Peptide bond, cleavage, chemistry

Since then, catalytic antibodies which catalyze different chemical reactions have been described. The reactions range from ester or carbonate hydrolysis to carbon-carbon bond forming reactions, bimolecular amide formation or peptide bond cleavage, so the application of catalytic antibodies to general synthetic organic chemistry seems to be very promising [22]. 

Where peptide chemistry can make a contribution toward the proof of protein structure is in the application and continued formulation of degrada-tive techniques. Since fragmentation of the protein molecule to smaller peptides is probably the key reaction in degradative processes, the search for specific reagents for the selective cleavage of various peptide bonds and the standardization of existing techniques is of prime importance (Katsoyannis, 1961). 

Fig. 19. Topography of the NBS cleavage of the six tyrosyl peptide links of native and

The actual oxidizing species present depends on pH and is either chlorine or hypochlorous acid (HOCl). Apparently, the hypochlorous acid is the more active species on hair given that degradation is greater at lower pH. Although the chemistry of these interactions was not examined, one would expect disulfide bond cleavage and peptide bond fission similar to the effects shown for the reaction of chlorine and wool fiber [42]. 

A major advance was devised by Pehr Edman (University of Lund, Sweden) that has become the standard method for N-terminal residue analysis. The Edman degradation is based on the chemistry shown in Mechanism 25.3. A peptide reacts with phenyl isothiocyanate to give a phenylthiocarbamoyl (PTC) derivative, as shown in the first step. This PTC derivative is then treated with an acid in an anhydrous medium (Edman used nitromethane saturated with hydrogen chloride) to cleave the amide bond between the N-terminal amino acid and the remainder of the peptide. No other peptide bonds are cleaved in this step as amide bond hydrolysis requires water. When the PTC derivative is treated with acid in an anhydrous medium, the sulfur atom of the C=S unit acts as an internal nucleophile, and the only amide bond cleaved under these conditions is the one to the N-terminal amino acid. The product of this cleavage, called a thiazolone, is unstable under the conditions of its formation and rearranges to a phenylthiohydantoin (PTH), which is isolated and identified by comparing it with standard samples of PTH derivatives of known amino acids. This is normally done by chromatographic methods, but mass spectrometry has also been used. 

Peptide map analysis of a protein containing two or more cysteine residues typically employs reduction and alkylation chemistry for efficient, reliable proteolysis, reproducible chromatographic profiles, and straightforward characterization by MS. However, when protease digestion is carried out on a nonreduced protein, the disulfide bonds in the protein will maintain the covalent linkage between the peptides that are involved in the disulfide bond. In many cases, it is then possible to choose a protease that will ensure one cysteine residue in each peptide upon cleavage, such that each disulfide bond will associate with a pair of proteolytic peptides. 

Carbobenzoxy derivatives play an eminent role in synthetic chemistry, because they can be cleaved by catalytic hydrogenation. Hydrogenolytic cleavage leaves intact bonds which are quite sensitive toward hydrolysis, e.g., peptide bonds (for the reactions involved cf. Chapt. III-l). 

III. Chemistry of the Modification and Cleavage of the Tryptophanyl Peptide Bond 323... 

FIGURE 5.18 Resins and linkers for synthesis of peptide amides using Fmoc/tBu chemistry. Chain assembly is effected after removal of the Fmoc group. Treatment with CF3C02H releases a peptide amide by cleavage at the NH-CH/CH2 bond. 

FIGURE 5.20 Resins for the synthesis of protected peptides using Fmoc/tBu chemistry. The first residue is esterified to the handle by reaction with the italicized functional group. The protected peptide is detached by cleavage of the ester bond with 1% CF3C02H for (A) and (B) and 10% CF3C02H for (C). 

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