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.

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