Chemists settle longstanding debate how methane made biologically

Chemists settle longstanding debate on how methane is made biologically

9:11 AM, 27th May 2016
Chemists settle longstanding debate on how methane is made biologically
Understanding how microbes generate methane might help scientists find ways to control pollution or make fuels.

ANN ARBOR, US: Like the poet, microbes that make methane are taking chemists on a road less travelled: Of two competing ideas for how microbes make the main component of natural gas, the winning chemical reaction involves a molecule less favoured by previous research, something called a methyl radical.

Reported in the journal Science, the work is important for both producing methane as a fuel source and tempering its role as a powerful greenhouse gas. Understanding how microbes generate methane might help scientists find ways to control pollution or make fuels.

"Methane is a greenhouse gas and, at the same time, one of the major sources of energy used worldwide," said study lead author Stephen Ragsdale, University of Michigan professor of biological chemistry. "Detailed knowledge of the microbial mechanism may lead to major breakthroughs for designing efficient catalytic processes for converting methane into other chemicals."

"We were totally surprised," said computational chemist Simone Raugei, a co-author at the Department of Energy's Pacific Northwest National Laboratory (PNNL). "We thought we'd find evidence for other mechanisms."

Ragsdale and his research team have been pursuing the answer to the methane question for 25 years.

Origins story

More than 90 percent of methane is (and has been) generated by microbes known as methanogens, which are related to bacteria. To make the gas, methanogens use a particular protein known as an enzyme. Enzymes aid chemical reactions in the biological realm like synthetic catalysts do in industrial chemical conversions. Also, the enzyme can run the reaction in reverse to break down methane for energy consumption.

Scientists know a lot about this microbial enzyme. It creates the burnable gas by slapping a hydrogen atom onto a molecule called a methyl group. A methyl group contains three hydrogen’s bound to a carbon atom, just one hydrogen shy of full-grown methane.

Energy block

To further substantiate their results, the team modelled the reaction computationally. They zoomed in on the action within the enzyme, known as methyl-coenzyme M reductase.

"We found that the methyl radical required the least amount of energy to produce, making that mechanism the frontrunner yet again," said Bojana Ginovska, a computational scientist part of the PNNL team.

In fact, one of the other intermediates required three times as much energy to make, compared to the methyl radical, clearly putting it out of the running.

Modelling the reaction computationally also allowed the team to look inside the reductase. Experiments showed that the reaction happens faster at higher temperatures and why: Parts of the protein that helped move the reaction along would move the nickel closer to the methyl-coenzyme M. Shorter distances allowed things to happen faster.

The team used supercomputing resources at two DOE scientific user facilities: EMSL, the Environmental Molecular Sciences Laboratory at PNNL, and NERSC, the National Energy Research Computing Center at Lawrence Berkeley National Laboratory.

The results might help researchers, including Ragsdale and Raugei, learn to control methane synthesis—either in the lab or in bacteria that make it in places like the Arctic—and how to break it down.

"Nature has designed a protein scaffold that works very precisely, efficiently and rapidly, taking a simple methyl group and a seemingly innocent hydrogen atom and turning it into methane as well as running that reaction in both directions," Ragsdale said. "Now how can chemists design a scaffold to achieve similar results?"

Raugei said that it would be a major breakthrough if they were able to devise a biomimetic strategy to activate methane, which means to turn it into more useful fuels.

"If nature figured out how to do it in mild conditions, then perhaps we can devise an inexpensive way to design catalysts to convert methane into liquid fuels like we use in our vehicles and jets," Ragsdale said.

This work was supported by the Department of Energy Offices of Science.

© University of Michigan News



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