Protip: Yankees can't drive in snow either

Any time it snows in the south, you can count on a few specific things happening. First, everyone goes to the grocery store to buy milk and bread (you know, for milk sandwiches). Second, your transplanted northern neighbor or friend laughs at that phenomenon (which is justified) and claims that because he's from the north, he "knows how to drive in snow." I tell you now, that man is lying. He lies without malice, to be sure—he honestly believes what he just told you. But he does not know how to drive in snow, and most especially he cannot drive safely in snow in the south.

As you probably know, there was a great big snowstorm in the northeast today. Doubtless you are imagining that plows rolled out like clockwork to clear the streets, but that's not what happened. Instead, as the snow fell, almost all the schools and businesses let out early simultaneously, resulting in what I always think of as the Raleigh Effect, a case of traffic paralysis resulting from an seemingly manageable winter weather event. The source of the problem in this case? Yankees who thought they could drive on snow. The result? Well, traffic was barely moving on South Street. Ralph's friend spent two hours going one block. And this is in Waltham MA.

The truth is that Yankees can't drive on snow because they almost never get a chance to learn how. The northeastern states all have very capable infrastructure that usually clears ice and snow off the roads fairly promptly. When that doesn't happen, in this case because plows can't clear roads that are full of cars, Yankee drivers are just as helpless as the rest of us. Your Yankee friend probably does know how to drive on roads that are a bit slushy, but he's almost certainly not equipped to drive on snowy roads in the South, where snowplows and salt trucks are about as common as an egg cream. Do not let him get in his car; he is in danger.

Now I know what you're thinking: "That may be true of citified Yankees, but what about those who come from the rural regions? They probably know how to drive on the powder." And you're right—New Englanders who don't come from the city are much more likely to be able to drive on actual snow. However, you must not let them drive on snow in the South! They are almost certain to wreck, though not out of any fault of their own. You see, these proud country men and women will get into their vehicles, drive confidently out onto the snowy streets, and promptly be hit by some jackass Southerner who thinks his 4 wheel drive means he knows how to drive in snow. Unless they're lucky, in which case they'll get hit by the southerner who thought his Honda was light enough to stay on top of the snow.

This is the painful truth your friend has not yet learned: Most likely, he actually doesn't know how to drive on a snowy road. Even if he does, this amounts only to overconfidence that will result in an accident due to the inevitable chaos of Southerners (who know even less about driving on snow than city Yankees) trying to get to the store because they've run out of fixin's for their milk sandwiches. Dissuade that man from getting in his car if you can... driving on snow, especially in the South, will only result in dents, dings, or a totaled car.

Posts the next couple of weeks will be sporadic as I get some travel in around the holidays. I shall return with more commentary in the new year.

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The Hierarchy of Motion in Adk

Well, the papers for which Ming produced his fantastic molecular artwork came out in Nature last week. There were two, as some of you might have noticed. Although the larger paper was probably more technically impressive, I'm going to skip over it and talk about the second Henzler-Wildman et al. In the interest of full disclosure, I will point out that although I did not work on this paper, those who did are in my lab. So, either I am a homer or this stuff is so exciting that I still want to write about it even after hearing it rehashed endlessly for more than a year. The question at hand is the nature of protein conformational changes. Specifically, the paper is meant to address whether motions on the timescale of nanoseconds to picoseconds are indicators of slower motions, and if so, what kind of indicators they are.

I don't mean to set up a false dichotomy here, but in order to set up this discussion it's most convenient to describe two extremes of an expected spectrum of behaviors. At one extreme of the spectrum we have a sort of "ball-and-string" model of protein behavior, in which slow motions generally reflect coherent motions of larger structural units with intervening regions of flexibility serving as "hinges". This would tend to produce the energy landscape shown at left, with two minima separated by a single large energy barrier, with perhaps a very low population of an intermediate state. Such a model predicts true two-state behavior in the slow time regime. On the fast timescale, dynamic behavior will be heterogeneous, with residues in the "ball" showing rigidity while residues in the "strings" are flexible.

As an alternative extreme, one could imagine a "jello" model of protein dynamics. In this model, domains or subdomains "wiggle" into new positions primarily through incoherent motions that occasionally produce a coherent shift. Thus, two well-populated minima might be separated by several intermediates with relatively low energy barriers (example energy diagram at right). If this is the case, one would expect the behavior in the slow time regime to be less clearly two-state (because the intermediates are all populated) and for the fast timescale dynamics to be fairly homogeneous and reflect significant flexibility. In the ball-and-string case the transition rate is governed by a monolithic energy barrier, while in the "jello" case the transition rate is limited by frustration.

I want to re-emphasize that this is not an either-or proposition. It is likely that both extremes are present in nature. Also, the ball-and-string extreme is really just a special case of the jello view. So what this paper cannot do is establish "how proteins move". However, it can establish how a particular protein moves and also indicate what techniques to apply to answer the same question in other cases.

