NMR Spectroscopy in Protein and Nucleic Acid Research

Unraveling Our Operating Instructions

The publication of the first complete human genome in 2003 marked a milestone in biological research, with tremendous potential to contribute to fields as diverse alternative energy and personalized medicine. It’s amazing to think that miniscule tangles of amino or nucleic acids could hold the key to controlling – or even completely eradicating – devastating diseases like cancer or debilitating neuromuscular diseases or HIV.

In truth, the success of the Human Genome Project was just a first step. There’s a long way to go before everyone gets customized vaccines or gene therapies. Knowing what’s there isn’t the same as understanding how the individual pieces interact – or how they function given different environments or stimuli.

Reading the Manual

Untangling how, when, and why genes are expressed, and how the resulting proteins function alone and together in the human body is key to realizing the vast potential of the user manual that is our DNA, in concert with the molecules that transcribe it and the proteins it encodes.

Nuclear magnetic resonance (NMR) spectroscopy is an important tool in the structural biologist’s toolbox. It’s the second most common experimental method used to characterize the more than 100,000 proteins, nucleic acids, and protein/nucleic acid complexes listed in the Protein Data Bank. And since structure relates to function, such research can shed light on various diseases as well as normal processes.

For example, researchers recently used a combination of magic-angle spinning (MAS) solid-state NMR spectroscopy with a comprehensive multiphase probe and 1H/1H radiofrequency-driven dipolar recoupling to resolve the spectra of oligomers of the amyloid-β protein which forms the plaque so characteristic of Alzheimer’s disease. NMR spectroscopy can resolve large molecules as well; using a variety of enhancements, such as selective nucleotide labelling, researchers used two-dimensional solid-state NMR spectroscopy to determine the structure of RNA from the extremophile Pyrococcus furiosus.

But NMR spectroscopy can be used to do much more than determine the structure of a protein or nucleic acid. It is also being used to shed light on molecules at work; researchers have used time-resolved 31P MAS NMR spectroscopy to detect biological processes like ATP hydrolysis in E. coli.

Other examples of NMR spectroscopy in protein and nucleic acid research include:

• Determining the structure and function of membrane proteins – prime drug targets – in diseases ranging from the 1918 influenza virus to the latest drug-resistant tuberculosis strain
• Identifying possible methods for inhibiting the development of the HIV virus
• Using NMR spectroscopy to inhibit cancer cells
• Using 19F NMR spectroscopy to explore ligands involved in various protein-protein interactions

Electron paramagnetic resonance (EPR) spectroscopy has also found uses in protein and nucleic acid research. For example, researchers used EPR spectroscopy in conjunction with spin labelling to study protein-protein and protein-oligonucleotide interactions.

How NMR Brings Molecules into Focus

NMR spectroscopy has already made significant contributions to the study of proteins and nucleic acids due to its ability to analyze both solid samples and samples in solution, and the fact that crystallization is not necessary for successful structure determination – in fact, protein structures can be determined in vivo.

However, NMR’s most useful days lie ahead. The use of labeling, of everything from atoms to nucleotides to electron spins, in combination with the wide variety of NMR techniques available, can reveal a vast amount of information regarding protein and nucleic acids, including their structures, dynamics, and interactions.

Another exciting innovation is the development of processes and protocols for simplifying and automating the use of NMR data in structure analysis, enabling high-throughput protein structure determination. (See also these articles from eMagRes and Proc Natl Acad Sci.) In addition, NMR spectroscopy is being used to help speed the development of in silico research by validating simulations of molecular dynamics. From the basic research of molecular biology through to its translation into tomorrow’s therapies, NMR provides an essential toolset for discovery at every step along the way.