First Computer Simulation of Structure of RNA-Molecules

The manifold biological importance of small RNA-fragments has only been recognized in the last years: they have important regulatory and catalytic functions within the cell.

What scientists had only been able to examine in experiments so far, has now been simulated on a computer for the first time by Dr. Dietmar Paschek, a chemist of Technische Universität Dortmund, together with his American colleague, Prof. Angel Garcia. Their innovative method describes the complex folding process of RNA-molecules, which happens on the microsecond-scale, to be viewed in detailed single steps with atomic resolution.

A standard personal computer would have to run for 35 years to simulate the complex process. That is why Paschek teamed up with his colleague from Rensselaer Polytechnic Institute in Troy, New York (USA), as this institute currently owns the world’s biggest university-based computer cluster. The simulation was only made possible by using a parallel computer code developed in Dortmund. For the first time the molecular environment, including the solvent water, was described in a very realistic way.

This offers the chance to observe the behavior of an RNA-molecule within its natural environment and provides clues regarding the function and possible reactions of different RNA-molecules in the cell. Small RNA fragments have been shown to be able to specifically disable genes in laboratory tests. A discovery, for which the US-scientists Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for Medicine.

Even if the simulation work of Paschek and Garcia, which could build the basis for research into and further development of this and other ways of using RNA, still is singular pioneering, it could become routine in some years in view of the exponentially increasing computer power. But they can already be sure of their colleagues’ recognition.

In the latest edition of the prestigeous “Journal of the American Chemical Society” the two scientists present their results. Moreover, Dietmar Paschek was invited to report about their innovative simulation methods within the scope of a plenary lecture at this year’s American Chemical Society national meeting in New Orleans.