The particular protein being studied in this paper is adenylate kinase, which I will refer to as Adk, a highly conserved protein that is present in nearly all forms of life. Its function is to convert one ATP and one AMP molecule into two ADP molecules and vice versa. Adk has two interesting properties. The first is that it is an equilibrium enzyme, which is to say that it catalyzes the phosphotransfer equally well in both directions. This is a useful feature to have in NMR studies. Additionally, although it is highly conserved, the slight differences in sequence between Adk from the intestinal bacterium E. coli (mesoAdk) and the hyperthermophile A. aeolicus (thermoAdk) produce enzymes that have very different thermal stabilities and activities.

Adk is a single fold with three subdomains: a "core" and two "lids", one of which typically binds AMP and the other ATP. It has previously been shown that the opening of these lids is the rate-limiting step of Adk catalysis, for both mesoAdk and thermoAdk. More recent research, published in a separate letter to Nature last week, indicates that these lids open and close even when the substrates are not present. The question then is whether the motion of the lids more closely resembles the ball-and-string model or the jello model. Henzler-Wildman et al. modeled thermoAdk and mesoAdk fast-timescale dynamics in order to resolve the question.

I have shamelessly stolen their first figure for your benefit. The order parameter S² is shown on the structure of mesoAdk (A) and thermoAdk (B). Both datasets were taken at 20 °C, a temperature at which mesoAdk is very active and thermoAdk is not. Just to orient the non-NMR people, for a structured protein one expects most of the bond vectors to have order parameters between 0.8 and 0.9, so even the red residues in these structures are not really all that unusually flexible. Also note that the AMP lid is located at the right end of these structures (folding over at hinges 1-4) while the ATP lid is at the top (hinges 5-8). It should be immediately apparent that thermoAdk is more rigid than mesoAdk. A more subtle point is that many of the "hinges" identified from crystal structures have increased flexibility relative to their surroundings. Also, although the lids (especially the ATP lid) are more dynamic than the core, they retain order parameters characteristic of folded proteins.

This is in contrast to earlier research from the Meirovitch lab, which indicated substantial nanosecond flexibility in the ATP and AMP lids (LID and AMPbD in their description). The supplementary information for Henzler-Wildman et al. is freely available and contains a good discussion of the discrepancy. For those who find it too technical, it can be summed up as follows: the Meirovitch group improperly applied an isotropic global rotational diffusion model, and their SRLS results produce order parameters that are inconsistent with the domains being folded. Moreover, the correlation times they derive with their method appear to be too close together to be reliably distinguished with the NMR data they collected. The Henzler-Wildman results are consistent with the previous relaxation dispersion data for Adk and also with molecular dynamics simulations (contained in the paper). If Katie reads this, perhaps she can elaborate on the reasons why her data is superior. Commentary from the Meirovitch group is also welcome.

Let us will continue on with the paper. As I mentioned, there is a bit of MD in there which supports the NMR findings. What I found to be more interesting, however, was the way that the dynamics of thermoAdk reacted to temperature. Because thermoAdk melts at a very high temperature, it was possible to measure its dynamics all the way up to 80 °C, although glycerol had to be added to the solution at this temperature in order to bring the tumbling rate back down to a point where internal and global correlation times could be reliably separated. The results, which you will have to read the paper to see because I forgot to email myself the figure from work, indicate that as the temperature increases the order parameters decrease (expected) and become very similar to those of mesoAdk at 20 °C. This matches up nicely with the results of activity studies which indicate that the activity of thermoAdk at the high temperature is similar to that of mesoAdk at the low temperature. Because it is known that the lid opening is rate-limiting, and because local deformations at the hinges are required for the lids to open, it is likely that the increased fast-timescale flexibility of thermoAdk hinges at high temperature is directly related to the increased activity of the enzyme at that temperature.

The dynamic results in this paper seem to support the ball-and-string view of motions in Adk (by contrast, the Meirovitch results would suggest the jello view). Although the lids are not as rigid generally as the core, their order parameters are still within a reasonable range for a folded protein, and are for the most part higher than the order parameters of residues located at reasonably well-defined hinges. In Adk, motions on the μs-ms timescale appear to be enabled by flexible hotspots that lie between well-defined elements of tertiary structure, with the overall ensemble dominated by the two discrete endpoints. For this case and others like it, a combination of relaxation dispersion measurements and model-free analysis suffice to characterize the motions.

For cases which more closely match the jello view, many NMR approaches may prove difficult to implement. Relaxation-dispersion analysis of such motions is likely to be frustrated by endpoints that constitute a slim majority or plurality of the ensemble, high rates of interconversion between similar conformers, and possibly a low Δδ for these conformers. Fast-timescale studies will be difficult because the motions involved will be complex and may violate some model-free assumptions. In such cases, high-field measurements of R₁ dispersion (yes, I said it) may prove especially valuable as the dominance of ω_N in those measurements at least gives us a chance of distinguishing motions in the high-ns regime. Of course, the major difficulty for NMR will be if the jello motions result in intermediate exchange and excessive signal averaging — in these cases paramagnetic spin labeling or EPR studies may prove to be the only practical method.

