Proteins carboxyl terminal analysis

Amino acid analysis itself does not directly give the number of residues of each amino acid in a polypeptide, but it does give amounts from which the percentages or ratios of the various amino acids can be obtained (Table 5.2). If the molecular weight and the exact amount of the protein analyzed are known (or the number of amino acid residues per molecule is known), the molar ratios of amino acids in the protein can be calculated. Amino acid analysis provides no information on the order or sequence of amino acid residues in the polypeptide chain. Because the polypeptide chain is unbranched, it has only two ends, an amino-terminal or N-terminal end and a carboxyl-terminal or C-termuial end. 

Figure 39-15. The leucine zipper motif. A shows a helical wheel analysis of a carboxyl terminal portion of the DNA binding protein C/EBP. The amino acid sequence is displayed end-to-end down the axis of a schematic a-helix. The helical wheel consists of seven spokes that correspond to the seven amino acids that comprise every two turns of the a-helix. Note that leucine residues (L) occur at every seventh position. Other proteins with "leucine zippers" have a similar helical wheel pattern. B is a schematic model of the DNA binding domain of C/EBP. Two identical C/EBP polypeptide chains are held in dimer formation by the leucine zipper domain of each polypeptide (denoted by the rectangles and attached ovals). This association is apparently required to hold the DNA binding domains of each polypeptide (the shaded rectangles) in the proper conformation for DNA binding. (Courtesy ofS McKnight)...

The COOH-terminal amino acid of a peptide or protein may be analyzed by either chemical or enzymatic methods. The chemical methods are similar to the procedures for NH2-terminal analysis. COOH-terminal amino acids are identified by hydrazinolysis or are reduced to amino alcohols by lithium borohydride. The modified amino acids are released by acid hydrolysis and identified by chromatography. Both of these chemical methods are difficult, and clear-cut results are not readily obtained. The method of choice is peptide hydrolysis catalyzed by carboxypeptidases A and B. These two enzymes catalyze the hydrolysis of amide bonds at the COOH-terminal end of a peptide (Equation E2.3), since carboxypeptidase action requires the presence of a free a-carboxyl group in the substrate. 

This technique gives information about the protein s primary structure, which may include its amino and/or carboxyl terminal groups (Edman, 1950). For recombinant DNA-derived proteins, this analysis serves to confirm the amino acid sequence predicted by the DNA sequence. The analysis can also be useful to determine the protein s homogeneity. 

Extensive chemical analysis of peak 11 protein was also carried out in our laboratory from many standpoints, such as the amino acid composition, fatty acid content, and contents of the peptidoglycan components. These studies clearly demonstrated that the protein of peak 11 has the exact chemical structure as the lipoprotein shown in Fig. 9, except that it does not contain any components of the peptidoglycan. Furthermore, most recently, the peak 11 protein was highly purified, and its carboxyl-terminal amino acid sequence was identified as -Tyr-Arg-Lys. This is extremely important because this carboxyl-terminal sequence would not be expected if... 

Sequential analysis of amino acids in purified peptides and proteins is best initiated by analysis of the terminal amino acids. A peptide has one amino acid with a free a-amino group (NH2-terminus) and one amino acid with a free a-carboxyl group (COOH-terminus). Many chemical methods have been developed to selectively tag and identify these terminal amino acids. 

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