Amino acids evolution during

Gobbetti, M., Simonetti, M.S., Rossi, J., Cossignani, A., Corsetti, A., Damiani, P. 1994. Free D- and L-amino acid evolution during sourdough fermentation and baking. J Food Sci 59 881-884. 

Benner, S. A., Cohen, M. A., Gonnet, G. H. (1994) Amino acid substitution during functionally constrained divergent evolution of protein sequences, Protein Engineering 7 1323-1332. 

Biological systems depend on specific detailed recognition of molecules that distinguish between chiral forms. The translation machinery for protein synthesis has evolved to utilize only one of the chiral forms of amino acids, the L-form. All amino acids that occur in proteins therefore have the L-form. There is, however, no obvious reason why the L-form was chosen during evolution and not the D-form... 

The paired box is another sequence motif that is very well conserved during evolution and is found in a number of genes known to be of developmental significance in lower organisms. The paired box encodes the 128-amino acid paired domain, which binds DNA(Chalapakis et al., 1991), and shows similarity, with a helix-tum-helix motif, to the homeodomain. 

Finding close agreement between the result of a calculation and an established body of empirical data is a delightful experience. To those of us who have witnessed the evolution of the computational tools during their own lifetime, the process has at times appeared like a revolution and a mutation of chemistry (Schafer 1983G, 1991G). The reference section given at the end of this chapter demonstrates that ab initio calculations of amino acids and peptides are at the base of a very active field and have become a powerful source of information on these important molecules. 

General acid catalysis is schematized in Fig. 7J,b. Here, an acid A-H increases the polarity of the carbonyl group and, hence, the electrophilicity of the carbonyl C-atom. For entropy reasons, the reaction is greatly facilitated when it is an intramolecular one (Fig. 7J,b2), in other words, when the general acid catalyst is favorably positioned within the molecule itself. Such a mechanism is the one exploited and refined by nature during the evolution of the hydrolases, with the general acid catalyst and the H20 molecule replaced by adequate amino acid side chains, and the enzymatic transition state being de facto a supermolecule (see Chapt. 3). 

Pinho, O., Ferreira, I.M.P.L., Mendes, E., Oliveira, B.M. and Ferreira, M. (2001). Effect of temperature on evolution of free amino acid and biogenic amine contents during storage of Azeitao cheese. Food Chem., 75, 287. 

Many examples of catalytic nucleic acids obtained by in vitro selection demonstrate that reactions catalyzed by ribozymes are not restricted to phosphodiester chemistry. Some of these ribozymes have activities that are highly relevant for theories of the origin of life. Hager et al. have outlined five roles for RNA to be verified experimentally to show that this transition could have occurred during evolution [127]. Four of these RNA functionalities have already been proven Its ability to specifically complex amino acids [128-132], its ability to catalyze RNA aminoacylation [106, 123, 133], acyl-transfer reactions [76, 86], amide-bond formation [76,77], and peptidyl transfer [65,66]. The remaining reaction, amino acid activation has not been demonstrated so far. 

In the third model (2, right), the colored residues are those that are located on the surface and occur invariably (red) or almost invariably (orange) in all known insulins. It is assumed that amino acid residues that are not replaced by other residues during the course of evolution are essential for the protein s function. In the case of insulin, almost all of these residues are located on one side of the molecule. They are probably involved in the binding of the hormone to its receptor (see p.224). 

Plants and microorganisms are able to synthesize all of the amino acids from scratch, but during the course of evolution, mammals have lost the ability to synthesize approximately half of the 20 proteinogenic amino acids. These essential amino acids therefore... 

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