Chaperonins: Open and Shut Case

_{Cornelius Hunter

January 29, 2010

Intelligent Design}

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A protein is created in the cell by copying its DNA gene, making any necessary edits to the copy, and passing the copy to the ribosome machine which uses the genetic code to translate the copy (a series of nucleotides) into the protein structure (a series of amino acids). But the story does not end here. The final step, after translation, is to fold the protein into its three dimensional structure. It is a step that is difficult to monitor and difficult to predict. The chain of amino acids folds up in a tiny fraction of a second and the final shape it assumes is not obvious. And sometimes the folding process is literally hidden as the nascent protein chain is hidden inside the cavity of a chaperonin machine with the lid shut. Read more

Comments

And the evidence for these purely imaginative hypotheses is…?
Oh, Mung. Don't be silly. You know very well that I was pointing out the false dichotomy presented in the original post.
What sort of function is this? A function that more or less functions, resulting in more function, or less function?
Again with the silliness.hrun0815_{January 30, 2010
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Your article suffers from the binary thinking of function/non-function in proteins, not less function/more function across a continuum.
What sort of function is this? A function that more or less functions, resulting in more function, or less function?
A protein now considered misfolded may still have had enough function to survive in the cells of several billion years ago. At the same time, if helping a protein fold does improve function, then chaperonins would be strongly selected for, and strongly conserved. This seems to be the case.
If helping a protein fold improves the function of WHAT? He's talking about the function of chaperones, and you're talking about the function of whatever it is that chaperones assist through their functioning. Apples. Oranges.Mung_{January 29, 2010
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Or, of course, there is a third scenario: The existence of a key enzyme, even if only a fraction of the peptide chains fold into a functional conformation increase fitness over not having the enzyme at all. In a second step, the presence of chaperonins, which increase the ratio of properly folded proteins over the total amount leads to a further increase in fitness.
And the evidence for these purely imaginative hypotheses is...?Mung_{January 29, 2010
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Dr Hunter, Your article suffers from the binary thinking of function/non-function in proteins, not less function/more function across a continuum. A protein now considered misfolded may still have had enough function to survive in the cells of several billion years ago. At the same time, if helping a protein fold does improve function, then chaperonins would be strongly selected for, and strongly conserved. This seems to be the case. Looking at chaperonins themselves, not so much lucky mutations but gene duplications seems to have built them up from smaller units. To better understand their evolution, we would need to understand what these subunits can do on their own. Is being a chaperone an exaptation of another function they once had? The Wikipedia page on GroEL offers some insight. The hand in hand evolution of proteins and chaperonins isn't quite so surprising if we find that chaperonins help a wide variety of proteins fold, which it seems they do. We also know that there are other kinds of chaperonin such as heat shock proteins which may have helped folding in the absence of larger chaperonins such as you discuss. Finally, some questions you didn't ask: if chaperonins help other proteins fold by enclosing them, what helps the chaperonin fold? ;)Nakashima_{January 29, 2010
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These are questions that young evolutionists are prone to ask (evolutionists are constantly probing and trying to falsify their own theory). In their lack of experience they miss the obvious solution: Evolution simultaneously evolved both the chaperonins and the proteins that need their help. The reluctant proteins were never clogging the works, and the chaperonins never lacked for something to do.
Or, of course, there is a third scenario: The existence of a key enzyme, even if only a fraction of the peptide chains fold into a functional conformation increase fitness over not having the enzyme at all. In a second step, the presence of chaperonins, which increase the ratio of properly folded proteins over the total amount leads to a further increase in fitness.hrun0815_{January 29, 2010
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Not to be picky but sometimes the amino acid chain gets edited before the folding process. (You know Art Hunt will bring that up)Joseph_{January 29, 2010
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