Saturday, December 31, 2011

The End Draws Near....

....for 2011, at least.

I really don’t have much to add about the recent charges in the UCLA lab safety case, especially given the posts elsewhere (most of which are collected at The Safety Zone here: 1; 2; 3 ). As I can easily count the small molecule syntheses I’ve done since my undergraduate days on my hands with room to spare, I am definitely not someone who can offer hard-earned advice on safety in synthetic chemistry labs based on extensive personal experience.

I will note that – obviously due to my biological inclinations – that lab safety can be just as much as insulating your experiment from you as protecting you from any hazards. Which, given one’s perspective on human nature, might be a more effective means of motivating compliance with lab safety standards.

Onto cheerier subjects….

My plan to bring up Helmholtz when Gibbs is mentioned did not quite pan out this year. I don’t think it’s going to happen. I’ll have to be contrary in some other manner in the future.

I did get back to blogging and commenting a bit this year, and I intend to keep it up next year. While the notion of doing substantive ResearchBlogging is a reasonable one, it would entail winding back the semi-regular sarcasm a bit for thoughtful commentary. I’m not sure if my system could endure the shock. It might happen, though. Having said that, if one has any substantive questions where my thoughts might be of interest, ask away.

Best wishes to all for a happy, healthy, and productive New Year! Read more!

Thursday, December 22, 2011

Trust but verify.

The question of how much to trust computational methods is brought up here at Chemiotics II. My answer is that it depends on what one is looking for in the first place.

If one is looking for some sort of completely accurate and precise way to have all biological phenomenona fall out of "first principles," well, I wouldn't hold my breath. Of course, I don't think anyone is really waiting for that. At least I hope not. I believe my feelings on these sorts of issues are best described by personal experiences I've had with computational methods.

In grad school, I had an interest in this one mid-sized protein (somewhere between 40 to 60 kDa) that was known to bind this particular ligand. There was a crystal structure of the protein with and without ligand, although of course it was hardly the entire story (which is why it was the subject of my research attentions). In any case, collaborators did some MD simulations, and it was consistent with what we had found and was known. In their next bit of work, they mentioned that they found something new regarding the mechanism of ligand binding. This was going on the same time as I was doing some work, and as it turned out, my data did not rule it out. And so new research was inspired for those who took up the project after I left.

Currently, I am embroiled in a sordid and complex tale of transmembrane signaling involving the receptor and varying amounts of soluble cytoplasmic proteins that propagate that signal. There was a fairly recent paper detailing MD studies of the signaling process. Well, part of it, I suppose - huge chunks on either end of the transmembrane receptor were not included, and none of the cytoplasmic proteins that bind and are modified by the receptor were included in the study. Certainly a daring attempt, but it's hard to get too worked up over it when it doesn't resemble anything that I actually work with on a daily basis.

In short....I think properly used, it can be a useful way to bridge what is measured experimentally with the metaphors we use to describe processes. (For example - people love using descriptions involving simple machines, but what is actually measured are thermodynamic or spectroscopic quantities. Of course, "force spectroscopy" looks to change this, but when you yank apart a protein, you are no longer just gently playing around at kT or sub-kT conditions to see what kinds of deformations you get naturally or as a response to some stimulus. Anyway....) Certainly, for small enough systems, I am inclined to give them a proper reading, and in cases where the system might be larger but is somewhat well characterized, the same applies. In giant systems where they toss out a number of critical components or oversimplify to the point of absurdity, I am generally far more skeptical.

Merry Christmas to those who celebrate, Happy Hanukkah to those who celebrate, and a delightful winter holiday season to the rest. Read more!

Saturday, December 10, 2011

Chemists, controls, and computing.

I have no experience with drug discovery, so I suggest one reads the excellent commentary offered over at The Curious Wavefunction and In the Pipeline inspired by a recent article on the role of computer simulation in pharmaceutical research, presuming that they haven’t already done so. What I thought was interesting enough to post about in response is in Wavefunction’s blog post.

They are reluctant to carry out the kind of basic measurements … which would be enormously valuable in benchmarking modeling techniques.

