Aug 182009
 
This post continues my series about selected articles from the dynamics-focused topical issue of JBNMR.

ResearchBlogging.orgIt is helpful, in examining some NMR articles, to understand that NMR spectroscopists have a long and resilient tradition of giving their pulse sequences silly names. You can think of it as the biophysical equivalent of fly geneticist behavior. From the basic COSY and NOESY experiments (pronounced “cozy” and “nosy”) to the INEPT spin-echo train, to more complicated pulse trains such as AMNESIA and DIPSI (which, I am not making this up, is used in an experiment sometimes called the HOHAHA), the field is just littered with ludicrous acronyms (look upon our words, ye mighty, and despair). A team from Josh Wand’s lab now joins this club by developing a multiple optimization for radially enhanced NMR-based hydrogen exchange (AMORE-HX) approach. The name is ridiculous, but the experiment fills an important role and illustrates a very active area of technical development in NMR.

The experiment they developed is intended to measure the rate of hydrogen/deuterium exchange at amide groups on the backbone of the protein. This sort of exchange reaction proceeds pretty quickly for most residue types, and can be either acid- or base- catalyzed. For it to happen, however, two things must be true. One of them is that the amide proton must not be in a hydrogen bond already. Also, the site of the reaction must be accessible to water. These requirements should indicate to you that HX measures the rate of local unfolding and can therefore be interpreted as a measure of fold stability at each NH group on the backbone. This data is of obvious interest to researchers studying protein folding. In addition, because some structural transitions are proposed to involve an unfolded state this may have explanatory power for protein interactions and regulation.

A typical HX experiment involves taking your protein, switching it rapidly into >75% D2O buffer, then placing it in the magnet and taking a series of HSQC or HMQC spectra that separate signals from backbone NH groups by the proton and nitrogen chemical shift. These spectra can be taken with very high time resolution (<2 min each), and the rate of exchange can then be measured by the decay of peak intensity as hydrogen is replaced by deuterium. Assuming that the chemical step occurs significantly faster than the rate of local unfolding and refolding, this decay can be directly interpreted as a local unfolding rate. This works quite well, but as proteins get larger there is a significant likelihood of signal overlap. It would be nice, with these large proteins, to separate the hydrogen signals using an additional chemical shift — say, that of the adjacent carbonyl. Unfortunately, taking these decay curves using 3-dimensional spectra like the HNCO turns out to be impossible because of the way these experiments are collected. Multidimensional NMR spectra rely on a series of internal delays during which a coherence acquires the frequency characteristics of a particular nucleus. In a typical experiment, the delays are multiples of a set dwell time, the length of which is determined by the frequency range one wishes to examine. Typically the collection proceeds linearly through the array, so for m y dwell times and n z dwell times you would collect 1D spectra with the delays:

0,0 0,y 0,2y 0,3y … 0,my

then

z,0 z,y z,2y z,3y … z,my

and so on until

nz,0 nz,y nz,2y nz,3y … nz,my

This is called Cartesian sampling, and it has some advantages. The numerous data points typically do a good job of specifying resonance frequencies, and processing this data is a fairly straightforward proposition. The glaringly obvious disadvantage is time, of which a great deal is required. Completely sampling either one of these dimensions separately can take less than 30 minutes, but sampling both can push a triple-resonance experiment into the 60 hour range. Most annoyingly, because triple-resonance spectra can be really rather sparse, this extremely long experiment often over-specifies the resonance frequencies. That is, much of this time is spent collecting data you don’t need.

Because spectrometer availability and sample stability are not infinite, there is considerable interest in making this process more efficient. One of the methods for doing so is called radial sampling. In this approach, the spectrum is built up from a series of “diagonal” spectra that lie along a certain defined angle with respect to the two time domains (imagine the above array as a rectangle with sides of my and nz to get a rough idea of what this means). If these angles are judiciously chosen, the spectrum can then be rebuilt from just a few of them with only modest losses in resolution. Gledhill et al. apply this approach as a means of addressing their time-resolution problem. Guided by a selection algorithm, they use just four angles (at 500 MHz) to resolve more than 90% of the peaks possible in myelin basic protein. As a result, they were able to collect HNCO-based HX data with 15-minute resolution. This isn’t enough to catch the fastest-exchanging peaks, but it’s more than sufficient to catch core residues.

Gledhill et al. used some additional tricks to gain extra speed in the experiment, however. Using band-selective excitation, they cut down the experiment’s relaxation delay to 0.6 s, which is important because this delay is a considerable portion of the duration of each transient. Having done this, they started to get really clever. Because this experiment is being used to measure the intensities of known frequencies, it is possible to significantly reduce the amount of processing required by employing the 2D-FT only for those regions that contained actual peak intensity. Moreover, they could extract peak intensities from each individual angle plane. Because they did not interleave the collection, this enabled them to substantially increase the time-resolution when necessary.

For peaks that exchanged quickly Gledhill et al. took relaxation data from the individual angle spectra, to maximize the time-sensitivity of the data. For slowly-exchanging peaks, they averaged the data from the angle spectra to maximize the signal-to-noise ratio. The resulting intensity curve seems a bit noisy, but this is an acceptable price to access new peaks. More importantly, the precision of the overall rate (as opposed to the instantaneous intensity) appears to be on par with simpler methods of measuring HX.

Successful use of the AMORE-HX experiment will depend on a wise selection of acquisition angles, a process that may benefit from further optimization. Because the HNCO has relatively good dispersion, the pulse sequence should enable HX measurements for just about any protein that is suitable for NMR. This would allow for a direct assessment of large enzymes and complexes, as well as a measurement of local stabilities in domain-domain interfaces.

Gledhill, J., Walters, B., & Wand, A. (2009). AMORE-HX: a multidimensional optimization of radial enhanced NMR-sampled hydrogen exchange Journal of Biomolecular NMR DOI: 10.1007/s10858-009-9357-4

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