Henzler-Wildman, K.A., Lei, M., Thai, V., Kerns, S.J., Karplus, M., Kern, D. "A Hierarchy of Timescales in Protein Dynamics is Linked to Enzyme Catalysis" Nature 450 (2007) p913-916.

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Tin Man: recycled

As Tin Man, the Sci-Fi Channel's "re-imagining" of The Wonderful Wizard of Oz entered its fifth hour, I found myself wishing that I was watching The Wiz instead. I don't mean that The Wiz was a better piece of cinema than the new mini-series, though arguably it was more visually inventive. However, it shared an important virtue with the book and the original movie musical that the present adaptation lacks: it knew what it was. The Oz story is not a sophisticated adult story about contemporary morality, it is a child's story about wonder and adventure. It can be turned into something more sophisticated, with enough effort, but that's a task at which Tin Man manifestly failed.

The presentation looked more sophisticated, I grant. But dressing people up in black leather does not, in fact, make for a sophisticated story. All this dark, steampunk set-dressing looks pretty cool, but it doesn't really fit with the theme of magical little girls who save their world with the power of love. The more adult visuals simply didn't mesh with the story that was presented. As a result, I felt a certain dissonance, as if I were seeing Strawberry Shortcake depicted as a dominatrix.

And while the story was unsatisfying on its own merits—a tale of a counterproductive MacGuffin fetch quest that heavily involves amnesia, of all damn things—it was even less satisfying as a re-imagining of Baum's original. When you re-imagine something, you ought to say something new, otherwise you're just making fan fiction. But Tin Man is essentially childish in its presentation of good and evil, and the only adaptations it makes to Baum's world are to insert stock elements from other sci-fi worlds and movies, as well as importing Nurse Ratched's hair. You can read Wizard of Oz crossovers at fanfiction.net if that's what you want; there's no reason to make a movie out of them.

Don't misunderstand me, Tin Man isn't bad. It looks nice, and the actors largely do a good job (although the child who plays little DG was not very good). The music leaves something to be desired, but doesn't offend. But Tin Man just feels unnecessary, a superfluous bit of fluff trying to staple a grown-up look onto a childish and irrelevant story.

The Sci-Fi channel is a curious contradiction. Most of its original series (at present, anyway) are actually pretty good, and their re-imagining of Battlestar Galactica may be the best scripted show on television. Their original movies, however, are largely pathetic drivel starring actors that have washed up on this shore after fading from better careers. And then there are the mini-series, which are typically of very high quality, probably because many of them are adapted from books. In this case, it seems, the movie quality bled into the mini-series. Although the production values of Tin Man were high, the writing was poor, and in the end, you'd be better off watching the original, rather than this fanfic.

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Child's Play, again... plus, game reviews!

I went over to the Child's Play site this morning to check out how things were progressing. Apparently, they're up to $450k, with several weeks left to go. If you haven't already, please add your own 5 or 6 bucks to the pot. Readers in North Carolina will be pleased to know that Children's Hospital of North Carolina (in Chapel Hill) now has their own wish list available. Coverage of the 50 states seems to be increasing daily, so if you're concerned with giving locally, check it out. Most of the eastern states have at least one hospital you can give to. Canadians, Brits, and our friends down under in Australia and New Zealand have hospitals on the list, too. If you don't want to give games or gaming systems, remember that there's also a huge demand for (non-absorbent) toys, books, board games, and DVDs. Just click on a hospital you like, or the PayPal direct donation link.

You don't have to like the Penny Arcade guys (hey, plenty of people don't) to like what they're doing. The recent game-reviewing spat (exacerbated by Gerstmann's suspicious firing) is really relatively tame compared to their past feuds with, say Jack Thompson. Anyway, I think it comparatively obvious that Gabe is right—game reviews have adopted the approach of newspaper movie reviews and devolved to being dominated by their metrics. This is the same phenomenon that creates those movie print ads that heavily feature 5-star raves and "two thumbs up". Some gaming companies adopt the same approach, touting 10/10 scores and the like, to the exclusion of giving any idea what the gameplay is about. Consider Kane and Lynch, for example, the game that kicked off the present controversy. The advertisements feature a bunch of cutscene violence that looks decent, so I know the game is about killing dudes with reasonable graphical fidelity. But what's the story? How does it feel to play the game? Why is 'killing dudes with reasonable graphical fidelity'—a property shared by no less than 50% of extant games—their marketing focus? This is different from asking why it was their development focus; that's a question for its own post.

The length and breadth of most gameplay, paired with the diversity of personal goals associated with a person's approach to gaming, calls for a more measured and less numeric approach. Prince of Persia: The Sands of Time is a fantastic platformer wedded to a charming story and a dull combat system. For the platforming enthusiast it is a game sent from heaven, but someone who loves RPGs, fighting games, or 3rd person adventures might justifiably hate it. Game reviewers need to consider an alternative approach to reviewing games, one that pays less attention to a dubious and corrupt quantification scheme and puts more effort into opening a window for the reader onto the experience of playing.

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