The Swine Flu Song

I haven't posted on here in a long time, but I just saw this and got an idea that I wanted to share with the world.

A San Francisco man named Stephan Zielinski, who is NOT a biochemist, decided to turn the sequence of swine flu hemagglutinin into a song.

Someone totally needs to take his algorithm and incorporate it into a plugin for one of the structure viewers like Chimera. Then, artists can create audiovisual works in which not only is a protein "played" musically, but the side chain of each amino acid flashes in the 3-D structure simultaneously with its respective sound. In this way, a linear piece of music is made to correspond with a path through 3-D space... How mindblowing.
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Membrane protein structures--part 3

I haven't posted here for a long time, so I decided to summarize a little of membrane structural biology over the last few months.

By far the most exciting advancements have occurred in the field of GPCRs. The Stevens group at The Scripps Research Institute (who also published the adrenoceptor structure mentioned a few posts ago) published a new structure of the same receptor, but with a different antagonist (3D4S). In this structure, a cholesterol molecule was observed in a slightly different location from in the previous one, which led to the discovery of a putative cholesterol recognition motif. Also, Schertler and colleagues at the MRC laboratory in Cambridge solved the structure of the turkey beta1 adrenoceptor with yet a third antagonist (2VT4).



One might think that with the first structures of "real" pharmacologically relevant GPCRs being solved, the relevance of rhodopsin, the previously prototypical member of the superfamily, might be on the way out. However, this is most definitely not a conclusion to jump to automatically, as a recent structure (3CAP) from Park et. al. demonstrates. This is the structure of opsin, which is rhodopsin without the covalently attached light-absorbing molecule retinal. Many of the helices show a change in conformation relative to rhodopsin, and based on some biochemical data showing constitutive activity in opsin, the authors propose that this structure may represent the long-sought active state of the receptor. This structure shows changes of a significantly greater magnitude from dark state rhodopsin than any other structure previously proposed to be activated, and this makes me more inclined to believe that it could actually be active. In fact, I am guessing the shift observed in opsin may be TOO large to represent normal activation, and may represent a partial unfolding of the receptor due to complete loss of the stabilizing effect of retinal. Though much less notable, for the sake of completeness I will add that a structure of squid rhodopsin has also been published (2Z73).

As for ion channels, a bacterial homologue of the Cys-loop superfamily, to which nicotinic and GABA(A) receptors in animals belong, has been solved (2VL0). The ligand of this receptor is unknown, and the low homology with other Cys-loop receptors along with the mediocre resolution mean that this structure will most likely not be useful for modeling studies. Also, this is not recent, but the structure of the acid-sensing channel ASIC1 (2QTS) provides insight into a new fold of ion channel. The most intriguing property of this structure is the fact that the homotrimeric channels show each monomer to be in a different conformation, with some of the differences being large (almost 10 Angstroms). This may be an artifact of the crystal structure, but if not, this would be an unprecedented finding.

In the area of transporters, not that much has happened, although there is a structure of a sodium-galactose transporter by a group at UCLA due to be released soon. Intriguingly, this transporter is related to LeuT, despite a lack of sequence similarity aside from conservation of a few glycines at proposed hinge regions. The fact that this transporter is in the inward-facing conformation, as opposed to LeuT, which was in the outward-facing conformation, should provide insight into the transport mechanism.
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Transmembrane pump structure

We are clearly now fully in the era of the membrane protein crystal structure--it's clear that even being in the greasy environment of the cell membrane isn't going to protect proteins much longer from the X-ray beams of determined structural biologists. This time, the structure is of the sodium potassium pump, also known as the Na+/K+ ATPase, which sets up the sodium and potassium gradients necessary for numerous cellular functions, from simple maintenance of osmotic balance to uptake of nutrients and nerve impulse transmission. Pharmacologically speaking, this protein is also the target of the simultaneously highly toxic and medically useful cardiac glycosides.

I am not nearly as surprised at the publication of this structure as I was at the adrenoceptor structure mentioned in my last post, or the structure of the amino acid transporter LeuT mentioned on here over a year ago, since multiple structures of a functionally very similar ion pump, namely the sarcoplasmic/endoplasmic reticulum Ca2+ ATPase, had been published years ago (interestingly, some newer structures of this Ca2+ ATPase were just released as well).

