Biomolecules, particularly proteins, fold and form unique three-dimensional structures that determine their function in living creatures. Nowadays, molecular dynamics simulations are an essential tool in biology to know how these folds occur. However, these tools need many calculation resources, so they can only cover a short period of a molecule's life.
The first experiment that allows manipulating a single molecule at computer simulation speed has been carried out in a study, published in the journal Science. Participating researchers belong to the University of Barcelona (UB) and the French National Institute of Health and Medical Research (INSERM), of Aix-Marseille University. Manel Puig Vidal, professor from the Department of Electronics of UB and author of the article, explains that "it is the first time that a direct comparison between experimentation and simulation takes place; it has been established that the physical state of a molecule, or a cell, is as important as its biochemical state."
Many life processes involve physical changes, for instance the mechanic action observed during muscle contraction. The study analysed titin, a protein that is a molecular spring in muscle sarcomeres and it is important in striated muscle functions. Consequently, its mechanical behavior is directly related to its physiological function, absorption and force transmission. "Generally speaking, we are learning important things about the protein folding process by studying its unfolding," concludes Puig Vidal.
In order to carry out the experiment, researchers used high-speed atomic force microscopy (HS-AFM); this technique allows imaging biomolecules at video rate through miniaturization of its components. It is similar to high-speed force spectroscopy (HS-FS), a technique developed by these researchers too. According to Laura González, doctoral student at UB and author of the article, "it enables to measure protein unfolding at speeds up to 4,000 microns per second." This is faster than conventional measures by 2.5 orders of magnitude and reaches current limits for steered molecular dynamics (SMD) simulations.
There is evidence that protein distortion may play an important role in biology and medicine, and particularly in mechanotransduction, which includes many biological mechanisms by which cells turn mechanic stimuli into chemical activity. In short, protein mechanics remains quite unknown, so there are still many important questions to be answered. This kind of studies, like the one carried out by physicists from UB and the team led by Professor Simon Scheuring, from INSERM, are important in order to take a step towards knowing how protein distortion affects their function and their dynamic behavior.
- F. Rico, L. Gonzalez, I. Casuso, M. Puig-Vidal, S. Scheuring. High-Speed Force Spectroscopy Unfolds Titin at the Velocity of Molecular Dynamics Simulations. Science, 2013; 342 (6159): 741 DOI: 10.1126/science.1239764
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