Polypeptide fragments

The standard protocol for analysis of the amino acid composition of proteins is discussed in Section 5.1. Results of such analyses allow the researcher to anticipate which methods of polypeptide fragmentation might be useful for the protein. 

Such a process led to the full assignment of the sequence of the cytochrome c" protein shown in Figure 5.17, in which the polypeptide fragments generated by enzymatic digestion with endoproteinase Lys-C and Glu-C are also indicated. 

Figure 7.8 Activation of clot formation by endotoxin. The presence of endotoxin causes stepwise, sequential activation of various clotting factors present naturally within the amoebocytes of the American horseshoe crab. The net result is the generation of the polypeptide fragment coagulin, which polymerizes, thus forming a gel or clot...

Figure 12.5 Proteolytic cleavage of prothrombin by factor Xa, yielding active thrombin. Although prothrombin is a single-chain glycoprotein, thrombin consists of two polypeptides linked by what was originally the prothrombin intrachain disulfide bond. The smaller thrombin polypeptide fragment consists of 49 amino acid residues, and the large polypeptide chain contains 259 amino acids. The N-terminal fragment released from prothrombin contains 274 amino acid residues. Activation of prothrombin by Xa does not occur in free solution, but at the site of vascular damage...

Reches, M., and Gazit, E. (2004). Amyloidogenic hexapeptide fragment of medin Homology to functional islet amyloid polypeptide fragments. Amyloid 11, 81-89. 

Lyampert, I.M., E.N. Semenova, V. Sanina, N.G. Puchkova, and A.V. Nekrasov, Immunogenicity of a polypeptide fragment of the streptococcal group A M protein conjugated with an acrylic acid N-vinylpyrroli-done copolymer. Biomed Sci, 1991. 2(4) 410-14. 

Intracellular protein degradation is not random. Different proteins have quite different half-lives, which are related to specific structural features. Imperfectly folded proteins and polypeptide fragments are frequently degraded most rapidly. In eukaryotes, lyso-somes play a major role in protein degradation. 

Usually, owing to insolubility or unacceptable buffers, large protein fragments are not beneficially analyzed by ESI-MS. However, the identity of stable domains of protein molecules can still be inferred from the accurate mass measurements of the smaller polypeptide fragments obtained from limited proteolysis. This provides a basis for resolving the compact domains for proteins in situations where matrix-assisted laser desorption ionization (MALDI) data are ambiguous and ESI-MS of the large protein may be precluded. 

SDS-PAGE, together with the Coomassie brilliant blue coloration, is used to quantitatively determine the sample purity with respect to dimers, larger covalent aggregates, and polypeptide fragments. The SDS-PAGE protein separation can be combined with the Western blot analysis, which is used to determine the presence of an electrophoretic band (Figure 13.2 see color section). 

The EGF receptor was first isolated by Downward et al. [1] in sufficient quantity to determine directly the primary amino acid sequence of several short polypeptide fragments. Since the molecule has an apparent molecular weight of 175000 it was clearly too large to determine its complete sequence by this approach. Rather, the... 

Tryptic hydrolysis of cytochrome yields a polypeptide fragment which carries the heme and has a molecular weight of approximately... 

Among the human prion diseases, Pi-p " polypeptide fragments can vary in number (typically 1 to 3), molecular weight, and the ratio of the three glycoforms. Based on these criteria, Prps<" is classified into three operational groups called type 1, type 2 (a and b), and GSS-type (Table 29.2, Figure... 

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