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Bio-Complexity paper: Similarity of enzyme structure does not guarantee ease of interconversion


Doug Axe and Ann Gauger have a new peer-reviewed paper up at BIO-Complexity which provides a quantifiable measure of how many mutations are required for a relatively simple biological innovation – the functional conversion of one enzyme to that of its closest structural neighbor.

The authors argue that their results show that similarity of structure does not guarantee ease of interconversion, and that that goes to the root of all Darwinian trees based on such similarity.

Here’s the abstract:

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs–the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations–transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution. 

I opened the paper and my eyes started to bleed. But wouldn't this be highly relevant to the thread at: https://uncommondesc.wpengine.com/intelligent-design/enzymes-complex-from-the-get-go/ Mung
This paper really goes to the heart of the refuting neo-Darwinian evolution. I hope gppuccio is still around to see this paper, for he clung to the idea that there was a fair amount of flexibility within protein families themselves, whilst he knew that unique classes of protein folds were far to rare in sequence space to be arrived at by Darwinian means. This paper would have let me show him the extreme constraint placed on variation of even seemingly similar proteins. bornagain77

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