Freethought & Rationalism Archive

lpetrich · 10-29-2002, 10:31 PM

Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code

Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh

Nontechnical "translation" of abstract from <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=122708 92&dopt=Abstract" target="_blank">ISCID's Most Feared Source</a>:

These researchers reconstructed a large number of "Archean Park" proteins, those belonging to the inferred common ancestor of all cellular life. They worked out amino-acid frequencies in these proteins and then compared those frequencies to present-day ones.

The ancestral proteins had more of the amino acids that are abundantly produced in prebiotic-chemistry experiments and less of those that are rare or absent in such experiments.

Which is consistent with amino acids having been appropriated from some "Primordial Soup"; what reason would some intelligent designer have for creating proteins with this pattern of abundances?

[ October 30, 2002: Message edited by: lpetrich ]</p>

monkenstick · 10-29-2002, 11:44 PM

delicious

theyeti · 10-30-2002, 05:40 AM

Here's another interesting paper dealing with the amino acid composition of proteins:

<a href="http://www.pnas.org/cgi/content/full/99/21/13549" target="_blank">PNAS. USA, Vol. 99, 21, 13549-13553, Oct. 15, 2002</a>

Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set.

Quote:

We developed an effective strategy to restrict the amino acid usage in a relatively large protein to a reduced set with conservation of its in vivo function. The 213-residue Escherichia coli orotate phosphoribosyltransferase was subjected to 22�cycles of segment-wise combinatorial mutagenesis followed by 6�cycles of site-directed random mutagenesis, both coupled with a growth-related phenotype selection. The enzyme eventually tolerated 73�amino acid substitutions: In the final variant, 9�amino acid types (A, D, G, L, P, R, T, V, and Y) occupied 188�positions (88%), and none of 7�amino acid types (C, H, I, M, N, Q, and W) appeared. Therefore, the catalytic function associated with a relatively large protein may be achieved with a subset of the 20�amino acid. The converged sequence also implies simpler constituents for proteins in the early stage of evolution.

The authors here took a modern protein and replaced many of its amino acids such that it had a reduced set. Yet the protein still functioned fine. This shows that primitive proteins near the OOL might have had a reduced amino acid set that was later expanded as the genetic code grew.

theyeti

P.S. That was an excellent find LP! Very interesting.

[ October 30, 2002: Message edited by: theyeti ]</p>

10-29-2002, 10:31 PM	#1
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Ultimate Ancestor's Amino Acids Much Like Prebiotic Ones Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh Nontechnical "translation" of abstract from <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=122708 92&dopt=Abstract" target="_blank">ISCID's Most Feared Source</a>: These researchers reconstructed a large number of "Archean Park" proteins, those belonging to the inferred common ancestor of all cellular life. They worked out amino-acid frequencies in these proteins and then compared those frequencies to present-day ones. The ancestral proteins had more of the amino acids that are abundantly produced in prebiotic-chemistry experiments and less of those that are rare or absent in such experiments. Which is consistent with amino acids having been appropriated from some "Primordial Soup"; what reason would some intelligent designer have for creating proteins with this pattern of abundances? [ October 30, 2002: Message edited by: lpetrich ]</p>

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10-29-2002, 11:44 PM	#2
monkenstick Regular Member Join Date: Jul 2002 Location: Australia Posts: 214	delicious

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