Methods development research can be difficult to support. Even obtaining modest funding can be difficult. It’s one reason why it can usually seem incremental in nature, as it’s easier to scrounge a few small devices or specialty materials to use with existing research infrastructure. This one is near and dear to my heart, as I have two such projects going on at the moment, and a third which is still in the planning stages. Unfortunately, it’s not the kind of stuff one could convince people it needs to be funded and generously at that. That was really more just me griping. But that is par for the course for me here at my blog…..

Unlike chemists, engineers are usually more naturally inclined to learn programming and mathematical modeling. Most engineers I know know at least some programming. Even if they don't extensively write code they can still use Matlab or Mathematica, and this is independent of their specialty (mechanical, civil, electrical etc.). …The lesson to be drawn here is that programming, simulation and better mathematical grounding need to be more widely integrated in the traditional education of chemists of all stripes, especially those inclined toward the life sciences.

I of course agree, but am inclined to mention a few things. This may be an artifact from my recollection/experience and is no longer the case, but I’ve seen a tendency for computational methods & applications courses intended for chemists to be heavy on the typical computational chemistry aspects (basic electronic structure calculations, a dash of MD, some molecular mechanics) along with a fair bit of introductory programming. Not that there’s anything wrong with that….but wait, actually, it is problematic.

I would think a more useful course might still contain some introductory programming and some of the typical computational chemistry, but I’d like to think that one could also take the time to introduce the students to chemo/bioinformatics as well as a module on proper data fitting. Of course, it might be claimed that it’s better suited for an upper-division chemistry laboratory, which would be fine. The important thing is to get people weaned from MS Excel and to actually start fitting data, not algebraically torturing your data until it’s in a format that can be linearly plotted and then fit with Excel.

Also, given that I have this notion of this course being something that all students will probably find useful in the future, the programming and software elements should be those that will easily lend themselves to a broad range of applications and uses in the future. I would imagine that introducing students to something like Origin or Igor Pro would be useful, as well as (re)introducing them to Mathematica, Matlab, Maple, or other comparable software. While the power of Fortran is well established for the numerical-heavy applications in computational sciences, I feel it would be better to have students introduced to something like Python. You can leave the Fortran for those who want to do the computationally intensive theoretical chemistry, while I’m sure the majority can use Python as a useful tool in their work.

This above is clearly influenced by personal biases (I'm a bio/physical chemist who is in the process of adding "systems biologist" if he keeps it up for much longer), but I think that sort of mix in a "computers & chemistry" course would serve a good cross-section of the chemical community. Any and all commentary, feedback, suggestions, and brutal eviscerations of my points are welcomed. Read more!

Wednesday, October 5, 2011

Cackling in Glee.

I actually can't muster up any of my lazy man's wit for this year's chemistry Prize - is it physics? Physical chemistry? Materials science? Just sublimely wonderful and scoffs at the narrow cognitive categories that spring up on occasion. It also emphasizes that as chemists, we have fellow travelers in numerous allied pursuits - remember, if we want to continue blaring the "we are the central science" mantra, we have to recognize chemistry of all sorts whatever its ostensible classification.

The comments at ChemBark brought up two questions in my mind -

(1) - what do we consider chemistry?


(2) - why did it seemingly not catch anyone's attention as a candidate for the Chemistry Prize?

I've mentioned - in the vein of Roald Hoffmann - that chemistry stands on the pillars of structure, reactivity, and synthesis. Anything that causes us to reevaluate our understanding of even one of those pillars is noteworthy, as quasicrystals surely did in terms of understanding structure. That they can also occur naturally would indicate that our understanding of geochemistry can stand some fleshing out.

Now, if you had asked me about quasicrystals yesterday, I'd have thought that they'd be a Physics Prize one of these years, given that most of what I had heard about them was through physics seminars I'd attended over the years. But it used to be that the gap between physics and chemistry was far smaller - Rutherford (he of the physics vs. stamp collecting joke) picked up his Nobel in Chemistry way back when, and van der Waals was a Physics laureate. This year's Prize is a nice throwback in that regard. I think there might also be something to the comments on ChemBark that solid state chemistry is something of an underexposed topic in undergraduate curricula here in the US, and many of us just don't have that proper background in the field (which is certainly my case - most of what I know is because I stumbled into having learn something about the field in grad school). There might also be an echo chamber effect going on in the chemistry blogosphere. ;)

Now to start preparing for next year's betting pool! Read more!

