton from receiving a Ph.D. at Harvard, where he studied from 1951 to 1954 after earning an A.B. from Princeton. He was still publishing at the time of his death. In fact, he had promised to deliver a book chapter over this Thanksgiving weekend. Over his latter years at Princeton, in the early 1970’s, his annual production of papers averaged the middle 20’s. He kept up the same pace at Universität Erlangen-Nürnberg in Germany from 1976 to 1992. From 1993 to 1997, when he had appointments at both Erlangen-Nürnberg and the University of Georgia, he was in the 40’s. When fully at Georgia, after 1997, he gradually slacked off, publishing only 16 papers this year. Altogether he had 1277 publications, when a really productive chemist with ready access to students and postdoctoral fellows hopes to have 200–250 in a full career.

Another way to consider Paul’s productivity is by how often his work had been cited (partly by his own later papers but mainly by the papers of others). A 1981–1997 survey reported that he was the third most cited chemist in the world. Althogether his works were cited over 75,000 times. His h-index is 126 in the Thomson Reuters Web of Science database, meaning that he had 126 publications that were cited at least 126 times, an astounding number.

I first met Paul in the fall of 1958, two years after I arrived at Princeton. I needed to find someone to supervise my junior paper, a ritual common to all Princeton undergraduates doing A.B. degrees. I had originally approached Edward Taylor, a somewhat older chemistry professor, but when I told him that I was somewhat interested in becoming a chemical engineer, he directed me to Paul. Paul was 28 at the time, but he seemed older to me (I supposed all professors did). He was tall, with dark black hair combed to the side over his forehead. He had a scar on his cheek and talked very precisely.

My father met him once and came away asking if he had been a German U-boat captain during WWII.

I must say that I spent a sizable part of the next two years being terrified of Paul. He had a laboratory in the second floor of the southwest corner of Frick Chemical Laboratory. The benches were full of glassware, to the point where it seemed hard to do any research. However, the item that spooked me the most was a cauldron full of boiling black liquid, supposedly mainly nitric acid, in which dirty glassware was submerged to be cleaned.

Paul gave me a project to research the incidence and properties of the benzyne intermediate, a short-lived benzene ring with a triple bond. This was my first exposure to research beyond short papers for classes, and I suppose that I did well enough for him to invite me to do a senior thesis with him. The topic was to determine the mechanism by which an obscure organic chemical rearranged itself. The title of the thesis that came from a year’s dogged effort was “A Study of the Cleavage Products of 2,5-Dimethyltetrahydropyran-2-Methanol”, but what I mainly made was black goop. Paul’s written comments to me started with the statement that he was sorry that the problem was so intractable, but at least he liked my writeup. I still have the thesis (and the junior paper). Back in 2007 I was contacted by the Princeton University Library, which had lost its copy. They asked if I could send them mine so that they could microfilm it, which of course I did.

I remember that at least four of us chemistry majors spent much of our senior years in a very large and empty laboratory working on our theses under Paul’s direction. I must say that the various chemicals that I worked on smelled a lot better than the ones that you dealt with. I used to take weekend dates up to the laboratory to show them where I worked, and I would open one of your very small tubules, I think containing butyl mercaptan. Its smell still permeated the room on Mondays. (Editor’s note — people used to look at their shoes when I walked into the eating club after working with n-Bu-SH or similar compounds).

Despite my lack of success on my thesis, I learned from it how to do research. My chemical engineering major professor at the University of Pennsylvania was hard to contact, so much of my doctoral dissertation was done without much supervision. Between the two experiences, I had a good foundation for my 46 years of being a chemical engineering professor, six at the University of Nebraska-Lincoln and 40 at Iowa State University after four years at DuPont in southern New Jersey.

I only saw Paul four times after leaving Princeton. The first was when I returned there for a short visit. The second time was at my 25th Princeton reunion, when one of his daughters was graduating. A third time was when he visited the Iowa State chemistry department to present a prestigious lecture. The fourth and last time was in 2005 when I visited the University of Georgia for a meeting. Paul spent about 30 minutes telling me about his latest research, of which I understood very little.

I will close with a little story. When I told Paul during my senior year that I wanted to go to graduate school in chemical engineering, he asked why I wanted to become a pipe-fitter. Probably because of my chemistry background at Princeton, my research was always chemistry- and biology-based, first in fermentations at Penn and Nebraska (with a detour to chloro- and fluorocarbons at DuPont), and then in enzymes and carbohydrates at Iowa State. I moved more and more into computation late in my career, and when Paul visited around 2002 I told him that I would be sending a manuscript to the Journal of Computational Chemistry, which he and Lou Allinger at Georgia had founded and were still editing. Being Paul, he immediately said in his deep voice that it had better be good. As it turned out, it sailed through the review process with hardly a blip, and I followed it up with a second manuscript a few years later.

