Publication n°72: Simulations on the millisecond timescale

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Protein folding simulation on the millisecond timescale has been a great challenge for many years. When Folding@Home was launched, the first objective was to cross the one microsecond barrier. The upper stage of a millisecond is one thousand times more difficult to reach, and represents a significant advance in molecular simulation.

Folding@Home researchers Vincent Voelz, Greg Bowman, Kyle Beauchamp, and Vijay Pande have managed to cross this limit. The animation below represents one of the trajectories folded during the study (the simulation starts non-folded, and ends in the folded state). These simulations have yielded some surprising new information about how proteins fold. For more details, I invite you to consult the publication "Molecular Simulation of Ab Initio Protein Folding for a Millisecond Folder NTL9 (1-39)".




But why is it so important?

This step is very important because most misfolding occurs over long time scales, and this simulation of a millisecond's worth of protein folding means the team have have successfully demonstrated their new Markov State Model (MSM) technology, and can now successfully simulate very long timescales. The study of protein folding has the advantage of having a large amount of in vitro experimental data to validate the simulations.

While this publication on the folding of proteins has only just come out, researchers are already using the MSM method to study the misfolding of the proteins implicated in Alzheimer's disease, following on from the result of work described in the 2008 publication "Simulating oligomerization at experimental concentrations and Long Timescales: A Markov state model approach". While the previous publication presented time scales long enough to observe small oligomers of molecular size, this new methodology portends advanced simulations related to Alzheimer's, and to study Abeta oligomers larger and more complex than it has previously been possible to.

Adapted from: Paper No. 72: Major new results from Folding@Home: Simulation of the millisecond timescale