Supercomputer Simulations Unravel Mystery of How RNA Contributed to the Origins of Life

101004151725-large A research team led by Jeremy Smith, who directs  the Department of Energy's Oak Ridge National Laboratory's Center for Molecular Biophysics used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms. Early life on Earth was composed of RNA, rather than deoxyribonucleic acid (DNA).

Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions — two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.

"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."

The research team found a theoretical explanation for why the Diels-Alder ribozyme needs magnesium to function. The concentration of magnesium ions directly impacts the ribozyme's movements. Computational models of the ribozyme's internal motions allowed the researchers to capture and understand the finer details of the fast-paced reaction. The static nature of conventional experimental techniques such as chemical probing and X-ray analysis had not been able to reveal the dynamics of the system.

"When there's no magnesium present, the mouth closes, the substrate can't get in, and the reaction can't take place. We found that magnesium ions bind to a special location on the ribozyme to keep the mouth open," Smith said.

Casey Kazan via materials provided by DOE/Oak Ridge National Laboratory.


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