So, we were fortunate to have Paul as a mentor during our formative years. He certainly wasn’t the sweetest guy, but he was brilliant, and hopefully a very small part of his brilliance rubbed off on us.”

Peter J. Reilly

How one membrane protein senses mechanical stress

Chemists (particularly organic chemists) think they’re pretty smart. So see if you can figure out how a membrane embedded ion channel opens due to mechanical stress. The answer is to be found in last week’s Nature (vol. 516 pp. 126 – 130 4 Dec ’14).

As you probably know, membrane embedded proteins get stuck there because they contain multiple alpha helices with mostly hydrophobic amino acids allowing them to snuggle up to the hydrocarbon tails of the lipids making up the lipid bilayer of the biological membrane.

The channel in question is called TRAAK, known to open in response to membrane tension. It conducts potassium ions. The voltage sensitive potassium channels have 24 transmembrane alpha helices, 6 in each of the tetramer proteins comprising it. TRAAK has only 8. As is typical of all ion channels, the helices act like staves on a barrel, shifting slightly to open the pore.

In this case, with little membrane tension, the helices separate slightly permitting a a 10 carbon tail ( CH3 – [ CH2 – CH2 – CH2 ]3 – ) to enter the barrel occluding the pore. Tension on the membrane tends decrease the packing of hydrocarbon tails of the membrane, pulling the plug out of the pore. Neat !! ! ! This is a completely different mechanism than the voltage sensing helix in the 24 transmembrane voltage sensitive potassium channels, and one that no one has predicted despite all their intelligence.

Trigger warning. This paper is by MacKinnon who won the Nobel for his work on potassium channels. He used antibodies to stabilize ion channels so they could be studied by crystallography. Take them out of the membrane and they denature. Why the warning? In his Nobel work he postulated an alpha helical hairpin paddle extending outward from the channel core into the membrane’s lipid interior. It was both hydrophobic and charged, and could move in response to transmembrane voltage changes.

This received vigorous criticism from others, who felt it was an artifact produced by the use of the antibody to stabilize the protein for crystallography.

Why the warning? Because MacKinnnon also used an antibody to stabilize TRAAK.

The whole idea of membrane tension brings up the question of just how strong van der Waals forces really are. Biochemists and molecular biologists tend to think of hydrophobic forces as primarily entropic, pushing hydrophobic parts of a protein together so water would have to exquisitely structure itself to solvate them (e.g. lowering the entropy greatly). Here however, the ‘pull’ if you wish, is due to the mutual attraction of the hydrophobic lipid side chains to each other, which I would imagine is pretty week.

I’m sure that these forces have been measured, and years ago I enjoyed reading about Langmuir’s work putting what was basically soap on a substrate, and forming a two dimensional gas which actually followed something resembling P * Area = n * R * T. So the van der Waals forces have been measured, I just don’t know what they are. Does anyone out there?

Nonetheless, some very slick (physical and organic) chemistry.

Could Alzheimer’s disease be a problem in physics rather than chemistry?

Two seemingly unrelated recent papers could turn our attention away from chemistry and toward physics as the basic problem in Alzheimer’s disease. God knows we could use better therapy for Alzheimer’s disease than we have now. Any new way of looking at Alzheimer’s, no matter how bizarre,should be welcome. The approaches via the aBeta peptide, and the enzymes producing it just haven’t worked, and they’ve really been tried — hard.

The first paper [ Proc. Natl. Acad. Sci. vol. 111 pp. 16124 – 16129 ’14 ] made surfaces with arbitrary degrees of roughness, using the microfabrication technology for making computer chips. We’re talking roughness that’s almost smooth — bumps ranging from 320 Angstroms to 800. Surfaces could be made quite regular (as in a diffraction grating) or irregular. Scanning electron microscopic pictures were given of the various degrees of roughness.

Then they plated cultured primitive neuronal cells (PC12 cells) on surfaces of varying degrees of roughness. The optimal roughness for PC12 to act more like neurons was an Rq of 320 Angstroms.. Interestingly, this degree of roughness is identical to that found on healthy astrocytes (assuming that culturing them or getting them out of the brain doesn’t radically change them). Hippocampal neurons in contact with astrocytes of this degree of roughness also began extending neurites. It’s important to note that the roughness was made with something neurons and astrocytes never see — silica colloids of varying sizes and shapes.

