Computational analysis of the amino acid residue sequences of amaranth and some other proteins.

Abstract

Amaranth belongs to a nutritious class of pseudocereals. The well balanced amino acid composition of amaranth compared with those of major cereals would indicate that it deserves a quantitative study of its chemical properties. This work was undertaken to compare Amaranthus (A.) caudatus with a number of other plants on the basis of the sequences of various proteins and the composition of their alcohol-soluble protein mixture and glutelins. Alcohol-soluble proteins were extracted with 55% isopropanol (2-ProOH) + 5% 2-mercaptoethanol (2-ME) and glutelin fractions were obtained with borate buffer + 3% 2-ME + 0.5% sodium dodecyl sulfate (SDS), pH 10. Protein fractions were then electrophoreded on sodium dodecyl sulfate polyacrylamide gels (SDS-PAGE). FASTA and TFASTA programmes were used for comparison of amino acid sequences. Dot matrix analysis and secondary structure predictions which were drawn by Plot-structure, were taken from the GCG package. Electrophoretic tests failed to indicate significant correlation between prolamins from cereals and other plants with the alcohol-soluble fractions from amaranth, proving that these proteins cannot represent the main fraction in amaranth. On the other hand, glutelins shared some common electrophoretic bands with other cereals and showed some identity by SDS-PAGE. Amino acid sequences of A. caudatus (100% identity) had degrees of similarity in the range of 71.4 to 52.2% with rice, garden pea, jobs' tears, maize, and yam. Rice glutelin had similarity in the range of 93.3% to 44.8% with oats, soybean, and pea. Secondary structures of A. caudatus (using conservative amino acid replacement), jobs' tears and rice glutelins, oat globulin, and pea legumin sequences were predicted. Some relationship was shown among electrophoretic patterns of alcohol-soluble proteins and glutelins of A. caudatus.