Tuesday, October 4, 2011

Nobel Notes

Thumbs up to the Nobel Foundation for their decision regarding Ralph Steinman's laureate status. I always felt that the rule was to make sure nominations of those who have passed on were not submitted in the first place. Now, whether or not one agrees with this is a separate issue.

Given that my professional interests are not very immunological or astrophysical, I don't have any particularly incisive commentary about the Physiology/Medicine or Physics Prizes.

A followup to a comment elsewhere - Tom Wainwright passed away in 2007, so unfortunately he would be ineligible for a Nobel. Given that Aneesur Rahman and George Vineyard have also passed on, Alder is really the only "founding father" of MD who would be a possibility.

On the off chance it is a magnetic resonance Chemistry Prize this year, I will not be sarcastic and post "but it's just applied physics! Why are applied physicists winning Nobel Prizes?" I'll actually just write a short blurb on what was so cool about the new laureates' research. (All other fields of physical chemistry being recognized are fair game for such commentary, though.) Read more!

Tuesday, September 27, 2011

Surely you jest!

So, I strongly recommend everyone checks out this paper -

Accessing protein conformational ensembles using room-temperature X-ray crystallography

- which was just published in PNAS this week. The paper cites a 2004 paper by Bertil Halle (which I mentioned a while back) on the potential consequences of flash freezing and cryocrystallography.

Enjoy! Read more!

Tuesday, September 20, 2011

No, I am not going to talk about the recent paper on the success of Foldit. Mostly since if you can even get a crystal structure for something, it's probably not agonizingly painful enough for me to work on - as I've said before, give me your disordered, your poorly soluble, your aggregated masses yearning to be analyzed.

Anyway, I wanted to mention this interesting-looking paper:

Binding Leverage as a Molecular Basis for Allosteric Regulation. I haven't had a chance to really dig into the paper, but the idea itself is simple enough - ligand binding can couple to various collective motions in proteins to varying extents, due to which we observe allosteric modulation of enzyme function. There are obvious oversights (one example that they mention in the paper - the lack of attention paid to proteins that aren't enzymes such as signaling proteins of various types), and I'd want to pore through which structures they used in the PDB (e.g., how did they deal with the family of structures that are generated by NMR if applicable). Then again, I usually consider thought-provoking ideas worth the publication, even if a judiciously skeptical outlook may make them seem a little less lustrous. Read more!

Friday, September 9, 2011

As it’s that time of the year again to start speculating about potential Nobel laureates for 2011, I’ve already chimed in at The Curious Wavefunction and left a short note over at ChemBark.

While I’d be pleased to see another magnetic resonance prize (or five), there is a huge name which I’ve neglected, mostly since I was afraid that his time to be recognized had passed, but as he was the Welch Award recipient this year – John Waugh from MIT. Of course, if it were up to me, I bet I could come up with at least half a dozen trios of deserving recipients for magnetic resonance. But anyway…..

I’ve wondered about this earlier and I might as well bring it up again – what about the Kavli Prizes? Currently, they’re awarded for astrophysics, nanoscience, and neuroscience – will see ever see a dual Kavli and Nobel laureate? Or will being recognized with one put you out of the running for the other? Having said that, I know people were predicting someone getting a Nobel for semiconductor nanocrystals, so perhaps if Lou Brus is recognized by the Nobel committee, we’ll see one this year.

Quantitative biochemistry is not giving me quite as much of a headache. Although I'm hardly done with it just yet. I do envision there being an extremely dense biochemistry publication in my future. Speaking of which, back to working up data.... Read more!

Saturday, August 27, 2011

A few quick thoughts.

