Amino acid sequence evolutionary characteristics

The unique characteristic of each protein is the distinctive sequence of amino acid residues in its polypeptide chain. The amino acid sequence is the link between the genetic message in DNA and the three-dimensional structure that performs a protein s biological function. The sequence comparison among analogous proteins yields insights into the evolutionary relationships of proteins and protein function. 

The two characteristics required for protein native-state structures to be targets of an evolutionary process are stability and diversity. Stability is needed because one would not want to mutate away a DNA molecule able to code for a useful protein, and diversity is needed to allow evolution to build complex and versatile forms. The mechanism for natural selection arises naturally in this context DNA molecules that code for amino-acid sequences that fit well into one of these predetermined folds and have useful functionality thrive at the expense of molecules that create sequences that are not useful. Indeed, in this picture, sequences and functionality evolve in order to fit within the constraints of these folds, which, in turn, are immutable and determined by physical law. 

Lambda chains are also distinguishable by deletions or insertions (as compared with k chains) occurring at characteristic positions in the amino acid sequence (Chapter 4). These represent a striking structural feature because many of the same deletions and insertions have been seen in all X chains studied, including those of the chicken as well as several mammalian species (118). Thus, deletions or insertions, once established, may be almost irreversible evolutionary events, probably because they cause important structural alterations. Their presence provides a strong basis for characterizing a polypeptide chain of a species under investigation as k or X. 

Once sufficient numbers of intrinsically disordered and ordered protein sequences were collected, it became possible to compare them directly. The sequences in these databases were examined for dilferences in amino acid composition, sequence attributes, and evolutionary characteristics. 

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