Release date: 2016-05-23

There are two competing views on how bacteria make the main component of natural gas, methane. According to a new study, researchers from institutions such as the University of Michigan found that contrary to previous research, the dominant view involves the chemical reaction of methyl radicals. Understanding how bacteria produce methane may help scientists find ways to control pollution or make fuel. The results of the study were published in the issue of Science on May 20, 2016, entitled "The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase".

Stephen Ragsdale, a co-author of the paper and professor of biochemistry at the University of Michigan, said, “Methane is a greenhouse gas, and at the same time it is one of the main energy sources used worldwide. A detailed understanding of the mechanism by which bacteria produce methane may lead to the design of efficient catalysis. The process has made a major breakthrough in converting methane to other chemicals."

Although other types of free radicals are more common, such as hydrogen peroxide and ozone, this study demonstrates that bacteria in nature use the highly reactive methyl radicals to make methane.

"We were very surprised," said Simone Raugei, co-author and energy chemist at the Pacific Northwest National Laboratory. "We thought we had found evidence of other mechanisms."

More than 90% of methane is produced by bacteria called methanogens. Methanogens use a protein called Methyl-coenzyme M reductase to make methane.

Scientists know a lot about this enzyme. It produces this flammable gas by adding a hydrogen atom to the methyl group. A methyl group contains three hydrogen atoms bonded to the same carbon atom, only one hydrogen atom less than methane.

To produce methane, this enzyme carries away the methyl group from an auxiliary molecule called methyl-coenzyme M. The function of coenzyme M is to insert a methyl group into a suitable site on the surface of the enzyme. What makes this site just right is a perfectly positioned nickel atom, which is responsible for transferring the last hydrogen atom.

However, it has been controversial how this nickel atom has done this in the highly complex chemical reaction environment over the past few decades. Different possible pathways produce different fleeting intermediate molecules, but for scientists, chemical reactions occur too quickly to determine which reaction pathway to choose.

The most supported reaction pathway for chemists involves the nickel atom in this enzyme directly attacking the methyl group, stealing it from the coenzyme M. This methyl-nickel molecule is transiently present, and then the methyl group in this molecule then steals a hydrogen atom from the working region of the enzyme, coenzyme B, into methane. Many experiments support the idea that an intermediate molecule is produced: methyl-nickel.

The second view is supported by only a few research teams involved in methyl free radicals. Free radicals are unstable molecules that contain an unpaired electron. The more common free radicals are hydrogen peroxide and ozone, which can cause a lot of damage by degrading the weaker chemical bonds in the molecule.

It is this unpaired electronics that creates problems. The chemical bond between atoms usually involves two electrons. This unpaired electron will snatch electrons from other paired pairs of electrons in order to find another unpaired electron, and this can cause a lot of problems.

In the second aspect, the nickel atom is bonded to a sulfur atom of the coenzyme M instead of the methyl group. This knocks out a methyl group, and the knocked out methyl group lacks an electron. The resulting methyl radical immediately captures a hydrogen atom from coenzyme B, thereby producing methane.

In this new study, in order to find out which mechanism is correct, the researchers came up with a way to rule out one of them. The first thing they have to do is to slow down the reaction. After the intermediate molecules were produced (the first step in the manufacture of methane), they slowed the reaction by a factor of 1000 by slowing down the second step of making methane (ie, methane produced by the intermediate molecules). Doing so will allow intermediate molecules to accumulate.

Subsequently, researchers at the University of Michigan used electron paramagnetic resonance spectroscopy (EPR) techniques for biochemical analysis, allowing them to distinguish which intermediate molecule (ie, methyl-nickel in the first view) , and the methyl radical in the first view). If this reaction produces a methyl-nickel molecule, the methyl-nickel molecule will appear as a spike in their instrument. If this method produces methyl radicals, then the methyl radical molecule will still bind to the protein - actually the nickel bound to coenzyme M (also translated as this protein) Coenzyme M)--- combined with nickel atoms, so it will not be recorded in the instrument.

The researchers did not find a spike in the EPR spectrum of the product after the reaction, which means that the most likely intermediate molecule is methyl radical. However, in order to confirm this, they further carried out biochemical analysis, excluding other potential molecules. They also carried out other biochemical tests and confirmed that the structure of the main intermediate molecule is nickel-binding coenzyme M: if this reaction takes the intermediate route of methyl radicals, then this is the expected result.

Raugei said, “The effects of free radicals on living matter (such as biomaterials) are destructive. But for methyl radicals, one of the most unstable free radicals, it’s really amazing. In 100% of the time, this protein has to perform and control this reaction with extremely high precision, placing methyl radicals specifically on only one atom - a hydrogen atom bonded to the sulfur atom of coenzyme B --- Nearby."

To further validate these results, the researchers used computational methods to model this approach. They focused on this methyl-coenzyme M reductase.

Bojana Ginovska, co-author and computational scientist at the Pacific Northwest National Laboratory, said, "We found that the production of methyl radicals requires the least amount of energy, which again makes this mechanism dominant." In fact, compared to methyl radicals, Another intermediate molecule (ie methyl-nickel) requires three times the energy.

Modeling this reaction also allowed the researchers to observe the interior of the methyl-CoA reductase. Through experiments, they found that this reaction occurs faster at higher temperatures and the reason for this: a partial fragment of this reductase that assists in this reaction brings the nickel atom closer to the methyl-CoA molecule. Shorter distances allow the reaction to occur faster.

These findings may help scientists learn to control methanol synthesis in the laboratory or in bacteria, and how to degrade methanol. Raugei said it would be a major breakthrough if they were able to design a biomimetic strategy to activate methanol, which meant turning it into a more useful fuel.

Source: Bio Valley

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