Saturday, January 10, 2009


Another week, another post. So, in my last post, there was that interesting looking Hhyperfine term that describes the interaction between the nuclear spins and any unpaired electrons in the environment. I will make a few points about paramagnetic NMR and something I've been reading up on as of late in the biochemistry/biophysics field. And a random comment or two, of course, at the end.

NMR of paramagnetic species, while a topic of growing interest and fruitful research over the past couple of decades, still tends to get people not involved in the field to look at you and think, “But what about the enhanced relaxation, broadened lines, and paramagnetic shifts? It just sounds really hard!” To anyone who might be thinking that as they read this, I would like to note that a number of the metals involved in biological systems are, in fact, quadrupolar nuclei. Also, something like one-third of all elements can exhibit paramagnetism. So, you can pick one challenge or another, it appears. Life may not be easy, but think about it like this. Since there hasn't been a whole lot of work done compared to other areas, it's a growth field with plenty of opportunity. Besides, as the bioinorganic chemistry folks like to remind us, the number of metalloproteins in nature probably hovers around at least 20 to 25%, if not a bit higher. I hardly think neglecting all of the proteins out there is a good idea just because you're terrified of some hard work. To say nothing of potential applications in materials science and chemistry!

One thing to keep in mind is that the effects aren't necessarily the same in every direction. If you have a paramagnetic center which isn't isotropic, and there's a distinct anisotropy, one could have two marker peaks that are the same distance from the metal but only detect one because of the anisotropy. If you've ever done any EPR, or have any familiarity with it, one can – in principle – resolve the components of the g-tensor. (Determining the angles between the g-tensor and the molecular frame is far more challenging from my understanding, though, and not something I've ever done.) Sometimes there will be axial symmetry (where two of the components are equal to one another), other times all three components of the g-tensor will be different. In any case, while there is practically always the averaging of the electron magnetic moment, distance matters when dealing with paramagnetic systems. If you're close up, you'll not only experience more of the effect, but it's more sensitive to any anisotropy. If you're further out, less effect, and it looks more isotropic.

So, experimentally speaking, one can decompose an observed chemical shift from a paramagnetic sample, δ obs, as follows:

δ obs = δdiamagnetic + δcontact + δ dipolar.

The nomenclature here can get a bit confused, so step-by-step, and hopefully not too confusing, here we go. δdiamagnetic is the “base” diamagnetic chemical shift, what you would get if there was no metal there. δcontact is the so-called contact shift (or Fermi contact shift) – this is what one gets from the average delocalized electron density on the nucleus interacting with the nucleus's nuclear spin magnetic moment. δ dipolar is also known as the pseudocontact or dipolar shift – this is what you probably think it is, just a through-space dipolar interaction between the nuclear spin and the electron spin. Now, there are all sorts of neat computer programs that can incorporate paramagnetic restraints for structure calculations/refinements, determine magnetic susceptibility tensors from NMR data, and other related pursuits.

If any of this sounds interesting to you, please let me know. I can pump out a lit post with a number of citations without much difficulty during the week, it would be my pleasure. Or if you'd rather receive an email, let me know. However, for a starting point, I would strongly recommend a look at the work done by Ivano Bertini, Claudio Luchinat, and coworkers at the University of Florence here. That should keep you busy for a while.....

I've gotten interested in the entire “intrinsically disordered proteins” topic as of late. It's interesting for a couple of reasons, some related to my current research, others simply since it's a neat topic. It makes one more careful in one's thinking that proteins just fold to some structure and stay there – proteins actually have functions, which are connected to other macromolecules and their functions. A protein can bind a ligand/substrate, where it may adopt a restricted ensemble of conformations. That protein's function may be modulated by interacting with another ligand or with another protein (for instance, an electron transfer protein), which could alter its structure. It may finally need to adopt another conformation to release the ligand or product. So whenever someone says, “Well, I've determined the structure of a protein,” what you should really be thinking is, “That person has determined the structure of a protein at a particular point along its functional pathway.” It also serves as a handy thing to bring up in the inevitable protein folding discussions that crop up every so often offline and online. Not every protein comes away from translation and adopts its active conformation right away, after all. As a short and hopefully accessible example, if we'll remember our blood clotting biochemistry, there are a whole bunch of zymogens (or proenzymes, if you will) involved in the process. They're activated upon trauma in healthy individuals – there's no need for them to be active when you're not bleeding, after all. There's a somewhat recent paper I'm still digesting here on a model involving intrinsic disorder with coupling allostery between binding sites. It's an interesting topic, mostly since I've been focused on shorter-range interactions earlier on in my education/research, and am now becoming more intrigued on what I will facetiously call “structural systems biology” - what is the structural and dynamic underpinnings of all these neat things that happen in cell biology and physiology from a physical chemistry/biophysics perspective?

I'm always intrigued by the interplay between solution and solid state NMR, and how one tends to delve into the other in order to get information that is typically denied to them in their home territory. You have the solution NMR folk introducing residual dipolar couplings, you have the solid state NMR people trying to minimize the effect of the geometric/angular effects in measuring certain parameters, it's all kinds of fun. I will probably comment on this here and there in the future, I think it's endlessly fascinating despite no longer actively in the magnetic resonance community.

There was an interesting post on equipment (the abundance or lack thereof, and of varying quality) at In the Pipeline the other day here. I've since moved onto a postdoc in an honest-to-Buddha biochemistry/biophysics lab since my graduate school days in a (biphysical/NMR) chemistry lab, and have had use of pre-made kits on occasion. I think it depends on one's perspective and background – it can be a crutch to use them, but I don't plan on doing a great deal of molecular biology while I'm here. Is it really the best use of my time or the lab's money to pour my own gels (as I did in grad school) or prepare my own DNA plasmid purification materials, especially if I'm not going to be doing it week in and week out for the next 2 to 3 years?

The one thing I did miss in graduate school, compared to my undergraduate institution, was the presence of a professional research-grade electronics shop. I especially missed it in my last two years of graduate school, when I seemed to get problems with instrumentation about every three to four months. While we managed to get a good amount of support from our department's NMR facility, it's not quite the same as having a facility capable of not only repairing instruments but also helping one devise potential work-arounds or new solutions. Of course, it is a character-building process, taking apart an NMR probe, diagnosing the problem, and then fixing it (at least until it fluxes up again).

In any case, a substantial enough second post, I think. Best wishes to all!

Disclaimer - Any arguable/unrigorous point in the above post is 99.9% me being lazy about it.

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