I skimmed through the paper in which the Na+/K+ ATPase structure is described, and curiously the authors make absolutely no mention of the cardiac glycoside binding site, despite the fact that there is a clearly visible pocket among the amino acid side chains known to be involved in the binding of these inhibitors. Maybe, a discussion of this site was omitted either due to the modest resolution (3.5 A), and/or because the K+ occupied form of the protein, which is (assumed to be) mimicked by the rubidium ions in the crystal structure, is known to have a lower affinity for cardiac glycosides than the unoccupied form. It seems to me that groups like Qiu et. al. were very much on the right track, though.
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Shout it from the rooftops...

... a new G-protein coupled receptor (GPCR) has been crystallized!!! This one is actually pharmacology relevant, and closely homologous to the targets of many clinically important drugs. Namely, it's the beta2 adrenoceptor, bound to the partial inverse agonist ("beta blocker") carazolol. Immediately following a publication of the structure of the receptor complexed with carazolol and an antibody at modest (3.4 A in the plane of the membrane, 3.7 A along an axis normal to this plane) resolution in Nature, Brian Kobilka and colleagues published a high (2.4 A) resolution structure obtained by insertion of T4 lysozyme into the third intracellular loop, which yielded better-diffracting crystals. Congratulations to the Kobilka lab!

Those who have any kind of interest in structure-based drug design will most undoubtedly know how big this news is without me spouting all kinds of hype, and most others probably don't care anyway, so I won't give a long explanation. If you would like some more introduction, Keith Robison at Omics!, Omics! has a post on this. Any pharmacology or structural biology bloggers who actually read this should feel free to link here, write their own post if they think mine sucks, or of course can link directly to the articles as I have done.

The structures are not available from the PDB yet, and I haven't even examined the figures in the paper with the high resolution structure yet (beyond the new Kobilka lab front page graphic, which I just stumbled upon)--I want to see how much I can predict before I actually view the structure in detail. Nevertheless, once they are, I (and undoubtedly dozens of others) will be creating new models of other adrenoceptor complexes, as well as of other receptors in the amine subfamily. It is almost certain that these will be substantially more correct than the previous rhodopsin-based models, however illuminating the latter have been (and what I know about the new structure seems to say that they were not THAT far off).

...Whew! I haven't blogged in over five months, but I just had to say something about this. After a week that started with the southern California wildfires (I didn't have to evacuate, but I was close enough to see the smoke, and the campus has been closed), I receive notice of this. If someone had asked me last week to make a bet, I would have said I would have finished grad school before a drug-bound GPCR structure was published ( I just started this fall--note also that my area of grad study has nothing to do with GPCRs, crystallography, or pharmacology--this is just a personal area of interest). On the other hand, the structure of LeuT a little over two years ago totally caught me off guard too. I guess we're finally coming into the era of the membrane protein crystal structure. Any guesses as to when the first GPCR agonist complex structure will be published?
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A little puzzle

Here's something for whoever reads this blog to try and figure out. Below I have posted what I have tried to make look like an excerpt from a story (it actually isn't from any story). The "plot" is a little disjointed at times I will admit, but there is something "special" about this piece of writing, and that something has to do with the 30 underlined phrases. As a small hint, as I bet many people will think along these lines, the phrases do NOT unscramble to spell something--at least not that I intended. I specifically tried to use a lot of phrases that were unlikely to occur in normal text and/or used rare words--there are many other phrases of the same type I could have used that make sense by themselves, but that wouldn't have been as much of a challenge. I wonder if anyone will leave a guess in the comments.

On to the "excerpt":


"Where shall we direct our forces, at Colombo, in the Niagara provincial territory?"

"It's that or Segovia".

"It doesn't really matter", Davis interjected. "As of now we lack the technology to swiftly encircle the territory. If we attempt our mission like this, word of our approach is certain to reach them in no time, and our attack is sure to be thwarted."

"But in order to make any difference we would need to increase our maneuverability by a thousandfold. Even with state-of-the-art vehicles running on specially nanoformulated fuel, and ultra-multiplexed communication transponders to coordinate the whole process, I don't know if we could do it."