Now is when it gets interesting. The plaques of Alzheimer’s disease have surface roughness of around 800 Angstroms. Roughness of the artificial surface of this degree was toxic to hippocampal neurons (lower degrees of roughness were not). Normal brain has a roughness with a median at 340 Angstroms.

So in some way neurons and astrocytes can sense the amount of roughness in surfaces they are in contact with. How do they do this — chemically it comes down to Piezo1 ion channels, a story in themselves [ Science vol. 330 pp. 55 – 60 ’10 ] These are membrane proteins with between 24 and 36 transmembrane segments. Then they form tetramers with a huge molecular mass (1.2 megaDaltons) and 120 or more transmembrane segments. They are huge (2,100 – 4,700 amino acids). They can sense mechanical stress, and are used by endothelial cells to sense how fast blood is flowing (or not flowing) past them. Expression of these genes in mechanically insensitive cells makes them sensitive to mechanical stimuli.

The paper is somewhat ambiguous on whether expressing piezo1 is a function of neuronal health or sickness. The last paragraph appears to have it both ways.

So as we leave paper #1, we note that that neurons can sense the physical characteristics of their environment, even when it’s something as un-natural as a silica colloid. Inhibiting Piezo1 activity by a spider venom toxin (GsMTx4) destroys this ability. The right degree of roughness is healthy for neurons, the wrong degree kills them. Clearly the work should be repeated with other colloids of a different chemical composition.

The next paper [ Science vol. 342 pp. 301, 316 – 317, 373 – 377 ’13 ] Talks about the plumbing system of the brain, which is far more active than I’d ever imaged. The glymphatic system is a network of microscopic fluid filled channels. Cerebrospinal fluid (CSF) bathes the brain. It flows into the substance of the brain (the parenchyma) along arteries, and the fluid between the cellular elements (interstitial fluid) it exchanges with flows out of the brain along the draining veins.

This work was able to measure the amount of flow through the lymphatics by injected tracer into the CSF and/or the brain parenchyma. The important point about this is that during sleep these channels expand by 60%, and beta amyloid is cleared twice as quickly. Arousal of a sleeping mouse decreases the influx of tracer by 95%. So this amazing paper finally comes up with an explanation of why we spend 1/3 of our lives asleep — to flush toxins from the brain.

If you wish to read (a lot) more about this system — see an older post from when this paper first came out — https://luysii.wordpress.com/2013/10/21/is-sleep-deprivation-like-alzheimers-and-why-we-need-sleep-in-the-first-place/

So what is the implication of these two papers for Alzheimer’s disease?

    First

The surface roughness of the plaques (800 Angstroms roughness) may physically hurt neurons. The plaques are much larger or Alzheimer would never have seen them with the light microscopy at his disposal.

    Second

The size of the plaques themselves may gum up the brain’s plumbing system.

The tracer work should certainly be repeated with mouse models of Alzheimer’s, far removed from human pathology though they may be.

I find this extremely appealing because it gives us a new way of thinking about this terrible disorder. In addition it might explain why cognitive decline almost invariably accompanies aging, and why Alzheimer’s disease is a disorder of the elderly.

Next, assume this is true? What would be the therapy? Getting rid of the senile plaques in and of itself might be therapeutic. It is nearly impossible for me to imagine a way that this could be done without harming the surrounding brain.

Before we all get too excited it should be noted that the correlation between senile plaque burden and cognitive function is far from perfect. Some people have a lot of plaque (there are ways to detect them antemortem) and normal cognitive function. The work also leaves out the second pathologic change seen in Alzheimer’s disease, the neurofibrillary tangle which is intracellular, not extracellular. I suppose if it caused the parts of the cell containing them to swell, it too could gum up the plumbing.

As far as I can tell, putting the two papers together conceptually might even be original. Prasad Shastri, the author of the first paper, was very helpful discussing some points about his paper by Email, but had not heard of the second and is looking at it this weekend.

It’s why I don’t read novels

You can’t make up stuff like this. A nephrologist whom I consulted about our daughter-in-law’s bout with pre-eclampsia, asked me about her brother-in-law when she found out I’d been a neurologist. Long out of practice, I called someone in my call group still practicing, only to find out that his son (who was just a little guy when we practiced) is finishing up his PhD in Chemistry from Princeton. Put this in a novel and no one would believe it.

