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Nylonase


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#1 AFJ

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Posted 29 October 2011 - 05:24 AM

From a chemical perspective, the enzymes "6-Aminohexanoate-dimer hydrolase (EII), responsible for the degradation of nylon-6 industry by-products, and its analogous enzyme (EII*)" (1), is microevolution in action. The derivative of nylon, 6-aminohexanoate, which flavobacterium was discovered digesting in pond waters, is an oligomer, or analogue of the amino acid lysine (2).

The following shows a Lewis diagram comparison between the two molecules.

Posted Image
6-aminohexanoate acid


Posted Image
2,6-diaminohexanoic acid--Lysine

As you can see (if you turn them both horizontal), both are a 6 carbon chain with an amine (NH2) on one end, and an acid (carboxyl) on the othere end (COOH). The only differences between them is the amino acid lysine has another amine on the number 2 carbon (i.e. 2,6 there are amines). And the wedge in the Lysine diagram represents the 3D shape coming toward you, and would be caused by London forces from the amine bonded to the #2 carbon.

What you may find interesting is that bacteria have been used industrially for quite sometime to produce lysine (4). This is because, unlike mammals, many bacteria can syntheize lysine. Mammals have to consume lysine for energy, and protein production.

That said, the analogous enzymes that "evolved" by means of an identified insertion and plasmid into a repeating 10 base sequence, thus causing a frameshift mutation (5) was a unique situation. One where each of three possible frameshifts (because the reading frames are 3 bases each), would not cause a stop codon, nor cause the protein binding domains to be ruined. Moreover, there is other research that provides a third analogue. http://www.jbc.org/c...4.full.pdf html

As for initial breakdown of nylon in an en vivo environment, it is commonly known that nylon, being technically an organic molecule (carbon chained), is subject to hydrolysis via an acid environment. Many bacteria produce acids as wastes.

There is a common precursor (solid phase) material between lysine and nylon, which I read about, but can not currently find (because my wife is beside me talking--lol). If someone wants to do the research for the precusor it would be appreciated.

At any rate, this is only intended to define the actual evolution of nylonase enzyme or enzymes and the chemical "closeness" of what they break down. I feel sufficient information and citing has been given. I'm asking for arguements/evidence from both sides that either shows justification for a mechanism of macroevolution, or why it is that it is not a mechanism of macroevolution.

#2 jason777

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Posted 29 October 2011 - 10:45 AM

X-ray crystallography is an empirical method, so I'm certain it falsified the first assumption of a frameshift mutation. All that was observed was an additional two amino acids to a pre-existing enzyme.

I didn't know lysine and nylon were so chemically similar. Thanks for sharing.




Enjoy.

#3 AFJ

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Posted 29 October 2011 - 05:35 PM

X-ray crystallography is an empirical method, so I'm certain it falsified the first assumption of a frameshift mutation. All that was observed was an additional two amino acids to a pre-existing enzyme.

I didn't know lysine and nylon were so chemically similar. Thanks for sharing.




Enjoy.

Were they additional or substitutions? I thought I read substitions, but may be wrong.

Not to nitpick, but the aminohexanotate acid is not nylon. It is a derivative, and that's what the flavobacterium actually digests. "Nylon eating" is not correct.

#4 jason777

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Posted 29 October 2011 - 06:14 PM

Yeah, your correct; it was a substitution. And I'm beginning to wonder if the bacteria could digest 6-aminohexanoate acid already and the amino acid substitution was just some random mutation that occurred afterwards and inferred as the means. Do you know for certain? The nylon and lysine are so similar that it got me thinking. The paper says that it's the enzyme responsible for the degradation of nylon, but I don't know if they have observed other bacteria feeding on it without those two amino acid substitutions or not.




Thanks.

#5 AFJ

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Posted 30 October 2011 - 05:23 AM

Yeah, your correct; it was a substitution. And I'm beginning to wonder if the bacteria could digest 6-aminohexanoate acid already and the amino acid substitution was just some random mutation that occurred afterwards and inferred as the means. Do you know for certain? The nylon and lysine are so similar that it got me thinking. The paper says that it's the enzyme responsible for the degradation of nylon, but I don't know if they have observed other bacteria feeding on it without those two amino acid substitutions or not.




Thanks.

6-Aminohexanoate-dimer hydrolase should be responsible to actively break down 6-Aminohexanoate, and not the full nylon molecule, which is much longer. I was looking for a complete lewis structure for nylon that I could paste here. I found one structure but I couldn't paste it. http://www.polymerpr...ymers/PA66.html

You will see in general the nylon molecule is much longer. In detail, you can see what becomes, after reactions, 6 aminohexanoate. If you look at the first part of the nylon molecule structure, you see (CH2)6. This is a 6 carbon chain with each carbon having 2 bonded hydrogens, the other two bonds carbons on each side. That is except on the 2 end carbons of (CH2)6, which is a carbon on one side two H's bottom and top and NH on the end of the chain.

If you break this (CH2)6 off, add an amine (NH2) on one end, and a carboxyl (COOH) on the other, you have 6 aminohexaoate. All amino acids have the same thing, a carbon/H structure, with an amine and carboxyl at opposite ends. So it is basically lysine, without the amine on the #2 carbon.

I'll bracket this in quotes, letting you know I did it. You can verify it by simple chemistry, and the things I already cited in the OP.

(CH2)6
H H H H H H
-C-C-C-C-C-C-
H H H H H H

Nylon molecule bonds NH on each end carbon atom. Both NH's bonded to carboxyls in a polymer chain.

6 Aminohexanoate bonds NH2 on one end, and COOH on other. Just like an amino acid.

It specifically says, even on Wiki, that the flavobacterium was digesting "by products" of nylon. Just as an aside, in a strong enough acid environment, nylon itself can go through hydrolysis--chemically with no enzyme required. Hydrolysis adds an H2O between the peptide bonds (amine/carboxyl) between the amino acids, or monomers in a polymer. This breaks the peptide bond.

#6 gilbo12345

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Posted 30 October 2011 - 10:57 AM

What you may find interesting is that bacteria have been used industrially for quite sometime to produce lysine (4). This is because, unlike mammals, many bacteria can syntheize lysine. Mammals have to consume lysine for energy, and protein production.


Thanks for the info AFJ.

I'll just add that the above is Biotransformation, a type of Biotechnology whereby bacteria is used to produce, (quite cheaply), complex molecules due to the secondary metabolic pathways bacteria access in their stationary phase of growth.

#7 AFJ

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Posted 30 October 2011 - 01:32 PM

Thanks for the info AFJ.

I'll just add that the above is Biotransformation, a type of Biotechnology whereby bacteria is used to produce, (quite cheaply), complex molecules due to the secondary metabolic pathways bacteria access in their stationary phase of growth.

Not much debate here. Kind of suprising when this is supposed to be evidence of "evolution in action." I call it prokaryote adaptation to a chemical environment.




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