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Researchers have also presented the first platform for atomic-level simulation of nucleic acids
The Molecular Modeling and Bioinformatics Lab at the Institute for Research in Biomedicine (IRB Barcelona) has developed a new model to simulate DNA on an atomic level that allows researchers to discover DNA dynamics “with extraordinary accuracy,” according to study researchers. The work, published in Nature Methods, was conducted in collaboration with the Barcelona Supercomputing Center (BSC) and laboratories in England and the United States.
Molecular dynamics uses simulation to see what can't be observed directly through experiments. This technique simulates DNA movements, its chain folding and even its interactions with proteins or drugs. And it was the focus of study of this group of IRB researchers devoted to developing theoretical methods to better understand the behavior of bio-macromolecules and, in particular, of nucleic acids and their applications in biomedicine and bionanotechnology.
The new technique, developed over 5 years and tested with more than 100 DNA systems, allows scientists to study processes that take place on time scales ranging from picoseconds to minutes, and are applied to molecular systems of varying sizes, from nanometers to one meter. The data from the study is stored on a public website, which already has more than 4 Terabytes of information. It can be accessed through the Spanish Institute of Bioinformatics (INB) or the ELIXIR-Excellerate network (the largest collection of life sciences data in Europe).
“A force-field has never previously allowed the study of such diverse structures in time scales relevant for understanding biological phenomena,” says Pablo Dans Puiggròs, researcher at IRB Barcelona and lead author of the article with Ivan Ivani, a PhD student in the same laboratory. In addition to the new simulation model, the authors have also presented the first platform to date to focus on atomic-level simulations of nucleic acids that can “predict DNA properties, which can then be compared directly with experiment,” explains Modesto Orozco, director of the project.
The study, which is the fruit of the joint Computational Biology research program (IRB Barcelona and BSC) and funded by the European Research Council (ERC Advanced Grant), the Ministry of Economy, the Government of Catalonia and the Spanish Institute for Bioinformatics, will help advance understanding of the biological function of DNA, from protein-recognition mechanisms to improving drugs targeting nucleic acids. “Advances in simulation are bringing us closer to the definition of a theoretical model that will allows us to simulate key aspects of cell life, therefore approaching the dream of being able to describe the behavior of organisms only based on the basic rules of physics and chemistry,” says Orozco.