Structural characterisation of proteins and peptides

Solution NMR data on peptides can be acquired at concentrations > 0.1mM for a 1D or to get structural information >1-2mM in aqueous buffers with 10% D2O. Phosphate buffer is an economical non-protonated buffer, and there also are a variety of perdeuterated buffers (d-Tris, d-HEPES) available that do not obscure protein NMR signals. Protein preparation for NMR gives further details on how to optimise the buffer conditions for your sample.  

As for peptides, protein spectra can be acquired at concentrations >0.1mM for a 1D or 2D 15N HSQC. Typically, isotopically labelled protein samples (usually 15N and/or 15N/13C) are required for structural characterisation. A protocol for labelling in E. coli can be provide upon request. For proteins with MW > 20 kDa, deuteration may be also needed. In general, the degree of deuteration required is largely dependent on spectral quality, the size and modularity of the system studied and the types of experiment performed. However, very high levels of deuteration (>90 %) are usually required for proteins with molecular weights of the order of 35 kDa or greater.

The acquisition of standard NMR spectra takes from a few minutes (1D spectra) to 3/4 days (3D or 4D spectra) for each experiment. A full set of experiments for protein structure determination usually takes about 7-14 days. In the case of relatively small proteins, recent advanced multidimensional data acquisition schemes have been successfully used to reduce experimental acquisition time by up to an order of magnitude or more.

The first NMR experiments acquired will investigate the state of the protein and it's suitability for further study (protein folding and  aggregation state) at the selected NMR protein concentration, acquiring 1D 1H and/or 2D 15N HSQC spectra. This will take about 1 day, depending on sample concentration. These preliminary data will allow us to evaluate the time and the experimental conditions (i.e. kind of labelled nuclei, optimal protein, buffer concentration and pH) needed to obtain a high resolution structural determination on the user’s protein.

In addition to the structural characterisation of proteins the facility also offers high-throughput protein-ligand screening. Typically, 10-20μM of protein is needed with a 100-fold excess of ligand Using  automation large numbers of compounds can be quickly screened. Hits can be further verified using protein-detect methods  (1H-15N or 1H-13C HSQC). 

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