On Tuesday, February 28, 2023 at 7:25:13 AM UTC-5, Ernest Major wrote:
HT Derek Lowe (In The Pipeline blog)
https://www.biorxiv.org/content/10.1101/2022.06.14.495995v2.full.pdf
I had previously suspected that choice of proteinogenic amino acids was influenced by availability in abiotic media and by selection for
chemical differences between members of that set. This paper concludes
that selection for lower solubility and more regular folding was involved.
--
alias Ernest Major
Here I was ready to complain about the paper but it's actually pretty good.
The paper is an interesting one. It explores a few hypotheses about factors that may have driven selection of inclusion and exclusion (and evolutionary selection) of amino acids within the development of the modern canonical Genetic Code.
Their introduction is somewhat limited in that it relies on an incompletely characterized model for factors that could have contributed to early
selection. In one simplistic treatment, it seems to consider rather random selection from extant abiotically synthesized molecules to be followed by
those that were synthesized by a proto-organism.
This seems to ignore the argument that the selection of L-amino acids
as part of the code is an indication that the important bioamino acids
were catalytically synthesized by enantiomerically selective catalysts
and not from some random pool of non-specific abiotic synthesis (which
would not have shown a preference for one enantiomer).
That and a few other complaints aside for now, they did some interesting experiments to show that the amino acids that appear to have been
early components of the precursor Genetic Code have in common the
ability to form regular secondary structure (alpha helixes and beta
sheets) with good packing that would contribute to stable folding.
This follows our current understanding of a key point of significance
in protein folding: the collapse of an oily hydrophobic core that 'hides'
from water. This simultaneously speeds and stabilizes the folding of
proteins. This 'feels' like a good explanation. An early primitive version
of the Genetic Code focused on amino acids that were good at generating polymers with good folding propensities.
One thing I think is lacking is a consideration of the role of the primitive Genetic Code prior to significance of folded proteins. For that, the model
I like is the role of smaller peptides in stabling RNA and expanding the folding repertoire of ribozymes with peptide stabilizers/co-factors. This
would have been one of the earliest functions of the most primitive
translation systems that gave rise to the genetic code, perhaps at the
stage of 3 to 4 originally encoded amino acids, or 3 to 4 families of closely related amino acids, perhaps not discriminating between Val, Leu, and Ile,
or between Ser and Thr, or Gln, Glu, Asn and Asp.
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