Amino acid sequence in protein molecules

Since each protein molecule consists of a long chain of amino acid residues, linked to each other by peptide bonds, the hydrolytic cleavage of all peptide bonds is a prerequisite for the quantitative determination of the amino acid residues. Hydrolysis is most frequently accomplished by boiling the protein with concentrated hydrochloric acid. The quantitative determination of the amino acids is based on the discovery that amino acids can be separated from each other by chromatography on filter paper and made visible by spraying the paper with ninhydrin. The amino acids of the protein hydrolysate are separated from each other by passing the hydrolysate through a column of adsorbents, which adsorb the amino acids with different affinities and, on washing the column with buffer solutions, release them in a definite order. The amount of each of the amino acids can be determined by the intensity of the colour reaction with ninhydrin.

To obtain information about the sequence of the amino acid residues in the protein, the protein is degraded stepwise, one amino acid being split off in each step. This is accomplished by coupling the free α-amino group (―NH₂) of the N-terminal amino acid with phenyl isothiocyanate; subsequent mild hydrolysis does not affect the peptide bonds. The procedure, called the Edman degradation, can be applied repeatedly; it thus reveals the sequence of the amino acids in the peptide chain.

Unavoidable small losses that occur during each step make it impossible to determine the sequence of more than about 30 to 50 amino acids by this procedure. For this reason the protein is usually first hydrolyzed by exposure to the enzyme trypsin, which cleaves only peptide bonds formed by the carboxyl groups of lysine and arginine. The Edman degradation is then applied to each of the few resulting peptides produced by the action of trypsin. Further information can be gained by hydrolyzing another portion of the protein with another enzyme, for instance with chymotrypsin, which splits predominantly peptide bonds formed by the amino acids tyrosine, phenylalanine, and tryptophan. The combination of results obtained with two or more different proteolytic (protein degrading) enzymes was first applied by English biochemist Frederick Sanger, and it enabled him to elucidate the amino acid sequence of insulin. The amino acid sequences of many other proteins subsequently were determined in the same manner.