May 2, 2007

Molecular visualization of the bioconversion process

The tools available for the hunt for renewable energy are very 21st Century. In place of wildcatting subterranean petroleum deposits using multi-million dollar rigs and oil crews, much of the ground-breaking research is taking place with meticulous precision at government labs in collaboration with universities and industry. New tools include robotics, mass spectrometers, laser imagers, and data collection and analysis devices. As a result, communications can be digital and more visual than ever before, speeding questions and understanding at warp speed around the globe.

The Society of Industrial Microbiology convened their 29th Symposium on Biotechnology for Fuels and Chemicals in Denver this week which was hosted by the federally-financed National Renewable Energy Laboratory (NREL) situated in nearby Golden, Colorado. One of the highlights of the symposium was a tour of NREL's groundbreaking facilities. The tour included visits to its biochemical and thermochemical labs and pilot plants for converting an array of feedstock (particularly corn stover for now) into sugars and ethanol.

One stop was in a research area where high tech imaging devices are employed to analyze cell and molecular structures involved in the bioconversion process. At right is a picture of the X8 Proteum - a new tool for conducting biological crystallography research. Data collected from this device can be used to build accurate models and animations to aid understanding.

Each tour group was treated to a 4 minute animation that zoomed from outside a corn plant into its stalk structures with an intricate graphic depiction of how molecules interact during the bioconversion process. It was built from data provided by NREL and visualized by the San Diego Supercomputer Center (SDSC).

In an article titled Tapping Plants for Fuel Cassie Ferguson, writing for the SDSC, explains the animation process this way:

To explore the intricate molecular dynamics of cellulase, researchers at NREL have turned to CHARMM (Chemistry at HARvard Molecular Mechanics), a suite of modeling software for macromolecular simulations, including energy minimization, molecular dynamics, and Monte Carlo simulations. The widely-used community code, originally developed in 1983 in the laboratory of Martin Karplus at Harvard University, models how atoms interact.

In the cellulase modeling, CHARMM is used to explore the ensemble configurations and protein structure, the interactions of the protein with the cellulose substrate, and the interactions of water with both. Not only are the NREL simulations the first to simultaneously model the cellulase enzyme, cellulose substrate, and surrounding water, they are among the largest molecular systems ever modeled. In particular, the researchers are interested in how cellulase aligns and attaches itself to cellulose, how the separate parts of cellulase—called protein domains—work with one another, and the effect of water on the overall system. And they are also investigating which of the over 500 amino acids that make up the cellulase protein are central to the overall workings of the "machine" as it chews up cellulose.

To the biochemists in the collaboration, the simulation is like a stop-motion film of a baseball pitcher throwing a curveball. In real-life the process occurs too quickly to evaluate visually, but by breaking down the throw into a step-by-step process, observers can find out the precise role of velocity, trajectory, movement, and arm angle. In simulations on SDSC's DataStar supercomputer, the researchers have modeled a portion of the enzyme, the type 1 cellulose binding domain, on a surface of crystalline cellulose in a box of water. The modeling revealed how the amino acids of the domain orient themselves when they interact with crystalline cellulose as well as how the interaction disrupts the layer of water molecules that lie on top of the cellulose, providing a detailed glimpse of this intricate molecular dance.

While this lengthy animation does not appear to be available online, another bioconversion cartoon (pictured at top) simulated by Dr. Mark Nimlosis (NREL) and visualized by Dr. Ross Walker and Amit Chourasia of SDSC is available for download.

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