I am still trying to unenviably navigate an n-dimensional parameter space, attempting to optimize the biochemistry for the present bane of my existence in order to get to some proper structural & biophysical studies. It is further complicated that whenever I do seem to devise a plan, something odd crops up in my data in amidst the general experimental madness (remember, if you work with n components, you need to vary one and keep n-1 constant : easier said than done!).

In any case, I stumbled across this interesting paper. Given my innate worrying about structural data obtained under cryogenic conditions, this was right up my alley – utilizing mesoporous materials to confine proteins and their hydration waters, and then using your interrogation method of choice across a range of temperatures without having to worry about the effects of bulk water. I can envision that this would be an excellent way to more explicitly bridge the gap between cryocrystallography and dynamic/functional studies done under more physiologically relevant conditions.

There was a very long back-and-forth over at The Curious Wavefunction this past week. I basically have the opinion that expecting physics to “explain” chemistry and biology is perhaps a bit overly demanding. I mean, it’s not as if all physicists are just waiting to wrap up high-energy/elementary particle physics and then retire, after all! There are still a number of unresolved questions in physics, and as a number of them involve many-body systems, it would only seem reasonable that those are the ones that would likely be of the most immediate application to chemistry and biology.

Now to finish preparing for this inclement weather…..
Read more!

Thursday, July 7, 2011

As has been often noted about a number of topics, one’s biases will always skew one’s perspective.

On the one hand, we have this very interesting paper where the authors suggest correlated motions in ubiquitin over a distance of ~ 15 Angstroms (1.5 nm) based on further squeezing information from previously acquired NMR data with the help of computational methods. On the other hand, there is this other very intriguing paper where the authors put forth using gadolinium tags as a way to obtain structural constraints in proteins on the order of ~ 6 nm (60 Angstroms) via ESR/EPR techniques.

In the former, we’re looking at proposed long-distance correlations based on a bunch of relatively weak, short-range interactions (NOEs and RDCs), while in the latter we have nanometer-scale distance constraints being derived from a technique that is well matched to determining distances at the nanoscale. I figure the astute reader can figure where I stand on each given my tone.

Suffice it to say, it’s the reason why I’ve recently developed an interest in 19F NMR (oh, to work with a nucleus that has a decent gyromagnetic ratio and isn’t as common as protons in biological materials!), for one, as well as metal binding tags for paramagnetic relaxation enhancement studies.

In other news, my resolution for the second half of 2011 is to always try and work in a mention of the Helmholtz free energy into each discussion I am involved in that touches upon thermodynamics, as I think far too many chemists have gotten comfortable in their Gibbsian-oriented world.

I suppose this is one of those “it was bound to happen” things – one of the summer undergraduates who is in my lab at my current institution mentioned that the undergrad biochem lab uses a hexahistidine-tagged protein for overexpression & purification. I of course remember having to prep and subsequently grind up giant amounts of animal muscle to extract a protein in my undergrad biochem lab. I feel slightly dusty.

With that observation, I will call this blog post to an end. Read more!

Thursday, May 19, 2011

SAXS And Promiscuity - Or, What Your Biochemistry Text Doesn't Cover.

Glycolysis is one of those things you learn about as an undergraduate (in high school as well, to be fair, but in a good bit more detail in an undergraduate biochemistry course) and – at least in my experience – it was presented as a topic that had already been well-explored and thoroughly annotated. After all, if it hadn’t been, would they have put it down for posterity in a textbook?

Snickering aside, I was pretty intrigued to see the following paper the other day for more than just being another entry in my “clearly, plenty of mechanistic detail was glossed over in my biochem text” list. Basically, the research team utilized a combination of crystallography, small-angle x-ray scattering (SAXS), and computational model to develop a scheme for the mechanism of phosphoglycerate kinase. They propose that the enzyme has a preferred “open” conformation where substrates (1,3-bisphosphoglycerate and ADP) can bind (separated by over 15 angstroms), and then a “closed” conformation, where the domains “fold in” on one another, bringing the substrates together for chemistry and which exposes a hydrophobic patch, which they suggest drives the preference for the “open” conformation. In the supplemental info, they do have some movies for download which make for fun viewing.

