Protein Evolution

Evolution of Molecular Knowledge in Insulin

Finding the information contained in insulin is straight forward. The math is tedious, but the procedure is at least defined, and today insulin contains 189 bits of information. So how much of this information does insulin require to provide a selective advantage? This question is much more difficult to answer.

   This is where human insight is necessary. Some amino acids side chains have very similar chemical properties. Others are similar in size. Thus, some amino acid substitutions should be allowed even if they are not found. These are summarized below with the chemical trait given in parentheses:

Group1: leucine , isoleucine, valine, alanine, and methionine (do not like water, so they tend to cluster on the inside of the protein).
Group 2: tyrosine, phenylalanine, and tryptophan (very large amino acids that can influence protein folding).
Group 3: aspartate and glutamate (acidic - proton donors, like water).
group 4: histidine, arginine, and lysine (basic - proton acceptors, like water).
Group 5: glutamine and asparagine (charged and like water).
Group 6: serine and threonine (like water, tend to be found on the outside of protein).
Group 7: glycine (very small).
Group 8: proline (introduces a bend into the chain).
Group 9: cysteine (cross links peptide chains).


   Based on these properties, this chapter will propose the following procedure to calculate knowledge: if a column in a multiple alignment sequence like figure 4.3 only contains a single amino acid, or if the variation is limited to any one of the above 9 groups, then the column should be included in the calculation for molecular knowledge. If the column contains amino acids from different groups then it should be excluded.

   Furthermore, for the columns included in the molecular knowledge calculation, all amino acids in the same group must be included whether they are present in the alignment or not. For example, at position 19 in table 4.2, only isoleucine and valine are found. But because alanine, methionine, and leucine belong to group 1, it is assumed that these amino acids can be substituted at position 19 without destroying the function of insulin. With this procedure, table 4.2 becomes table 4.4. The parenthesis in table 4.4, represent amino acids that are not present in the multiple sequence alignment (figure 4.3). The positions that are assigned 0 bits all have amino acids from more than one of the 9 predefined groups.

  

Table 4.4: Molecular Knowledge in B chain of Insulin

                            Total = 76 bits

Example calculation: at position 3 val, ala and pro are found. Because these amino acids are in different groups, the knowledge is defined as zero bits. At position 16 only leu is found, but ala, val, ile, and met probably will not be that damaging to protein function because they are in the same group. The total number of codons that encode these 5 amino acids is 18. Thus, knowledge = 3.32 x log[ 64/18] = 1.8 bits.


  Comparing table 4.4 to table 4.2, it is clear that knowledge is much less than information (76 bits vs. 108 bits). The ratio of knowledge to information for the insulin B chain is thus 76/108 = 70%. The same procedure is repeated for the A chain as shown in table 4.5.

  
Table 4.5: Molecular Knowledge in Insulin A Chain

                           Total = 51 bits


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