Proteins stability polypeptide backbone

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). 

Why denaturants such as urea and GdmCl cause proteins to denature may be considered empirically. Those denaturants solubilize all the constituent parts of a protein, from its polypeptide backbone to its hydrophobic side chains. To a first approximation, the free energy of transfer of the side chains and polypeptide backbone from water to solutions of denaturant is linearly proportional to the concentration of denaturant.7,8 Because the denatured state is more exposed to solvent than the native state, the denatured state is preferentially stabilized by denaturant. Thus, the free energy of denaturation at any particular concentration of denaturant is given by... 

All the constituent amino acid side-chains in proteins are susceptible to free radical attack, but some are more vulnerable than others, as discussed in Chapter 2. Thus, exposure of proteins to free radical-generating systems may induce tertiary structural changes as a consequence of modifications to individual amino acid side-chains. As secondary structure is stabilized by hydrogen bonding between peptide groups, interactions of radical species with the polypeptide backbone and interference with the functional groups of the peptide bonds may cause secondary structural modifications. 

Conceptually, the amino and carboxyl termini of a polypeptide chain are flexible and amendable to form a peptide bond. The formation of the terminally linked peptide bond yields circular (cyclic) proteins with circular backbones. Cyclic peptides such as cyclosporin are known. These peptides tend to be less than 12 amino acids in size, contain modifled amino acids and are generally metabolic products. Whereas circular proteins are 14-70 amino acids in size, true gene products (encoded by DNA) with well-defined 3D structures. They occur in microorganisms, plants and animals, as products for an enhanced stability or involvement in host defense (Trabi and Craik, 2002). Several naturally occurring circular proteins are listed in Table 5.10. CyBase (http //research.imb.uq.edu.au/ cybase) is the curated database for cyclic proteins. 

Proteins have a covalently bonded backbone, as discussed before, in relation to amino acid sequence determination. But the 3-D shape or conformation is held together by weaker bonding of the noncovalent type. The linear form of the polypeptide backbone of the protein folds into a tightly held shape, which is chemically stabilized by weak bonds like hydrogen bonds, ionic bonds, and hydrophobic interactions among nonpolar amino acid side chains [19]. 

While the ability to evaluate the integrity and stability of protein structure based on the results of HDX MS measurements at the whole protein level are very useful, they do not provide any information on how the protection is distributed across the polypeptide backbone. Local information on protein hi er-order structure and dynamics can be obtained by carrying out proteoly-... 

On theoretical grounds, there seems no reason why conformational integrity should not be maintained well above temperatures at which all enzymes are known to lose activity rapidly, and degradation seems likely to set the upper limit for protein stability. However, at least some reactions responsible for degradation are dependent on the flexibility of the polypeptide chain backbone, and on the arrangement of amino acids. Thus protein may be able to evolve to minimi.se degradation. Recent results in our laboratory show that under the right conditions some enzymes can have half-lives of over 10 min at 125 °C. 

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