It is a nice example of what some in the structural biology field have been pulling for, an integration of high-resolution methods with lower-resolution methods that can provide additional insight into dynamics at the domain scale and above. Just as a representative example of this thinking is the SIBYLS beamline at Lawrence Berkeley Lab (SIBYLS – Structurally Integrated Biology for Life Sciences, where they possess the ability to do both crystallography and SAXS at the same station). They’ve also got a fairly lengthy review linked to on that page that describes the interplay between crystallography, SAXS, and computational methods.

In the spirit of Wavefunction’s link post the other week, at least, I stumbled across this recent paper on stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification today. I am still working through the paper, but – given that one of the authors has written rather extensively on atypical (non-Michaelis-Menten) kinetics in enzymes – he is putting forth a new set of organizing thoughts for understanding the unusual substrate binding and catalytic properties of detoxification enzymes (which frequently have multiple isoforms differentially expressed in tissues). These enzymes are not only promiscuous in terms of the substrates they’ll work with, but are also involved in multiple metabolic processes. So it's hardly as straightforward as biochem texts are fond of portraying with those nice, neat flow charts. I have occasionally considered this as a possible reason for all those secondary metabolites in plants that no one can figure out why they're present in the first place - you have a bunch of enzymes floating around in the cells and given enough time, stuff happens. But that is perhaps another post for another day. Read more!

Saturday, May 14, 2011

A modest update.

So, it appears that efforts in semi-quantitative biochemistry are approaching reproducibility, which is always interesting to observe. Of course, I have yet to surmount the final barrier of putting quantitative boundaries on both axes of my graphs (so far, there’s only the one axis that has actual numbers on it), so I suspect a couple more replications will be adequate to get it to a state where I will not dread being laughed at in public.

I suppose it will be something of a recurring theme in the future, but the crux of my interest in discussing protein dynamics is just how much territory that phrase covers, as what it implies varies from person to person, frequently corresponding to their own scientific interests. You have everything from the famed “protein dynamical transition” at around 180 K to research examining HD exchange in proteins, to studying the motion of various motifs in proteins as a function of a certain parameter, and extending all the way up to processes occurring at cell biology scales.

My current distraction (from reading things that are actually a bit more germane to my own work) is found here - a set of reviews on ion selectivity. It’s one of those topics I’ve found perpetually fascinating, although haven’t really worked in to any extent. Off to downloading! Read more!

Thursday, April 28, 2011

I feel like I should note this given my last post – the expositions of NMR that I can recall sitting through over the last decade have focused on the effects of judiciously applied B1 fields have on nuclear spin magnetic moments, not absorption/emission of electromagnetic quanta. I suppose the "absorption notion" – even if only intended in a handwavy pedagogical manner – is one that can feel fairly natural and not too extraordinary (given that spectroscopic methods that do involve actual absorption/emission of quanta are ubiquitous). But onto what I really wanted to discuss today.

The perils of quantitative biochemistry.

I have returned to contending with my old nemesis, sedimentation assays. Back in the day, I was interested in the interaction of a protein with a polymer, in particular the stoichiometry of said interaction (e.g., how many monomer units needed to bind one protein). While I eventually managed to get a reasonable-seeming estimate, it took a few tries to really pin down the optimal way to do it in a clear and reproducible manner. Nowadays, I am interested in the formation of a protein complex on the surface of a vesicle.

Once again, my latest attempt at quantification of a particular interaction was doomed to “no one with two neurons to rub together would trust anything on this gel.” Lesson learned yet again to not just double-check everything, but quadruple-think every step and every sample that is loaded, to say nothing of any assumptions about the entire process. In the vein of the old adage, one has to pick two of the following – quickly, easily, properly – to do their biochemistry. Being crunched for time, I naturally figured the first two would be best (as my brief attempt at doing this same basic type of measurement - same system, albeit with some modest differences) worked out somewhat well a few months ago).

One of the major issues is that reasonable-enough precautions (a particular wash step) one might take to improve the quality of said measurements is not feasible in this system since said precaution will cause unwanted (and functionality-inhibiting) aggregation. Alas. The major issue is that there are a number of little things that need to be done just right in order to ensure gloriously clear results and measurement-to-measurement reproducibility.

