Advances in Enzymology: And Related Areas of Molecular by Eric J. Toone
By Eric J. Toone
Advances in Enzymology and comparable parts of Molecular Biology covers the advances in enzymology, explaining the habit of enzymes and the way they are often applied to enhance novel medications, synthesize identified and novel compounds, and comprehend evolutionary processes.Content:
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Extra info for Advances in Enzymology: And Related Areas of Molecular Biology, Volume 75
B. HIERARCHY OF MODELS FOR MODELING ANCESTRAL PROTEIN SEQUENCES 1. Assuming That the Historical Reality Arose from the Minimum Number of Amino Acid Replacements In a world without knowledge, we would know nothing about sequences of any ancestral protein that lived in any ancient organism that went extinct millions of years ago. In particular, we would know nothing about the sequence of the ribonuclease that was biosynthesized by Pachyportax. But we have some knowledge. In particular, we know the sequences of some of the descendents of the ancient RNase as well as the sequences of descendents of its relatives.
SASSI, AND ERIC A. GAUCHER FIGURE 12. A maximum likelihood analysis infers an Asn at site 38 as the most probable residue. Note how the additional ‘‘prior’’ information alters the probabilities assigned to different amino acids at points throughout the tree. Note that the sum of the probabilities of Ser, Asn, and all other amino acids is unity at all points in the tree. information has increased. Now, a simple parsimony analysis assigns an Asn at the central node, with the model for the history of site 38 incorporating an Asn-to-Ser replacement along the branch leading from the central node to the RNase from swamp buffalo.
For example, we may incorporate into our theory the possibility that a site contained amino acids that are not found in any of the sequences derived, even though this requires some histories to have more than the minimum number of changes absolutely required to account for the amino acids in the sequences derived. Consider again site 39 of the ribonucleases from the swamp and river buffaloes. Even though the sequences of both RNases hold a Met at this site, it is conceivable that another amino acid (let us say Ile) occupied site 39 in the last common ancestor.