Piia Bartos from University of Eastern Finland has been studying RNA-binding proteins (RBPs), which may play a role in cancer treatment. RBPs have been found to play a role in cancer cells, particularly in drug responses and the development of drug resistance. More than 1,500 RBPs have been discovered so far. Changes in the function of these proteins can affect the level of cancer gene expression.
“We’re particularly interested in argonaute proteins which play an important role in RNA-mediated gene silencing. The most important of these is Ago2,” says Bartos.
When RNA is bound to Ago2 protein, this combination is called the RNA-Ago2 complex. Argonaute 2 protein binds microRNA molecules in cells.
“As argonaute-2 is a protein that’s vital for cell function, it’s likely to affect all types of cancer. If it is removed from the cells, the cells will not survive. If its activity could be eliminated in cancer cells, those cells would not survive. This would prevent the growth and spread of cancer cells.”
Molecular dynamics simulations provide insights into how biomolecules interact with each other at the atomic level. Because atoms are in constant motion, the forces between them are calculated and used to determine factors such as the new positions, velocities and energies of the protein atoms. This will provide new information for drug design. Simulations of molecular dynamics can be used to make a kind of video of the movements of Ago2-RNA complexes and to compare the differences between activating and silencing complexes.
The RNA sequence data used in the simulation was obtained from the A.I. Virtanen Institute for Molecular Sciences. Six RNA molecules were used in the simulations, three of which increased protein production and three of which decreased it. For all of these, molecular dynamics simulations were run for about 50 microseconds, or a millionth of a second per system. The simulations placed high demands on the computing resources of the Finnish ELIXIR Node, CSC – IT Center for Science.
Read more here:
ELIXIR is partly funded by the European Commission