In research led by Michael Summers, Professor of Chemistry and Biochemistry at the University of Maryland, scientists have been developing new techniques to overcome the present challenges involved in using NMR to study the structure of HIV. In some of those studies, the team has been able to develop new ways of inhibiting the virus.
One of the main problems with studying RNAs is that because only four types of nucleotide are present, signals tend to occur in very crowded regions of the NMR spectrum. This has meant that previously, it has only been possible to characterize RNAs made up of around 25 to 30 nucleotides.
To address this problem, Summers and colleagues have been developing labelling techniques and other strategies that have enabled structural information to be obtained about much larger RNAs, with some of the molecules studied reaching up to 700 nucleotides. The team is now trying to create tools that will enable three-dimensional modelling of these huge RNAs. The researchers have also started collaborating with Ad Bax using traditional NMR methods to take advantage of long range proton nitrogen scalar coupling so that three- and four-dimensional NMR can be introduced.
The team hopes this innovative research will lead to exciting new developments in the field of biomedical research. By solving the structure and dynamics of certain parts of the HIV particle, the researchers have realized there may be ways of preventing HIV maturation and have patented and licensed several inhibitors that companies are now interested in developing. Summers and colleagues are most excited about establishing how key parts of the virus fit together and how this relates to its function. They hope such findings about the basic principles of HIV virology may be of use to people focused on drug discovery, as well as to those across the biomedical community in general.
The researchers place great emphasis on how important their NMR instrumentation is to the success of their studies. Summers says: “We couldn’t do anything without our instrumentation… NMR is the central tool that we use.”
In the past, the team has attempted using other technologies such as trying to grow crystals of RNAs or protein RNA complexes, but this technique was unsuccessful. Now, through using NMR to look at larger, biologically functional RNAs, the researchers have learned that these molecules actually undergo conformational changes and are flexible, meaning the idea of them crystallizing was never likely to be realized. Summers and colleagues believe they have been able to learn more about these structures using NMR than they would be able to using any other technique.
To help move their research forward, the team is now interested in technological advances that might improve the signal-to-noise ratio and resolution they get at higher magnetic fields. Each time there is a significant increase in magnetic field strength, the researchers have noticed major benefits, with it being possible to interpret information at 800 megahertz, which would not be possible at 600 megahertz. The team is now focused on achieving a higher field strength, improved signal-to-noise ratio and a better resolution to further help them characterize the structure, dynamics and function of large RNAs.