Odds and Ends –

1.) A good chunk of my tax refund this year is going for my chronic science habit. Software, books, and single malt Scotch. Well, OK, the last might not properly qualify.
2.) I find the entire International Year of Chemistry thing to be charming. The efforts being made by various organizations is vaguely reminiscent of someone thinking that as long as they make an effort on their partner’s birthday and Valentine’s Day, things will work out. Your mileage may vary, but that's the feeling I get in the back of my mind. We should view the IYC as a beginning, not merely a window of opportunity, to educate, enlighten, and entertain those around us.
3.) I have this urge to discuss protein dynamics. Future posts, I suppose.

And with that, I’ll be off. Read more!

Tuesday, April 26, 2011

You spin me right round baby.....

I saw this come up in the comments here, and figured that it would make for a cute post. I will start off with the mundane, though.

One is frequently asked to picture electromagnetic radiation as an oscillating wave, with the electric and magnetic fields orthogonal to one another as it propagates. This, I imagine, does not come as a surprise to anyone reading this.

As is propagated in the above link, the NMR experiment is presented as utilizing radiofrequency (RF) waves to tickle the nuclear spin magnetic moments. Of course, that leads to the question presented in that post – how does an RF wave (with a wavelength on the order of meters) get absorbed at the scale of a single nucleus? One might also ask an analogous question on the other end of the experiment when one is recording a signal on your nearest friendly NMR spectrometer.

Now, for two related things to think about –

The first is the oft-neglected sibling in the magnetic resonance community, electron magnetic resonance (EMR, also known as ESR or EPR depending on who you speak to). One of the fun little things that you can shovel a sample into is a flat sample cell. This is exactly what it sounds like – your sample is basically sandwiched between two planes of quartz. It is helpful since you can position your sample (typically aqueous in this case, as they’re notoriously lossy) at a point of maximum magnetic field (high B1) and minimal electric field (low E1), which keeps the resonator Q-factor high as well as keeping your sample from heating up, which can make for sad spectroscopic pandas.

The second is the development of so-called “Low-E” probes for the biological solid state NMR community. Given that they are not infrequently studying aqueous samples with some amount of salts (aka lossy as hell), and the traditional need for high power decoupling to get adequately resolved spectra, minimizing sample heating has been a major focus of effort within the community. The result here is a probe that minimizes heating from the electric field, actually using some insights from the EMR/EPR/ESR community.

Now, if we think about what’s going on here….they’re trying to minimize the influence of the electric field (E1) by either judicious sample placement or probe design. We know from basic electromagnetism that an EM wave is composed of both electric and magnetic field components. It would seem that the absorption of EM radiation in magnetic resonance is not necessary for a successful experiment. It would, in fact, appear to be the case that what is important is the magnetic field that is generated by an appropriate EM source (RF for NMR/MRI, microwave for EMR) for the magnetic resonance experiment. The electric field appears to simply be a source of woe and frustration.

Of course, as noted in the comments to the above link, this is not new thinking. Hoult and his collaborators have been working on this topic in various ways and manners for over two decades now. There’s also that fun paper by Hanson regarding the necessity of quantum mechanics for understanding magnetic resonance. And more recently, there’s been a rather lengthy (and somewhat dense – I have a copy printed out, haven’t had a chance to really dig into it just yet) article on virtual photons in magnetic resonance, following up on Hoult’s suggestion from a while back.

Alright, back to things.... Read more!

Thursday, April 14, 2011

There's a discussion here on a variety of topics, and in the comments, the issue of "homegrown" versus "bought" talent comes up. Of course, as may be par for the course, I suspect I see schools somewhat differently than the majority of the commenters there (I think of how awesome their NMR people are, naturally, followed by their biophysical chemists), so I was like, "How can someone say School X has no homegrown superstars - Professor Y went from fresh assistant professor to NAS electee in like 15 years?" But anyway.

I am feeling uncommonly pleasant and motivated this evening, though. Small victories in lab will do that to a person. I suppose I should power on through and finally finish up my taxes. Read more!