Thursday, February 22, 2007

Douglas Axe - J.Mol.Biol.(2000) 301, 585-595

Thanks to "Smokey" for the paper.
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.

Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.

Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.

Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.

These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.

It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.

Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.

4 Comments:

Blogger Smokey said...

Andrew wrote:
"Thanks to "Smokey" for the paper."

You're welcome.

"Previous blog post here."

So where's the big controversy?

"This paper examines the idea that ...The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous."

Yes, but the binary code hypothesis is a structural hypothesis. Why did you lose interest in the evolutionary theory (neutral theory), in the context of which Axe also discussed his results?

Why on Earth would you blog about a mere structural hypothesis instead of the evolutionary theory addressed in the paper?

"...When roughly 1 in 5 of these [exterior] residues is changed this results in complete loss of function in both enzymes examined."

So is this really accurate? Did Axe check each enzyme for any function, or just for one function? I'm not saying that it is inaccurate in the context of the entire paper.

"Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive."

Inactive in what respect?

"Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features."

Axe also concluded that his results could be reconciled with neutral theory, and explicitly pointed out that he only assayed a tiny subset of possible evolutionary intermediates.

"These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues."

Wasn't there an important difference? Exterior vs. interior? Hydrophilic vs. hydrophobic?

"It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues."

Ah, so here's your chance to demonstrate your faith. What do YOU predict would happen if we changed a residue in the active site, which contacts the substrate, from an almost universally conserved residue (with one of the largest side chains) to a residue not found in nature (with the smallest side chain)? IOW, it's as radical as you can get wrt size.

"Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous."

Axe also concludes,
The fact that the amino acid differences between two closely related b-lactamase enzymes clearly are not functionally inconsequential might seem to contradict the notion that homologues are connected by a path of neutral substitutions. However, the neutral theory claims neither that most possible substitutions nor that most possible paths between close homologues are selectively neutral. It claims, rather, that the actual historical paths consist primarily of substitutions that each were neutral in their own context.

The findings of this work can be accommodated within the framework of the neutral theory by postulating that substitutions initially having no significant effect become invested with functional importance as further substitutions accumulate. The catastrophic disruption observed in the hybrids demonstrates a high degree of co-optimisation among the residues unique to either parent.


Isn't that the most relevant conclusion to someone interested in ID vs. evolution?

8:17 am  
Blogger Andrew Rowell said...

You asked:
"So where's the big controversy?"

Those opposed to ID accuse it of being a complete science stopper. Axe is a key figure in the ID movement. He has done some excellent work and is apparently continuing that work despite the difficulties his association with ID has resulted in.

This work is highly relevant in my view to some of the central issues of ID.

You said:
"So is this really accurate? Did Axe check each enzyme for any function, or just for one function? I'm not saying that it is inaccurate in the context of the entire paper."

It is a lot of work to check for one function. Are you expecting that there would have been several other functions among the variants?

You said:
"Wasn't there an important difference? Exterior vs. interior? Hydrophilic vs. hydrophobic?"

I am not sure I understand the Q here....

9:58 pm  
Blogger Smokey said...

Andrew wrote:
"Those opposed to ID accuse it of being a complete science stopper."

Andrew, this is utterly, completely false. There's nothing in the paper that threatens science, or MET, in any way. That's why I took issue with your previous misrepresentation of this paper. You conflated the paper itself with the attempts to spin it.

"Axe is a key figure in the ID movement. He has done some excellent work and is apparently continuing that work despite the difficulties his association with ID has resulted in."

Axe clearly states in this paper that the data in the paper are compatible with the neutral theory:

The findings of this work can be accommodated within the framework of the neutral theory by postulating that substitutions initially having no significant effect become invested with functional importance as further substitutions accumulate. The catastrophic disruption observed in the hybrids demonstrates a high degree of co-optimisation among the residues unique to either parent.

Simple question: do you agree with Axe or not?

"This work is highly relevant in my view to some of the central issues of ID."

Which ones?

"It is a lot of work to check for one function."

Yes, science is often hard work. Why not just admit that he didn't?

Since Axe didn't bother, did anyone else look for another function in these or similar mutants?

"Are you expecting that there would have been several other functions among the variants?"

The issue is not what *I* expect, Andrew; it's what the hypotheses predict.

What does ID predict?

"I am not sure I understand the Q here...."

You claimed that it was surprising in light of previous experiments that changed internal, hydrophobic residues. I am challenging you to explain why, because I don't find these results surprising. Interesting, yes. Surprising and a threat to science, no way.

So, please be honest and courageous enough to predict, based on your understanding of the data in Axe's paper (not spin), what would happen to an enzyme if I changed a residue:

1) in the active site
2) that directly contacts the substrate
3) that is nonpolar, with a relatively huge side chain (tyrosine)

http://z.about.com/d/chemistry/ 1/0/1/1/tyrosine.gif

to the residue with the smallest nonpolar side chain (glycine).

http://z.about.com/d/chemistry/1/0/4/1/glycine.gif

Does ID theory predict that the enzyme:
1) lose the wild-type activity?
2) gain an additional activity?
3) be completely inactive?

Note that 1 and 2 are not mutually exclusive. This is the most radical substitution one can make without changing charge.

Remember, this is important stuff, so it is extra important to reduce bias by making predictions instead of spinning existing data.

If you understand the Axe paper well enough to conclude that it supports ID, it would be spectacularly dishonest for you to avoid offering a prediction in this case.

6:59 pm  
Blogger Kerry Craig Wallker said...

Please read this and give any feedback.

Kerry
kerrycw1 at gmail.com

The Dawn of Intelligence

http://www.slideshare.net/superwhuffo1/the-dawn-of-intelligence-by-kerry-craig-walker-final-ds-numbered-pageslatestfinalfinalfinal

8:55 pm  

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