Polypeptidic backbone

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

M Claessens, EV Cutsem, I Lasters, S Wodak. Modelling the polypeptide backbone with spare parts from known protein structures. Protein Eng 4 335-345, 1989. 

The peptide linkage is usually portrayed by a single bond between the carbonyl carbon and the amide nitrogen (Figure 5.3a). Therefore, in principle, rotation may occur about any covalent bond in the polypeptide backbone because all three kinds of bonds (N——C, and the —N peptide bond) are sin-... 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

Whereas the primary structure of a protein is determined by the covalently linked amino acid residues in the polypeptide backbone, secondary and higher... 

FIGURE 6.43 The polypeptide backbone of the prealbnmin dimer. The monomers associate in a manner that continnes the /3-sheets. A tetramer is formed by isologons interactions between the side chains extending outward from sheet D A G H HGAD in both dimers, which pack together nearly at right angles to one another. (Jane Richardson)... 

A number of enzymes are in common use and each of these cleaves the polypeptide backbone adjacent to a particular amino acid residue. The one used for a particular investigation is therefore chosen for the specificity with which it will cleave the polypeptide backbone of the protein being studied. A number of the enzymes used for this purpose are shown in Table 5.4. 

Figure 5.12 Structures and nomenclature of the ions formed in the mass spectral fragmentation of peptides which involve scission of the polypeptide backbone. From Chapman, J. R. (Ed.), Protein and Peptide Analysis by Mass Spectrometry, Methods in Molecular Biology, Vol. 61, 1996. Reproduced by permission of Humana Press, Inc.

The proteolytic digestion of j6-lactoglobulin was carried out with trypsin which, as indicated in Table 5.4 above, is expected to cleave the polypeptide backbone at the carboxy-terminus side of lysine (K) and arginine (R). On this basis, and from the known sequence of the protein, nineteen peptide fragments would be expected, as shown in Table 5.7. Only 13 components were detected after HPLC separation and, of these, ten were chosen for further study, as shown in Table 5.8. 

The digestion of the protein, after heme removal, using Glu-C endoproteinase was also carried out. This enzyme cleaves the polypeptide backbone on the carboxyl terminus of a glutamic acid residue and in this case yielded twelve chromatographic responses. Despite two of these arising from unresolved components, molecular weight information was obtained from 15 polypeptides, one of which was the intact protein, covering the complete sequence, as shown in Table 5.10. 

Location of the Position of Attachment of a Glycan on the Polypeptide Backbone of a Glycoprotein... 

Engler AC, Lee HI, Hammond FT (2009) Highly efficient grafting onto a polypeptide backbone using click chemistry. Angew Chem Int Ed 48 9334-9338... 

The genes encoding the polypeptide backbones of a number of mucins derived from various tissues (eg, pancreas, small intestine, trachea and bronchi, stomach, and salivary glands) have been cloned and sequenced. These studies have revealed new information about the polypeptide backbones of mucins (size of tandem repeats, potential sites of N-glycosylation, etc) and ultimately should reveal aspects of their genetic control. Some important properties of mucins are summarized in Table 47-8. 

Figure 52-6. Diagrammatic representation of the structures of the H, A,and B blood group substances. R represents a long complex oligosaccharide chain, joined either to ceramide where the substances are glycosphingolipids, or to the polypeptide backbone of a protein via a serine or threonine residue where the substances are glycoproteins. Note that the blood group substances are biantenna ry ie, they have two arms, formed at a branch point (not indicated) between the GIcNAc—R, and only one arm of the branch is shown. Thus, the H, A,and B substances each contain two of their respective short oligosaccharide chains shown above. The AB substance contains one type A chain and one type B chain.

Figure 1. The three-dimensional structure of PelC. A. A schematic diagram illustrating the major secondary structural features of the PelC polypeptide backbone. The three parallel p sheets are represented by arrows in light, medium and dark gray.

Fig. 2. Sketch of the polypeptide backbone illustrating the Ramachandran angles...

Kallenbach and co-workers have recently demonstrated via CD spec-tropolarimetry and NMR spectrometry that a seven-residue alanine peptide adopts predominantly the PPII helical conformation in aqueous solution (Shi et al., 2002). Since alanine is nothing but backbone, such a finding indicates that the polypeptide backbone possesses an intrinsic... 

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