Assessment of similarities of pairs and groups of proteins using transformed amino-acid-residue data

Abstract

Using as a primary standard a representative set of 208 proteins whose amino-acid-residue mole frequencies have been accurately established, a set of standard distributions of mole frequencies is defined for each amino acids, in terms of which percentile values for the observed mole frequencies of the amino-acid residues in any other protein can be determined. Data so transformed have a distribution much closer to Gaussian than untransformed values, and allow meaningful determinations of correlations between the amino-acid-residue compositions of two proteins as well as between pairs of amino-acid-residues within groups of proteins. Of the 153 possible pairs of amino acids (Asx and Glx are used) 39 are significantly correlated at p less than or equal to 0.01 and 22 at p less than or equal to 0.001. A percentile table is included for those wishing to use the method with programmable calculators. The transformed data for amino-acid compositions have been used to perform principal components analyses on groups of proteins in order to determine if meaningful sub-groupings (observable clusters in scatter diagrams) were detectable. Such analyses are shown for the representative set of proteins and for a group of 184 globins. With regard to the globin chains, a correlation is observed for alpha chains in the first principal component projection (PCP), (accounting for 22% of the variance) with respect to the evolutionary time-scale while beta chains show such a correlation in the first and second PCPs (22% and 18% of the variance respectively). Thus, alpha and beta chains appear to diverge from a common progenitor, similar in position to globin chains from "primitive" forms. Furthermore, globins from "primitive" forms are nearer to one another than they are to globins from the vertebrates, a finding without a priori reason, suggesting perhaps that once a chain has reached a stable relationship with its environment, strong constrains are placed on the co-existing globin chains so that they maintain appropriate interaction with one another. In addition, positions of the epsilon, gamma and delta chains are in the order: epsilon (embryonal) more primitive than gamma (foetal) more primitive than delta equal to beta (adult).