NMR

Nuclear Magnetic Resonance (NMR) is a spectroscopic technique that can be used to elicit structural and dynamic properties of molecules by exploiting the behaviour of certain atoms when placed in very powerful super-conducting magnets (180 000 to 360 000 times stronger than the earths magnetic field for magnets at UConn Health). When NMR-active nuclei are placed in a strong magnetic field their nuclei align with the field and begin to process at a frequency dependent on the isotopes gyromagnetic ratio and the strength of the applied magnetic field, along with the chemical and physical environment of the atom. The component of the frequency that is dependent on the chemical and physical environment is called the chemical shift. NMR experiments perturb the alignment by applying short pulses of Radio Frequency (RF) energy to determine the chemical shift of each of the NMR active atoms in the molecule being studied. By using combinations of pulses and delays (this is known as a pulse sequence), additional information may be ascertained such as which atoms are bonded to each other, and which atoms are spatially close to each other. By utilising many different experiments it is possible to determine the three-dimensional structure of molecules, including large bio-molecules such as proteins.

High resolution NMR investigations are more feasible for proteins less than approximately 25 kDa in mass and soluble to around 0,5 mM. In certain cases it may be possible to investigate proteins or complexes of larger size or lower solubility. Membrane proteins are difficult to study using high resolution methods, but new techniques are emerging that may be applicable. Because NMR studies usually require labelling, the protein with stable isotopes 15N, 13C, and sometimes 2H (an expression system suitable for growth in labelled media), must be available. Proteins must be purified (typically >95% is required), folded, and at least marginally stable. Preliminary characterisation by circular dichroism and thermal or solvent denaturation is recommended.

This question is difficult to answer, as it is dependent on the questions being asked and the behaviour of the sample. Typically 300 µl (with specialised NMR tubes) to 600 µl of sample is needed. Protein concentrations for well behaved systems should be above 150 µM for structural studies, but lower concentrations may be used for other non structural studies. While 150 µM is a rough estimate for the lowest concentration to use for structural studies, it is advisable to make protein concentrations as high as possible and they should be limited by solubility and protein behaviour, not the amount of protein prepared. The amount of time used for running longer experiments to compensate for low concentrations, and the increased time to interpret NMR spectra, will almost certainly be longer than the time it takes to prepare an additional sample.

Once the sample has been sufficiently purified and dried, the next step is to choose a suitable solvent. Since deuterium is by far the most popular lock nucleus, the sample is usually dissolved in a deuterated solvent (a deuterated solvent is one in which a large proportion, typically more than 99%, of the hydrogen atoms have been replaced by deuterium). Commonly used deuterated solvents are acetone-d6, benzene-d6 and chloroform-d though many other solvents are available.

Factors to be considered when choosing a solvent are:

1. Solubility:

• Clearly more soluble the sample is, the better it is. This maximises the amount of sample within the sensitive volume which increases the sensitivity of the experiment. High solubility is particularly important if only small quantities of the sample are available.

2. Interference of solvent signals with the sample spectrum

• The solvent itself will inevitably produce NMR signals which will obscure regions of the spectrum. These ‘residual solvent peaks’ should not overlap with signals from the sample.

3. Temperature dependence:

• For experiments above or below room temperature a solvents melting and boiling points are also important factors. Furthermore the solubility of the sample is likely to vary with temperature.

4. Viscosity:

• The lower the solvent viscosity, the better the resolution of the experiment.

5. Cost:

• Clearly for routine NMR, where many samples need to be measured, solvent cost is an important consideration. As a rule of thumb, the price increases with the number of deuterated atoms.

6. Water content:

• Almost all NMR solvents contain water traces. Also many are hygroscopic (they absorb water from the atmosphere) and hence the longer they are stored the more water they contain. The presence of a water (HDO) peak will only serve to degrade the quality of the NMR spectra. The water level in the solvent can be greatly reduced by filtration through a drying agent or by storing the solvent over molecular sieves.
• The choice of solvent for a particular sample will be the best compromise between the various advantages and disadvantages of each. For precise details of specific solvents please refer to standard NMR text.