One of life's strongest bonds has been discovered by a science team researching biofuels with the help of supercomputers. Their find could boost efforts to develop catalysts for biofuel production from non-food waste plants.

Renowned computational biologist Klaus Schulten of the University of Illinois at Urbana-Champaign led the analysis and modeling of the bond, which behaves like a Chinese Finger Trap puzzle. "What's new is that we looked at the system very specifically, with the tools of single molecule force spectroscopy and molecular dynamics, computing it for the first time," Schulten said.

The research team, in particular Rafael Bernardi of the University of Illinois at Urbana-Champaign, used the computational resources of XSEDE, the Extreme Science and Discovery Environment, a single virtual system funded by the National Science Foundation (NSF) that allows scientists to interactively share computing resources, data and expertise.

"XSEDE allowed us to employ one of the fastest supercomputers to, in parallel, perform the simulations that helped us to reveal how the building blocks of the cellulosomes become ultrastable in harsh environments," Bernardi said. "The massive amount of computer time necessary to perform our study, and the fact that fast supercomputers are necessary to have a fast iteration with experimentalists, makes a study like this simply not feasible without support from public available supercomputers like Stampede."

"We looked at the system very specifically, with the tools of single molecule force spectroscopy and molecular dynamics, computing it for the first time."Klaus Schulten, University of Illinois at Urbana-Champaign.

The bond behaves like a Chinese Finger Trap, a puzzle made of a grippy tube of woven bamboo. Two fingers inserted into the ends of the puzzle become stuck when one tries to pull them out.

What's bonded together are two proteins, Cohesin and Dockerin. The bacteria Ruminococcus flavefaciens, which live inside the stomach compartment of cows, take Cohesin and Dockerin and piece them together to form a finger-like system of proteins called the cellulosome. Bacteria connect the cellulosome they assemble outside on their cell wall.

The point of all this machinery is to have scaffolding that hangs on to enzymes needed for bacteria, and ultimately the cow, to digest the variety of grass, wood chips, etc. that the animal finds to eat. "Just imagine (the cellulosome) like a hand, where the tips of the fingers contain different enzymes that can digest plant cell walls," explained Schulten. "The bacteria need to build those cellulosomes and those enzymes according to whatever plant material they encounter."

The rumen of a cow is a tough place to hang on to anything — there's enormous mechanical work being done in the form of contraction, expansion, and flows of liquid.

"There is some kind of puzzle, namely to piece the cellulosome together from its parts," said Schulten. That's because during construction, the forces holding together the pieces must not be very strong in order to permit flexible assembly and disassembly.

"But once the cellulosome starts to work and force is exerted on it, then the cohesion forces become very strong," he continued. "They become in fact almost as strong as complete chemical bonds that are real molecular connections between molecules. They can bond into a very strong connection, and you need to use very strong forces to break it."

Schulten's study co-author Hermann Gaub and his group at the University of Munich did just that, building and then stretching apart an XMod-Doc:Coh complex, the building block of the cellulosome. From that the scientists measured the force extension curve, the force needed to stretch a certain extension.

"That gives you information, not the detail that tells you what physical process is going on and that permits you to explain the physical properties," Schulten said. "For that you need to simulate them."

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.

This story is reprinted from material from The University of Texas at Austin, with editorial changes made by Materials Today. The views expressed in this article do not necessarily represent those of Elsevier. Link to original source.