Amino acid sequence composition comparisons

This work was extended by the important investigations of Weigert et al. (56,57) who investigated the amino acid sequences of the variable portions of twelve different X chains. All the tryptic peptides were aligned and their amino acid compositions determined. A comparison with the sequence reported by Appella permitted the ordering of amino acids. The polypeptide chains sequenced included X chains isolated from IgA myeloma proteins, as well as urinary Bence Jones proteins from mice with serum myeloma proteins of the IgA, IgM, and IgG2a classes. Two of the proteins were obtained from the transplantable tumors that were used by Appella and Perham. 

Light chains expressing specificities b4, b5, or b6 also have distinct C-terminal sequences (35,36a). (These are shown in Table 9.2 together with C-terminal sequences of human and mouse L chains, included for the sake of comparison.) In addition, Frangione and Lamm have isolated two small Internal peptides, adjacent to half-cystine residues, with amino acid sequences that differentiate the b4 and b5 alleles (36). The same amino acids that are involved in the sequence differences identified so far were also implicated by data on overall amino acid composition. 

The amino acid compositions reported for RBP preparations purified from these different species are generally quite similar to each other (see Table I). More than 90% of the amino acid sequence of rabbit RBP has been reported (Rask et al., 1981) in preliminary form. Of the 170 positions available for comparison with the sequence of human RBP, 160 were found to be identical. A comparison of the amino-terminal sequences of human and dog RBP, isolated from urine, has also been reported (Poulik et al., 1975). The two sequences were demonstrably different at only 5 of the first 49 amino-terminal positions. The amino-terminal sequence of 29 residues of bovine serum RBP has been reported... 

The data presented in Table 3, which includes the amino acid composition of baker s yeast and Candida krusei cytochrome c for comparison, show that Ustilago and Neurospora cytochrome c contain the same number of total residues. In seven instances, the number of residues of a particular amino acid/mole are identical. Thus, even in the absence of a sequence for the Ustilago cytochrome it can be concluded that this protein, unlike the siderochromes, has suffered little alteration in the progression from the Ascomycetes to the Basidiomycetes. This can be ascribed to the varying function of the two types of molecules. Cytochrome c must fit into a relatively specific slot bounded by a reductase and an oxidase and it has hence evolved much more slowly than the more freely acting transport agents where the specificity constraints are less demanding. 

Hence, we have made comparisons of amino acid compositions of a-lactalbumins (Table VI), mammalian c-type lysozymes (Table VII), and egg-white lysozymes (a variety of c type and one g type) (Table VIII). Where the sequence information is available, the compositions have been deduced from these results otherwise, the amino acid compositions are obtained from amino acid analysis of the protein. 

At least one aminoacyl-tRNA synthetase exists for each amino acid. The diverse sizes, subunit composition, and sequences of these enzymes vv ere be vildering for many years. Could it be that essentially all synthetases evolved independently The determination of the three-dimensional structures of several synthetases follo ved by more-refined sequence comparisons revealed that different synthetases are, in fact, related. Specifically, synthetases fall into tvv o classes, termed class I and class II, each of vv hich includes enzymes specific for 10 of the 20 amino acids (Table 29.2). Glutaminyl-tRNA synthetase is a representative of class I. The activation domain for class I has a Rossmann fold (Section 16.1.101. Threonyl-tRNA synthetase (see Figure 29.11) is a representative of class II. The activation domain for class II consists largely of P strands. Intriguingly, synthetases from the tvv o classes bind to different faces of the tRNA molecule (Figure 29.14). The CCA arm of tRNA adopts different conformations to accommodate these interactions the arm is in the helical conformation observed for free tRNA (see Figures 29.5 and 29.6) for class II enzymes and in a hairpin conformation for class I enzymes. These two classes also differ in other ways. 

Once a protein has been fully sequenced, it is usually saved in a publicly accessible database for on-line comparison. Researchers only have to determine the amino acid composition of their sample protein and compare this to the database. Very often, unambiguous identification of the sample protein is possible. Alternatively, the sample protein can be partially digested, for example by trypsin. The fragments of this tryptic digest are characteristic for a particular protein, in the same way as a fingerprint is characteristic for an individual. By comparison with an electronic database, unambiguous identification is often possible. 

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