Biological complexity: no life if no enzymes (Introduction)

by David Turell , Tuesday, April 17, 2018, 22:53 (2412 days ago) @ David Turell
edited by David Turell, Tuesday, April 17, 2018, 23:09

Enzymes manage all reactions in life. They are giant complex molecules that force the completion of biochemical reactions: An other enzyme structure is described:

https://www.sciencedaily.com/releases/2018/04/180417130122.htm

"Without enzymes, nature would come to a standstill. These tiny molecules accelerate biochemical reactions or make them possible in the first place. But how does this happen on a molecular level? "Understanding the exact function of enzymes is one of the greatest challenges of modern biochemistry," says Ville Kaila, Professor of Computational Biocatalysis at the Technical University of Munich.

"The research team led by Ville Kaila and Michael Groll, Professor of Biochemistry at the Technical University of Munich, have, for the first time, deciphered the mechanism of the enzyme aspoquinolone J (AsqJ), a dioxygenase that activates carbon bonds with oxygen.

"The enzyme AsqJ is particularly exciting as it catalyzes a cascade of chemical reactions that ultimately lead to the formation of antibacterial compounds. It was discovered only a few years ago in the Aspergillus nidulans fungus.

***

"'Our calculations illustrate how the enzyme catalyzes the formation of quinolone alkaloid," reports Kaila. "Tiny details have amazing effects: A slight change in the substrate, like the removal of a small chemical group, is sufficient to practically stop the reaction."

"Next, the team computationally designed a new variant of the enzyme that catalyzes the formation of quinolone alkaloids with the modified substrate. This new enzyme was experimentally produced in bacteria and tested for its functionality. "The results were impressive: the expected reaction took place after only a few seconds," recalls Bräuer."

Comment: The change in one amino acid in this giant molecule changed the way it controlled reactions, showing how precise each enzyme has to be to perform its proper function. These molecules must be present for life to exist with life's need for immediate results. The odds against chance evolution making such structures are enormous. Design is more logical.

Look at the illustration and the comment:

"While the difference between the natural and the modified AsqJ is only one amino acid, the reactivity is clearly different. The natural AsqJ (left) possesses a valine at position 72 (blue). The modified form possesses an isoleucine (red) at position 72. The substrate in the active site is green-colored, alpha-ketoglutarate yellow, the iron atom gray, and two histidine chains cyan and blue." (my bold)

Further here is an article about improving an enzyme by accident:

http://bigthink.com/brandon-weber/theres-a-plastic-eating-bacteria-and-its-now-on-stero...

"A few years ago, at an Osaka, Japan recycling plant, scientists discovered a bacteria called Ideonella sakaiensis that eats one of the most common forms of plastic, known as polyethylene terephthalate or PET. That form of plastic is found in water bottles, food containers, and polyester.

"Researchers from Britain’s University of Portsmouth and the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) were trying to model the enzyme and ended up with a mutant strain of the same thing, with a crucial difference: it eats plastic even better.

"'We hoped to determine its structure to aid in protein engineering, but we ended up going a step further and accidentally engineered an enzyme with improved performance at breaking down these plastics," said NREL's lead researcher Gregg Beckham."

Comment: This was study in a lab run by designing minds, but Darwin asks us to accept that nature does this by accident all the time. I don't accept that. Only design fits.