The reason for the post, is that Princeton’s new Chemistry building, built to the tune of .25 gigaDollars, isn’t working very well. According to his son not all the hoods are functional. There are other dysfunctionalities as well, lack of appropriate space etc. etc. All is not lost however, the building is so beautiful (if non-functional) that it is used as a movie set from time to time. Any comments from present or past inhabitants of the new building?

Here’s the old post.

Princeton Chemistry Department — the new Oberlin

When I got to grad school in the fall of ’60, most of the other grad students were from East and West coast schools (Princeton, Bryn Mawr, Smith, Barnard, Wheaton, Cal Tech etc. etc.), but there were two guys from Oberlin (Dave Sigman, Rolf Sternglanz) which seemed strange until I looked into it. Oberlin, of course, is a great school for music but neither of them was a musician. They told me of Charles Martin Hall, Oberlin alum and inventor of the Hall process for Aluminum — still used today. He profited greatly from his invention, founding what is today Alcoa, running and owning a lot of it. He gave tons of money to the Oberlin Chemistry department, which is why it was so good back than (and probably still is).

What does this have to do with Princeton? Princeton’s Charles Hall is emeritus prof Ted Taylor, whose royalties on Alimta (Pemetrexed), an interesting molecule with what looks like guanine, glutamic acid, benzoic acid and ethane all nicely stitched together to form an antifolate, to the tune of over 1/4 of a billion dollars built the new Princeton Chemistry building. Praise be, the money didn’t go into any of the current academic fads (you know what they are), but good old chemistry.

An article in the 11 May “Princeton Alumni Weekly” (yes weekly) about the new building contains several other interesting assertions. The old chemistry building is blamed for a number of sins e.g., “no longer conducive to the pursuit of cutting-edge science in the 21st century”, “hard to recruit world-class faculty and grad students to what was essentially rabbit warren” etc. etc. Funny, but we thought the place was pretty good back then.

When the University president (Shirley Tilghman, a world-class molecular biologist prior to assuming the presidency — just Google imprinting) describes Princeton Chemistry as ‘one of Princeton’s “least-strong departments” you know there are problems. Is this really true? Maybe the readership knows.

Grad school applications are now coming from the ‘very top applicants’ — is it that easy to rate them? This is said not to be true 10 years ago — wonder how those now with PhD’s entering the department back then feel about this.

Then there is a picture of a young faculty member “Abby Doyle” who joined the department 6 years after graduating Harvard in 2002. As I recall there was a lot of comment on this in the earlier incarnation of ChemBark a few years ago.

The new building is supposed to inspire collaboration because of its open space, and 75 foot atrium, ‘few walls between the labs and glass is everywhere’. Probably the article was written by an architect. The implication being is that all you need for good science is a good building, and that bad buildings can inhibit good science. Anyone out there whose science has blossomed once they were put in a glass cage?

It’s interesting to note that the undergraduate catalog for ’57 – ’58 has Dr. Taylor basically in academic slobbovia — he’s only teaching Chem 304a, a one semester course “Elementary Organic Chemistry for Basic Engineers” (not even advanced engineers)

Comments anyone?

No longer looking under the lamppost

Time flies. It’s been over 5 years since I wrote https://luysii.wordpress.com/2009/09/25/are-biochemists-looking-under-the-lamppost/, essentially a long complaint that biochemists (and by implication drug chemistry and drug discovery) were looking at the molecules they knew and loved rather than searching for hidden players in the biochemistry and physiology of the cell.

Things are much better now. Here are 3 discoveries from the recent past, some of which should lead to drugable targets.

#1 FAFHA — a possible new way to treat Diabetes. Interested? Take a long chain saturated fatty acid such as stearic acid (C18:0). Now put a hydroxyl group somewhere on the chain (the body has found ways put them at different sites — this gives you a hydroxy fatty acid (HFA). Next esterify this hydroxyl group with another fatty acid and you have a Fatty Acid ester of a Hydroxy Fatty acid (an FAHFA if you will). So what?

Well fat makes them and releases them into the blood, making them yet another adipokine and further cementing fat as an endocrine organ. Once released FAHFAs stimulate insulin release, and increase glucose uptake in the fat cell when they activate GPR120 (the long chain fatty acid receptor).

A variety of fatty acids can form the ester, one of which is palmitic acid (C16:0) forming Palmitic Hydroxy Stearic Acid (PAHSA) which binds to GPR120. if that weren’t enough PAHSAs are anti-inflammatory — interested read more [ Cell vol. 159 pp. 238 239, 318 – 332 ’14 ]. I don’t think the enzymes forming HFA’s are known, and I’m willing to bet that are other HFAs out there.

