There is an awful lot of information that can be obtained from an nmr experiment and, while the physics behind it makes my eyes go a bit squiffy, I think that it is all very cool.
The latest published protocol on protein nmr is: Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy and is useful for investigating the structures of the excited states of proteins. These conformations are usually “invisible” because they are short-lived and the proportion of molecules in them at any one time is very small.
The Procedure deals pretty much exclusively with the methods for preparing the labeled protein samples required for the NMR experiments (summarised here.
The NMR part of this protocol includes the Carr – Purcell- Meiboom – Gill (CPMG) relaxation dispersion NMR experiment. Now, as we all know, being able to type a name like that in a blog post does not mean that I have the slightest clue what it is. And, in this case, I did not.
So, Google to the rescue. My searches led me to the following web resource:
Advanced NMR web course – page maintained by Françoise Sauriol, and the page where the explanation for CPMG rests is that that deals with Spin-Spin Relaxation time (T~2~). I started to relax somewhat: those are all words that I can understand, and it jogs a memory regarding MRI scans… I did a google search to remind me, and the Wikipedia entry seemed to have the best description, though it could probably do with some more expert attention.
Another search led me to: The Basics of NMR, an electonic book by Joseph P. Hornak and I quickly read through the first three chapters. I think that the important thing to notice is that the decay of transverse magnetization is affected by molecular interactions experienced by the nucleus in question.
Okay, okay. Back to the question at hand (and the NMR web course page). Scroll down to CPMG. Hmm. Scroll up to Hahn Spin-Echo. Back down to CPMG. Gosh it seems complicated. Again, I think that the important thing is that the CPMG experiment allows us to get a “number” (the size of the echo) that is affected only by the spin-spin relaxation process of each nucleus (having the chemical shift associated with the radiofrequency of each pulse).
So we are looking at changes in the molecular interactions experienced by nuclei in the protein molecule.
The protocol itself does not have any figures (lots of tables though), but there was a publication by Prof Kay’s group in Nature a few years ago, and these figures might be illuminating. Follow the links!
My boss in Sydney gave a very accessible course in NMR for dummies. I should dig up my notes and see if I can still understand them! What I remember most is the dawning realization of how radio works.
Hi Richard,
Thank you for the comment! NMR is one of those things that I “understood” when I was an undergraduate, but seems to have gotten awfully complicated as I have gotten older.
I have just been reading your blog post on open access – what an interesting discussion!
Bye for now, B
PS Am looking forward to when Hap is old enough to enjoy building a little radio as I did not quite get to that when I was a child…
heh. Children are great for revisiting your own childhood. Reminds me, I’d promised the Pawns we’d build a laser beam…
Goodness gracious me! (humming Stars Wars theme for no particular reason…)