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ORNL Fundamental Discovery Casts Enzymes in New Light

A tree outside Oak Ridge National Laboratory researcher Pratul Agarwal’s office window provided the inspiration for a discovery that may ultimately lead to drugs with fewer side effects, less expensive biofuels and more.

Just as a breeze causes leaves, branches and ultimately the tree to move, enzymes moving at the molecular level perform hundreds of chemical processes that have a ripple effect necessary for life.

Previously, protein complexes were viewed as static entities with biological function understood in terms of direct interactions, but that isn’t the case. This finding, published today in PLoS Biology, may have enormous implications.

“Our discovery is allowing us to perhaps find the knobs that we can use to improve the catalytic rate of enzymes and perform a host of functions more efficiently,” said Agarwal, a member of the Department of Energy laboratory’s Computer Science and Mathematics Division.

Making this discovery possible was ORNL’s supercomputer, Jaguar, which allowed Agarwal and co-author Arvind Ramanathan to investigate a large number of enzymes at the atomistic scale.

The researchers found that enzymes have similar features that are entirely preserved from the smallest living organism – bacteria -- to complex life forms, including humans.

“If something is important for function, then it will be present in the protein performing the same function across different species,” Agarwal said. “For example, regardless of which company makes a car, they all have wheels and brakes.”

Similarly, scientists have known for decades that certain structural features of the enzyme are also preserved because of their important function. Agarwal and Ramanathan believe the same is true for enzyme flexibility.

“The importance of the structure of enzymes has been known for more than 100 years, but only recently have we started to understand that the internal motions may be the missing piece of the puzzle to understand how enzymes work,” Agarwal said. “If we think of the tree as the model, the protein move at the molecular level with the side-chain and residues being the leaves and the protein backbone being the entire stem.”

This research builds on previous work in which Agarwal identified a network of protein vibrations in the enzyme Cyclphilin A, which is involved in many biological reactions, including AIDS-causing HIV-1.

While Agarwal sees this research perhaps leading to medicines able to target hard to cure diseases such as AIDS, he is also excited about its energy applications, specifically in the area of cellulosic ethanol. Highly efficient enzymes could bring down the cost of biofuels, making them a more attractive option.

Funding for this research was provided by ORNL’s Laboratory Directed Research and Development program. Ramanathan was a graduate student at Carnegie Mellon University when this work began and now also works at ORNL. The paper is titled “Evolutionarily conserved linkage between enzyme fold, flexibility and catalysis.”

UT-Battelle manages ORNL for DOE’s Office of Science.
Caption: This cartoon-like image provides a representation for the internal motions coupled to the catalytic step of the enzyme Cyclophilin A. The substrate bound at the active site is shown in cyan sticks and the highly flexible regions in the enzyme are highlighted in a tube-like representation. The transparent tubes indicate the directionality of the motion. The colors on the tube indicate the extent to which these regions move,

with red and blue regions representing maximum and minimum mobility, respectively. Hydrogen bond interactions from the surface of the enzyme connect all the way to the active site and are indicated as yellow dashes. The interactions and the internal motions in Cyclophilin A are conserved from bacteria to humans.

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