PROTEINS AND THEIR AMINO-ACID COMPOSITIONS - UNIQUENESS, VARIABILITY,AND APPLICATIONS

Amino acid compositions (AAC) of proteins were analyzed in terms of th eir uniqueness and variability, Using several measures of convergence between the AACs of randomly chosen proteins versus those stored in pr otein 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 chromat ographic media prior to their fractionation on two dimensional (2D) ge ls, Subfractionations of proteins markedly enhance the chances for pro per identification of low-abundant proteins which rest inaccessible if the total protein extract of an organ is analyzed on 2D gels, Althoug h the amino acid composition versus protein identity (AAC-PI) method a llows identification with high confidence of unique proteins resolved on monodimensional SDS-PAGE (1D) gels and arrays of protein isoforms r esolved on two-dimensional (2D) gels, selective immunoblotting is stil l a more robust method, Thus, in principle, the AAC-PI method may allo w limiting the number of ''unknown'' spots on 2D gels which could be f urther investigated by microsequencing and/or mass spectroscopy, Howev er, to resolve certain ambiguities inherently linked with protein iden tities derived only from their AACs, the AAC-PI method must be sometim es aided by microsequencing and immunoblotting, especially in the cons truction of high-resolution 2D maps of proteins, A suite of algorithms which form the AAC-PI method are described in detail. (C) 1996 Academ ic Press, Inc.