Using Pressure to Understand RNA Dynamics

There is still a lot to discover when looking at biomolecules, which are one trillion times smaller than a meter.

At the Shirley Ann Jackson, Ph.D. Center for Biotechnology and Interdisciplinary Studies (CBIS) and Constellation Chair Professor of Bioinformatics and Biocomputation at Rensselaer Polytechnic Institute, Catherine Royer, is committed to comprehending the conformational landscapes of biomolecules and how they regulate cell function.

The atoms in biomolecules can rearrange and the biomolecule can change shape in response to certain stimuli. Understanding conformational dynamics is essential for drug development as their altered shape impacts how they operate in cells.

Royer and her group recently explored the structural dynamics of a human transfer ribonucleic acid (tRNA) under strong hydrostatic pressure in research just published in the Proceedings of the National Academy of Sciences.

The tRNA-excited states, ordinarily present at extremely low levels, increased in the population at high pressure, providing fresh information on tRNA function.

We are interested in observing the excited states because they lead to conformations outside of those that can be determined by X-Ray crystallography, nuclear magnetic resonance (NMR), or electron microscopy. We are beginning to understand that there are far more biomolecular structures than previously thought and, for the development of therapeutics, we need to understand what these states look like.”

Catherine Royer, Constellation Chair Professor of Bioinformatics and Biocomputation, Shirley Ann Jackson, PhD, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute

Instead of using the proteins she usually examines for this study, Royer employed human tRNA.

She added, “There has not been much work done on excited states of large RNA molecules, so that is what makes this research unique.”

Royer and his team discovered that the excited states are likely involved in HIV infection in addition to being important for tRNAs’ ability to translate messenger RNA into proteins normally. Each year, HIV infects roughly 1.5 million new people worldwide.

“The NMR revealed that the hydrogen bonds holding the tRNA together are weakened in these excited states. The small-angle X-Ray scattering at high pressure, which we did at CHESS, revealed that the shape of the tRNA changed in these excited states. The areas that were altered by pressure also happen to be the areas that get hijacked by HIV during infection,” Royer stated.

The sole synchrotron radiation facility in the United States that supports high-pressure small-angle X-Ray scattering (SAXS) experiments on biomolecules is CHESS, or the Cornell High Energy Synchrotron Source.

Royer and her team hypothesize that the invading viral RNA might use the excited state configurations of the tRNA they observed under pressure to start HIV reverse transcription. Viral contagiousness is connected to this process.

Dr. Royer’s research, together with her team, may advance our understanding of how HIV spreads. Further, over 80% of the microbial biomass on Earth exists at high pressure. Understanding how biomolecular sequences are adapted to function in high-pressure environments will yield new approaches for developing sturdier and more active biomolecules for biotechnology.”

Deepak Vashishth, Director, Shirley Ann Jackson, PhD Center for Biotechnology and Interdisciplinary Studies

Richard Gillilan of CHESS further stated, “People have known for some time that biomolecules do interesting things under extreme pressure, but, until very recently, technologies like high-pressure NMR and SAXS just were not available to the general research community. Now, we can start to see what pressure does in molecular detail, and there is a lot of interest from multiple scientific fields, including biomedicine.”