Proteins and Their Amino Acid Compositions: Uniqueness, Variability, and Applications

Amino acid compositions (AAC) of proteins were analyzed in terms of their uniqueness and variability. Using several measures of convergence between the AACs of randomly chosen proteins versus those stored in protein data banks, it was established that certain families of proteins have unique AACs despite the mutations of their sequences which were imposed in the process of evolution. AACs may be used to establish the identities of many proteins which were sorted through various chromatographic media prior to their fractionation on two-dimensional (2D) gels. Subfractionations of proteins markedly enhance the chances for proper identification of low-abundant proteins which rest inaccessible if the total protein extract of an organ is analyzed on 2D gels. Although the amino acid composition versus protein identity (AAC-PI) method allows identification with high confidence of unique proteins resolved on monodimensional SDS–PAGE (1D) gels and arrays of protein isoforms resolved on two-dimensional (2D) gels, selective immunoblotting is still a more robust method. Thus, in principle, the AAC-PI method may allow limiting the number of “unknown” spots on 2D gels which could be further investigated by microsequencing and/or mass spectroscopy. However, to resolve certain ambiguities inherently linked with protein identities derived only from their AACs, the AAC-PI method must be sometimes aided by microsequencing and immunoblotting, especially in the construction of high-resolution 2D maps of proteins. A suite of algorithms which form the AAC-PI method are described in detail.