Polypeptide/protein structures

The basic concept is the use of the fluorescence response of tryptophan residues, embedded in the polypeptide/protein structure, which is sensitive to changes in its microenvironment. Therefore, if a given protein interacts with a membrane surface and, due to this interaction, changes its 3D structure, it can be anticipated that... 

As more protein structures became available it was observed that some contained more that one distinct region, with each region often having a separate function. Each of these region is usually known as a domain, a domain being defined as a polypeptide chain that can folc independently into a stable three-dimensional structure. 

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. 

These results indicate that is it possible to change the fold of a protein by changing a restricted set of residues. They also confirm the validity of the rules for stability of helical folds that have been obtained by analysis of experimentally determined protein structures. One obvious impliction of this work is that it might be possible, by just changing a few residues in Janus, to design a mutant that flip-flops between a helical and p sheet structures. Such a polypeptide would be a very interesting model system for prions and other amyloid proteins. 

Many proteins consist of two or more interacting polypeptide chains of characteristic tertiary structure, each of which is commonly referred to as a subunit of the protein. Subunit organization constitutes another level in the hierarchy of protein structure, defined as the protein s quaternary (4°) structure (Figure 5.10). Questions of quaternary structure address the various kinds of subunits within a protein molecule, the number of each, and the ways in which they interact with one another. 

The folding of a single polypeptide chain in three-dimensional space is referred to as its tertiary structure. As discussed in Section 6.2, all of the information needed to fold the protein into its native tertiary structure is contained within the primary structure of the peptide chain itself. With this in mind, it was disappointing to the biochemists of the 1950s when the early protein structures did not reveal the governing principles in any particular detail. It soon became apparent that the proteins knew how they were supposed to fold into tertiary... 

The biological function of biopolymers such as polypeptides, proteins, nucleic acids etc. depends strongly on their ordered structure which is determined by the pattern of inter- and intramolecular interactions given by the primary structure. 

Chemical techniques for the isolation, purification and elucidation of the structure of toxins have evolved to the extent that it is frequently a routine procedure to identify the chemical nature of a newly discovered toxin once it has been purified, although difficulties arise when the toxin is a very large polypeptide, protein, or a very complex organic molecule. However, it is sometimes found that a toxin becomes progressively more labile and stabilizing contaminants are removed by the purification processes. An example of this is Cyanea toxic material which becomes increasingly labile with each purification step 111). 

Figure 1.3 Folding of a polypeptide chain illustrating the hierarchy of protein structure from primary structure through secondary structure and tertiary structure.

The N-terminal domain of the OCP is an orthogonal alpha-helical bundle, subdivided into two four-helix bundles (Figure 1.3a and c). These subdomains are composed of discontinuous segments of the polypeptide chain (gray and white in Figure 1.3c). To date, the OCP N-terminal domain is the only known protein structure with this particular fold (Pfam 09150). The hydroxyl terminus of the 3 -hydroxyechinenone is nestled between the two bundles. The C-terminal domain (dark... 

Raman optical activity is an excellent technique for studying polypeptide and protein structure in aqueous solution since, as mentioned above, their ROA spectra are often dominated by bands originating in the peptide backbone that directly reflect the solution conformation. Furthermore, the special sensitivity of ROA to dynamic aspects of structure makes it a new source of information on order-disorder transitions. 

Sasisekharan, V. 1962. Stereochemical Criteria for Polypeptide and Protein Structures, in Collagen, Ramanathan, N., ed. 39-78. Madras, India, Wiley. 

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