In this TACC podcast, Klaus Schulten of the University of Illinois at Urbana-Champaign describes the first-time analysis and modeling of the cellulosome bond. Computed on the The research could boost efforts to develop catalysts for biofuel production from non-food waste plants.
Schulten’s work champions computationally-guided research, and among his accomplishments are solving the structure of the AIDS virus with the Blue Waters supercomputer. “Only the simulations give us a view,” Schulten said. “The simulations are a kind of computational microscope that tells engineers this is what is happening. This is why it works. This is how we can improve it.”
The challenge of using molecular dynamics to simulate the Cohesin-Dockerin system was its size, which ranged in Schulten’s and Bernardi’s simulations between 300,000 and 580,000 atoms. What’s more, they had to simulate the computationally long timescales of half a microsecond. “That is impossible for us to reproduce. But we wanted to get as close as possible to it,” Schulten said.
Schulten used the NAnoscale Molecular Dynamics program (NAMD) to characterize the coupling between Cohesin and Dockerin. His group developed the widely-used scalable parallel molecular dynamics code in 1995, which he continues to update and is available for free. What’s more, his group also developed Visual Molecular Dynamics (VMD), also freely available and widely used to analyze and animate bimolecular systems in 3D.
This achievement that our program works in the most optimal way would only be possible because of the availability of staff helping us test programs, giving us advice, and also in the broad scope of the available resources in Texas, not only the Stampede computer, but also the graphics computer (Maverick) that is available there,” Schulten said. “It was real teamwork that made it possible, and the staff at TACC was always absolutely outstanding.”
Schulten said this research on the cellulosome has fertile ground for application to benefit society. Biofuels made from non-food plant such as corn stalks or straw are currently too costly to produce at scale because the enzymes needed to digest the tough material are expensive. Engineered bacteria might one day be able to lower that cost by more efficiently delivering enzymes to plant cellulose.
Understanding cellulosomes might actually allow us one day to design our own cellulosomes that we make just for the purpose of stable, long-time digestion of plant materials and other toxic materials. And in particular, you learn to take advantage of the modularity of a cellulose-type system that we engineer, particularly also making such strong bonds as we investigated in the experiments and in the simulations that would give us an incredibly versatile, mechanically stable, long-lived, robust tool in the hands of engineers. This is very important for sustainability, for cleaning the environment, etc…There is a really long perspective in this kind of work.”
The researchers published their results in the journal Nature Communications in December of 2014.