The growing role of NMR in structural biology

Gary Battle and Aleksandras Gutmanas EBI, EMBL

In June 2013, the number of structures available in the Protein Data Bank (PDB) determined using Nuclear Magnetic Resonance (NMR) spectroscopy passed the 10,000 mark. Since the first biomacromolecular NMR structure was archived in 1989, the number of NMR-derived structures in the PDB has grown steadily. In 2012 alone over 500 new NMR structures were deposited, more than in the first 10 years of NMR depositions combined. NMR-derived structures account for more than 10% of the PDB archive which itself will reach the 100,000 structure mark in 2014.

Far from merely being a last resort for failed crystallographic targets, biological NMR is increasingly recognised as a valuable technique for determining the three-dimensional structure of biomolecules at atomic resolution. Not only does it avoid the major bottleneck of having to grow crystals, but it also makes it possible to study a range of properties of a molecule, such as its flexibility and how it interacts with other molecules. NMR is uniquely poised to investigate the low-population (“invisible”) states of proteins and, as an earlier opinion piece pointed out, NMR can now be used to study macromolecules in live cells.

The main limitation of solution NMR has traditionally been the size of the structures that are amenable to structural investigations. NMR spectroscopists typically focus on molecules no larger than 20-30 kDa (about 200-300 amino acids) whereas X-ray crystallographers routinely solve structures many times this size. However, significant advances in instrumentation over the past decade, particularly solid-state magic-angle spinning (MAS) NMR,coupled to smart isotopic labelling schemes and ingenious new spectroscopic techniques are circumventing these limitations.

A typical NMR structure in the PDB consists of an ensemble of models. Nowadays, in addition to the structural ensemble, the wwPDB requires the deposition of the assigned chemical shifts as well as the geometric restraints used in the structure determination and refinement. The NMR structure ensemble and associated experimental data are presented by the wwPDB partner sites through their entry-specific pages (e.g., http://pdbe.org/2lpz shown below). Additionally, a number of NMR-specific tools and services help make information about the quality of NMR structures in the PDB accessible and interpretable by non-specialist users.

NMR is firmly established as a powerful technique in the field of structural biology thatcontributes unique biological insights that are difficult or impossible to obtain using other techniques.As the use of NMR continues to increase, the technique promises to offer many new and exciting possibilities for observing and understanding the structure, function, dynamics and interactions of biomolecules.

Structure of a bacterial type III secretion needle from Salmonella typhimurium (PDB entry 2LPZ; Loquet et al., 2012, Nature, 486:276) determined using a hybrid solid-state NMR and electron microscopy (EM)

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