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Author Topic:   Meyer's Hopeless Monster
markoo
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Message 183 of 207 (154121)
10-29-2004 11:35 AM


There's a passage in Meyer's paper that I have a question about:

quote:
Cassette mutagenesis experiments performed during the early 1990s suggest that the probability of attaining (at random) the correct sequencing for a short protein 100 amino acids long is about 1 in 1065 (Reidhaar-Olson & Sauer 1990, Behe 1992:65-69). This result agreed closely with earlier calculations that Yockey (1978) had performed based upon the known sequence variability of cytochrome c in different species and other theoretical considerations. More recent mutagenesis research has provided additional support for the conclusion that functional proteins are exceedingly rare among possible amino acid sequences (Axe 2000, 2004). Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 1077. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 1077.

I did read Elsberry's response in regards to Axe's citation here - interesting to say the least.

But I still have a couple of questions:

1. What is cassette mutagenesis, and how does it differ from other mutagenesis techniques?

2. I seem to have come across an abstract or two that seems to show that cassette mutagenesis certainly has its limitations:

quote:
To achieve a non-biased random replacement on the amino acid level, oligonucleotide-directed mutagenesis (5) and cassette mutagenesis (6,7) have been carried out. These methods are limited to a defined region of the gene and can not introduce mutations at random positions
http://www.humanapress.com/ChapterDetail...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}

Am I incorrect on my assessment? If I am correct, wouldn't Meyer's analysis also be on a limited scope here?

3. Anything else in this passage that might be a bit off or misleading?

This message has been edited by Adminnemooseus, 02-03-2005 17:22 AM


  
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