"A thousandfold is veneer compared to the solid gains in speed we could obtain with the necessary equipment. Meanwhile, you simply must put your energy into fourth gear and hope for the best. I'll send a request to our technology acquisition officials through the overnet to notify them that we are in need of an expanded arsenal.

"In terms of increasing energy reserves, what ever happened to the work of Dr. Ramirez? Do you remember what he did when he was still working for Phytovance? I was thinking about that the other day".

"He studied the prospect of using a novel biochemical mechanism, found in the chloroplasts of vacuolate cells in the newly discovered tropical Ephemerides fern, to store chemical energy at an unprecedented density."

"But how much energy could be stored in each single one of his devices, a picojoule?"

"That's possible, but considering how lightweight and compact the microscopic fuel cells he invented are, the discovery could still lead to some immensely profitable patents. It beats our current bio fuels by a decent margin. Just think if you could hold a device in your hand that would supply your average home with electricity for several days. However, I remember hearing allegations that he stole the idea from some other researcher, one who was lesser known in the field."

"Well, the fact that his research into exotic plants was funded using corporate money is a warning. Men do things under the money-moon that they would be wise enough not to under the daylight of pure intellectual discovery."

"Do you know where he lives now?"

"I believe down in Newport, at least that's what I heard from one of my friends who ran into him at a biodevices conference ".

"Hot as a candlewick, Newport is these days. It seems everyone is trying to start up their businesses in the area. In the western part of the city, at least two thirds of the population is parvenu."

* * * *

Egan Morris was flying back to the headquarters of the technological division when the overnet transmission reached him, watching the scenery through a window to take his mind off the stress of the many requests for assistance he had received that day: a heavy volume accumulated in only a little over an hour. The shallow water near the coastline formed a straight turquoise stripe. The spectacular mountain ranges down below stretched as far as the eye could see, and from this height they seemed almost stationary, serpentine valleys filling the gaps between them. As Morris's gaze fell upon them, he was reminded of a poem he had read many years ago:

In December, I on powdery snow-blanketed slopes will gaze
During Christmas and all of it's cheer
I go skiing while I enjoy all the days
'Til the starting of a brand new year

As February a religiosity brings
I do existential thoughts contemplate
Of of majesty and most wondrous things
Hoping springtime will not start too late

In March I meander through valleys and hills
The color of Isfahan granite
I've been lots of places for sure, but this still
Must be one of the best on the planet
My Connecticut

* * * *

Meanwhile, Lawrence Hamford was relaxing in front of the television. An injury sustained from a previous encounter with the enemy had left him with a badly infected cut on his left thigh. He still had not returned to his former condition, but it was nothing that a few days of streptomycin, hearty meals, and rest couldn't take care of. His wife was in the kitchen with their son Ryan, preparing some lunch. Ryan had just finished making himself some eggs.

"What kind are those?", she asked him.
"This is scramble, ma" he replied, the words muddled by the half-eaten piece of bread he held in his mouth.

Hamford got up from his seat and walked into the bathroom to inspect his wound in the mirror. The mirror was small and mounted above a scrappy vanity, one that looked like it had been constructed out of leftover pieces of wood sitting in someone's garage. There were more important things to think about, though, than home improvements.

"So, so calendar, have you got anything for me today", he said mentally to himself as he looked at the calendar on the wall of his kitchen as he walked by.

* * * *

By now the soldiers were in the process of marching across a desert plain. As the their heavy-duty boots impacted the ground, they made a rhythmic plodding sound: "EEFB EFFB FAFB FUFB, EEFB EFFB FAFB FUFB..."

It wasn't long before they encountered the first enemy troops, led by General Williamson. As men opened fire, the thunderous, digitally amplified voice of the General rang out over the plain:
"Philistines and feathered fowl, of war and by my words, to Styx is where you all will go!". General Williamson was a military Bacchus; he responded with such excessive celebration and revelry to the massacre of his opponents armies and to the leveling of their major cities that even his allies were disgusted.


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The many roles of the brain cannabinoid pathway

Now on a more celebratory note: In honor of 4/20, I will post a brief review of the multifaceted activity of the central cannabinoid receptor, CB1, which is expressed in the brain. The peripheral receptor, CB2, also has interesting roles, especially in regulating the immune system, though for the sake of brevity I will omit those here.

