Figure 3-25 Steps In Sequencing A Polypeptide

FIGURE 3-25 Steps in sequencing a polypeptide. (a) Identification of the amino-terminal residue can be the first step in sequencing a polypeptide. Sanger's method for identifying the amino-terminal residue is shown here. (b) The Edman degradation procedure reveals the entire sequence of a peptide. For shorter peptides, this method alone readily yields the entire sequence, and step (a) is often omitted. Step (a) is useful in the case of larger polypeptides, which are often fragmented into smaller peptides for sequencing (see Fig. 3-27).

To sequence an entire polypeptide, a chemical method devised by Pehr Edman is usually employed. The Edman degradation procedure labels and removes only the amino-terminal residue from a peptide, leaving all other peptide bonds intact (Fig. 3-25b). The peptide is reacted with phenylisothiocyanate under mildly alkaline conditions, which converts the amino-terminal amino acid to a phenylthiocarbamoyl (PTC) adduct. The peptide bond next to the PTC adduct is then cleaved in a step carried out in anhydrous trifluo-roacetic acid, with removal of the amino-terminal amino acid as an anilinothiazolinone derivative. The deriva-tized amino acid is extracted with organic solvents, converted to the more stable phenylthiohydantoin derivative by treatment with aqueous acid, and then identified. The use of sequential reactions carried out under first basic and then acidic conditions provides control over the entire process. Each reaction with the amino-terminal amino acid can go essentially to completion without affecting any of the other peptide bonds in the peptide. After removal and identification of the amino-terminal residue, the new amino-terminal residue so exposed can be labeled, removed, and identified through the same series of reactions. This procedure is repeated until the entire sequence is determined. The Edman degradation is carried out on a machine, called a sequenator, that mixes reagents in the proper proportions, separates the products, identifies them, and records the results. These methods are extremely sensitive. Often, the complete amino acid sequence can be determined starting with only a few micrograms of protein.

The length of polypeptide that can be accurately sequenced by the Edman degradation depends on the efficiency of the individual chemical steps. Consider a peptide beginning with the sequence Gly-Pro-Lys- at its amino terminus. If glycine were removed with 97% efficiency, 3% of the polypeptide molecules in the solution would retain a Gly residue at their amino terminus. In the second Edman cycle, 97% of the liberated amino acids would be proline, and 3% glycine, while 3% of the polypeptide molecules would retain Gly (0.1%) or Pro (2.9%) residues at their amino terminus. At each cycle, peptides that did not react in earlier cycles would contribute amino acids to an ever-increasing background, eventually making it impossible to determine which amino acid is next in the original peptide sequence. Modern sequenators achieve efficiencies of better than 99% per cycle, permitting the sequencing of more than 50 contiguous amino acid residues in a polypeptide. The primary structure of insulin, worked out by Sanger and colleagues over a period of 10 years, could now be completely determined in a day or two.

Large Proteins Must Be Sequenced in Smaller Segments

The overall accuracy of amino acid sequencing generally declines as the length of the polypeptide increases. The very large polypeptides found in proteins must be broken down into smaller pieces to be sequenced efficiently. There are several steps in this process. First, the protein is cleaved into a set of specific fragments by chemical or enzymatic methods. If any disulfide bonds are present, they must be broken. Each fragment is purified, then sequenced by the Edman procedure. Finally, the order in which the fragments appear in the original protein is determined and disulfide bonds (if any) are located.

Breaking Disulfide Bonds Disulfide bonds interfere with the sequencing procedure. A cystine residue (Fig. 3-7) that has one of its peptide bonds cleaved by the Edman procedure may remain attached to another polypeptide strand via its disulfide bond. Disulfide bonds also interfere with the enzymatic or chemical cleavage of the polypeptide. Two approaches to irreversible breakage of disulfide bonds are outlined in Figure 3-26.

Cleaving the Polypeptide Chain Several methods can be used for fragmenting the polypeptide chain. Enzymes called proteases catalyze the hydrolytic cleavage of peptide bonds. Some proteases cleave only the peptide bond adjacent to particular amino acid residues (Table 3-7) and thus fragment a polypeptide chain in a predictable and reproducible way. A number of chemical reagents also cleave the peptide bond adjacent to specific residues.

Among proteases, the digestive enzyme trypsin catalyzes the hydrolysis of only those peptide bonds in which the carbonyl group is contributed by either a Lys or an Arg residue, regardless of the length or amino acid sequence of the chain. The number of smaller peptides produced by trypsin cleavage can thus be predicted

Diabetes 2

Diabetes 2

Diabetes is a disease that affects the way your body uses food. Normally, your body converts sugars, starches and other foods into a form of sugar called glucose. Your body uses glucose for fuel. The cells receive the glucose through the bloodstream. They then use insulin a hormone made by the pancreas to absorb the glucose, convert it into energy, and either use it or store it for later use. Learn more...

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