Polypeptide backbone

The properties of a protein depend primarily on its three-dimensional structure. The sequence of amino acids in the polypeptide chain is termed its primary structure. Its secondary structure is the shape of the backbone polypeptide chain. Remember that each amide group is planar, but the chain can have various conformations about the bond between the a-carbon and the nitrogen. The tertiary structure is the overall three-dimensional shape of the protein, including the conformations of the side chains. 

The glycoproteins from the Antarctic fishes and the Arctic polar cod have repeated amino acid sequences of Ala-Ala-Thr in their backbone polypeptide structure. Furthermore, disaccharide groups are regularly attached to all the threonine residues through a link-... 

Synthetic poly(amino acids) possess advant s as well as disadvantages as enzyme models, when compared widi vinyl polymers. The greatest advantage is probably the structural similarity of the polymer backbone (polypeptide linkage), and conformational characteristics derived therefrom. On the odier hand, die syndietic problems are much greater than those of vinyl polymers. A review artide was recently published on tfiis subject (726). 

In other regions of the backbone polypeptide fold, the side chains of residues are involved in heavy-chain-light-chain interactions. These include residues 35, 37, 42, 43, 86, and 99 in the Vl and Cl, and residues 37, 39, 43, 45, 47, 95, and 108 in the Vh region of protein NEW (Poljak, 1975). 

The same antibodies were not at all inhibited by polylysine or by polyalanine, i.e., by the backbone polypeptide or by the first chain attached. These results again provide strong evidence that the most exposed portion of the molecule, in this case poly(Tyr,Glu), is also the most immunogenic. 

M.J. Sippl, M. Hendlich and P. Lackner, Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments. Protein Sci. 1 (1992), 625-640. 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

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)... 

The backbone of polypeptides and, more generally, proteins is made up of a linear sequence of amino acids. 

By means of a ring-opening polymerization of the condensation type Vlasov et al. [50] synthesized polypeptide based MAIs with azo groups in the polymeric backbone. The method is based on the reaction of a hydracide derivative of AIBN and a N-carboxy anhydride. Containing one central azo group in the polymer main chain, the polymeric azo initiator was used for initiating block copolymerizations of styrene and various methacrylamides. 

FIGURE 19.19 A representation of part of an a helix, one of the secondary structures adopted by polypeptide chains. The cylinder encloses the "backbone" of the polypeptide chain, and the side groups project outward from it. The thin lines represent the hydrogen bonds that maintain the helical shape. 

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. 

---