Biological complexity: How to make methane (Introduction)

by David Turell , Friday, May 20, 2016, 22:38 (3109 days ago) @ David Turell

There are organisms, called methanogens, which make methane naturally by a complex process involving an enzyme with a nickel atom:-http://phys.org/news/2016-05-chemists-longstanding-debate-methane-biologically.html-"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 hydrogens bound to a carbon atom, just one hydrogen shy of full-grown methane.-"To generate methane, the enzyme pulls the methyl group from a helper molecule called methyl-coenzyme M. Coenzyme M's job is to nestle the methyl group into the right spot on the enzyme. What makes the spot just right is a perfectly positioned nickel atom, which is largely responsible for transferring the last hydrogen.- ***-"They also performed another biochemical test and showed that the structure of the major intermediate was the nickel stuck to coenzyme M, the expected result if the reactions took the methyl radical path.- ***-"To further substantiate their results, the team modeled 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.-"Modeling 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.-***-"'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," he said."-Comment: Again enormous complexity. Enzymes are huge molecules and how did cell communities know to use a nickel atom? Note my bold. Maybe someday we'll be as smart as nature (or God).