#2 Maresin1 (7S, 14S dihydroxy docosa 4Z 8E 10E, 12Z 16Z, 19Z hexaenoic acid to you) is the way you start making Specialized Proresolving Mediators (SPMs). Form an epoxide of one of the double bonds and then do an SN2 ring opening with a thiol (glutathione for one) forming what they call a sulfido-conjugate mediator. It appears to be one of the many ways that inflammation is resolved. It helps resolve E. Coli infection in mice at nanoMolar concentration. SPMs further neutrophil recruitment and promote macrophage clearance of apoptotic cells and tissue debris. Wouldn’t you like to make a drug like that? Think of the specificity of the enzyme producing the epoxidation of just one of the 6 double bonds. Also a drug target. For details please see PNAS vol. 111 pp. E4753 – E4761 ’14

#3 Up4A (Uridine Adenosine Tetraphosphate) — as you might expect it’s an agonist at some purinergic receptors (PO2X1, P2Y2, P2Y4) causing vasoconstriction, and vasodilatation at others (P2Y1). It is released into the colon when enteric neurons are stimulated. Another player whose existence we had no idea about. Certainly we have all the GI and vasodilating drugs we need. If nothing else it will be a pharmacological tool. Again the enzyme making it isn’t known — yet another drug target possibly. For details see PNAS vol. 111 pp. 15821 – 15826 ’14.

There is a lot more in these 3 papers than can be summarized here.

Who knows what else is out there, and what it is doing? Glad to see people are starting to look

Watching electrons being pushed

Would any organic chemist like to watch electrons moving around in a molecule? Is the Pope Catholic? Attosecond laser pulses permit this [ Science vol. 346 pp. 336 – 339 ’14 ]. An attosecond is 10^-18 seconds. The characteristic vibrational motion of atoms in chemical bonds occurs at the femtosecond scale (10^-15 seconds). An electron takes 150 attoseconds to orbit a hydrogen atom [ Nature vol. 449 p. 997 ’07 ]. Of course this is macroscopic thinking at the quantum level, a particular type of doublethink indulged in by chemists all the time — https://luysii.wordpress.com/2009/12/10/doublethink-and-angular-momentum-why-chemists-must-be-adept-at-it/.

The technique involves something called pump probe spectroscopy. Here was the state of play 15 years ago — [ Science vol. 283 pp. 1467 – 1468 ’99 ] Using lasers it is possible to blast in a short duration (picoseconds 10^-12 to femtoseconds 10^-15) pulse of energy (pump pulse ) at one frequency (usually ultraviolet so one type of bond can be excited) and then to measure absorption at another frequency (usually infrared) a short duration later (to measure vibrational energy). This allows you to monitor the formation and decay of reactive intermediates produced by the pump (as the time between pump and probe is varied systematically).

Time has marched on and we now have lasers capable of producing attosecond pulses of electromagnetic energy (e.g. light).

A single optical cycle of visible light of 6000 Angstrom wavelength lasts 2 femtoseconds. To see this just multiply the reciprocal of the speed of light (3 * 10^8 meters/second) by the wavelength (6 * 10^3 *10^-10). To get down to the attosecond range you must use light of a shorter wavelength (e.g. the ultraviolet or vacuum ultraviolet).

The paper didn’t play around with toy molecules like hydrogen. They blasted phenylalanine with UV light. Here’s what they said “Here, we present experimental evidence of ultrafast charge dynamics in the amino acid phenylalanine after prompt ionization induced by isolated attosecond pulses. A probe pulse then produced a doubly charged molecular fragment by ejection of a second electron, and charge migration manifested itself as a sub-4.5-fs oscillation in the yield of this fragment as a function of pump-probe delay. Numerical simulations of the temporal evolution of the electronic wave packet created by the attosecond pulse strongly support the interpretation of the experimental data in terms of charge migration resulting from ultrafast electron dynamics preceding nuclear rearrangement.”

OK, they didn’t actually see the electron dynamics but calculated it to explain their results. It’s the Born Oppenheimer approximation writ large.

You are unlikely to be able to try this at home. It’s more physics than I know, but here’s the experimental setup. ” In our experiments, we used a two-color, pump-probe technique. Charge dynamics were initiated by isolated XUV sub-300-as pulses, with photon energy in the spectral range between 15 and 35 eV and probed by 4-fs, waveform-controlled visible/near infrared (VIS/NIR, central photon energy of 1.77 eV) pulses (see supplementary materials).”

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