For those who do not know, cannabinoid receptors are activated by a set of endogenous signaling molecules known as endocannabinoids, in addition to the marijuana compound THC and various synthetic molecules of multiple structural classes. The endocannabinoids are nearly all esters and amides of unsaturated fatty acids, and the most important are anandamide (arachidonyl ethanolamide) and 2-arachidonylglycerol.

First, probably one of the least surprising roles of CB1 is to control appetite. This has led to the development of CB1 antagonists, most notably rimonabant, as anti-obesity drugs.

In addition, the CB1 receptor is involved in suppressing the release of several neurotransmitters, including glutamate, GABA, acetylcholine, and norepinephrine. It appears that there is a close functional interconnection between the CB1 receptor and the mu opioid receptor, which binds opioid peptides such as endorphins and enkephalins in addition to opium alkaloids like morphine, in the regulation of neurotransmitter release.

The CB1 receptor has been found to reduce seizure-type activity in the brain, as shown here in the hippocampus. One possible mechanism that probably contributes to this effect is a reduction in the synchrony of neuronal firing, decreasing the probability of large spikes of electrical activity. Amnestic at Gene Expression gave a good explanation of this phenomenon a while back. On the flip side, this decreased synchronization may underlie the inhibition of memory by cannabinoids.

CB1 has also shown roles in neurogenesis (differentiation of stem cells to form neurons) as well as differentiation of neurons and astroglia. This points to an overall effect of CB1 activation to stimulate "building up" of the neural network in the brain.

Finally, on a completely different note, the CB1 receptor has shown a role in implantation of the blastocyst (a very early stage of embryonic development) in the uterus. In order for proper implantation to occur, the development of the blastocyst to the point where it is competent to implant, and the development of the uterus to the point where it is prepared to receive the blastocyst, must be synchronized. The blastocyst expresses the CB1 receptor, and the uterus expresses the enzymes necessary to synthesize the endocannabinoid anandamide. It was found that the effect of anandamide on the blastocyst was highly concentration-dependent, with promotion of implantation competence at low concentration and inhibition at high concentration, both of these being mediated by CB1.
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Reflections on Virginia Tech

I would like to say a few things regarding the massacre at Virginia Tech.

First, I think the "blame war" going on now around the incident is very counterproductive. As terrible as this incident was, it is still an isolated occurrence and I don't believe it can be attributed primarily to a general failure in the university, our society, or any other cause outside the specific life circumstances of the shooter.

While Virginia Tech could clearly have been more prompt in alerting students to the news of the dormitory shooting, it is understandable that school officials expected that to be an isolated incident. You can't expect someone to have predicted that the happenings at the residence hall were only the tip of an iceberg. The same goes for the strange plays Cho Seung-Hui wrote for English class. I'm sure there are many students with a macabre imagination who never go on to commit any crimes in the real world. While it certainly would have been kind of students in the class to ask Cho if something was bothering him, and in fact he was offered counseling, I doubt paranoia would have been justified. Finally, on the subject of gun control, he would have probably been able to obtain those weapons no matter how rigorous a background check was, since he (presumably) had no criminal record. Reason has a good article explaining how probably neither ultra-strict or ultra-loose gun control is the answer.


I don't believe that the true blame lies with anyone other than Cho Seung-Hui himself. His shooting was directed at random people, the majority of whom must not have wronged him in any way, so any idea that he was "getting even" is not fitting here, no matter how much he had been made to suffer previously.

However, while I do not "fault" them, I do believe that some circumstances in Cho's surroundings, including his bullying, had some role to play in him becoming angry enough to murder 33 people. It is also sad that he was provided no opportunity for releasing his anger before it built up to such a level. For many more reasons than just the possiblity of creating a murderer, I think we should all think carefully before labeling people "losers" or considering them less valuable just because they don't fit in socially. There is so much more to a person's worth.

I strongly hope that this incident will not lead to increased negative stereotyping of loners, misfits, people who act "strange" but nonviolent, etc. This can only make the problem worse, by making these people less likely to open up and seek help in addressing injustices they have faced. I also hope that more peaceful but weird-acting people will not start to be forced into psychiatric settings in an attempt to "catch the next school shooter". Psychiatry is already used as a means of denying rights to supposedly "crazy" people, though thankfully this is rare due to laws making involuntary treatment very difficult. I would like to see it stay that rare.
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