Scientists discover channel used by catalyst to produce ammonia, vital for food and fuel crops

May 08, 2014
Scientists discover channel used by catalyst to produce ammonia, vital for food and fuel crops
The open conformation of the nitrogen channel in a molybdenum-dependent nitrogenase.

(Phys.org) —Mother Nature's helper in turning nitrogen from the air into ammonia is an enzyme called nitrogenase that uses molybdenum and iron; scientists want to learn natural catalyst's secrets and apply them to synthetic catalysts. To do so, they first need to know how the nitrogen gas reaches the heart of the catalyst. While scientists have posited long, convoluted routes, a team from Pacific Northwest National Laboratory and Utah State University discovered the actual channel the nitrogen uses. It is short and direct. They discovered the channel by identifying groups of proteins on the catalyst's surface that guard access to the metal atoms, twisting aside to allow nitrogen in.

"Our channel is the only one anyone has seen in action," said Dr. Simone Raugei, a theoretical chemist at PNNL who worked on the study.

Producing ammonia for use in fertilizer is an energy-intense reaction, known as the Haber-Bosch reaction, that requires high temperatures, around 500 degrees Celsius. The reaction consumes hydrogen gas derived from fossil fuels. Nitrogenase takes fundamentally different process to produce ammonia, and this natural reaction happens quickly at room temperature. If a synthetic catalyst could be designed that operates efficiently at and consumes available protons and electrons instead of , it would greatly benefit both the agricultural and energy sectors. The discoveries made in this study provide vital information for designing such catalysts.

"We knew where the reaction happened," said Dr. Dayle Smith, a computational chemist at PNNL who conducted the study. "But, we didn't know how the nitrogen got there. Now we do."

Methods: The researchers modeled molybdenum-dependent nitrogenase, a fast, efficient, and prevalent enzyme. The natural catalyst drives a reaction that turns one nitrogen molecule into two ammonia molecules. The reaction happens at the active site, buried deep inside the molecule. To access the metals at the active site, must traverse channels from the surface to the active site.

Previously, scientists suggested three possible channels that directed the nitrogen to the . Each of these channels was long and convoluted. To determine the actual channel, the team ran submicrosecond atomistic molecular dynamics simulations using a supercomputer at EMSL. The simulations provide the location and trajectories of each atom as the enzyme catalyzes the .

"Being able to see how the atoms move-you can get a lot out of that," said Smith.

In analyzing the data, the team found the channel was short and not far away at all, but rather close to where the chemistry happens. The channel is covered by protein groups on the surface that act as flaps that open to allow the nitrogen to enter.

"Nobody could see it before because you had to have the protein moving to see it," said Smith.

The team further analyzed the viability of the channel by studying the energy required for the nitrogen to move through the catalyst. Their calculations showed that uptake occurs along a low-energy path.

Explore further: First view of nature-inspired catalyst after ripping hydrogen apart provides insights for better, cheaper fuel cells

More information: Smith D, K Danyal, S Raugei, and LC Seefeldt. 2014. "Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach." Biochemistry 53(14):2278-2285. DOI: 10.1021/bi40131

add to favorites email to friend print save as pdf

Related Stories

Recommended for you

Why plants don't get sunburn

23 hours ago

Plants rely on sunlight to make their food, but they also need protection from its harmful rays, just like humans do. Recently, scientists discovered a group of molecules in plants that shields them from ...

Viral switches share a shape

Oct 27, 2014

A hinge in the RNA genome of the virus that causes hepatitis C works like a switch that can be flipped to prevent it from replicating in infected cells. Scientists have discovered that this shape is shared by several other ...

'Sticky' ends start synthetic collagen growth

Oct 27, 2014

Rice University researchers have delivered a scientific one-two punch with a pair of papers that detail how synthetic collagen fibers self-assemble via their sticky ends.

Cell membranes self-assemble

Oct 27, 2014

A self-driven reaction can assemble phospholipid membranes like those that enclose cells, a team of chemists at the University of California, San Diego, reports in Angewandte Chemie.

Emergent behavior lets bubbles 'sense' environment

Oct 27, 2014

Tiny, soapy bubbles can reorganize their membranes to let material flow in and out in response to the surrounding environment, according to new work carried out in an international collaboration by biomedical ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.