Polypeptide chain random-coil conformation

The conformational behavior can be quite different in aqueous solution. Below pH 5, a sample of poly(L-glutamic acid) containing about 30 mol% azobenzene units adopts a P-structure that is not affected by light. Above pH 7, the polypeptide is random coil and the conformation is, once more, not affected by the photoisomerization of the azo side chains. However, at pH values in the range 5-7 (close to the pK of the conformational transition), irradiation causes a remarkable diminishing of the ordered structure, which is completely reversed in the dark.120,221... 

The structures of spiropyran-modified poly(L-glutamate)s are strongly affected by light or dark conditions, as demonstrated by the CD spectra in Figure 10. Before irradiation, the colored solutions show the CD spectrum of a random coil conformation. After exposure to sunlight, the colorless solutions display the typical CD pattern of the a-helix, thus indicating that the isomerization of the side chains causes a transition from coil to helix in the polypeptide chains. The photoinduced conforma-... 

Fig. 2. Temperature dependence of the partial specific heat capacity for pancreatic ribonuclease A (RNase), hen egg-white lysozyme (Lys), sperm whale myoglobin (Mb), and catalase from Thermus thermophilus (CTT). The flattened curves are for RNase and Lys with disrupted disulfide cross-links and for apomyoglobin, when polypeptide chains have a random coil conformation without noticeable residual structure (Privalov et al., 1988).

The study of the raesophases by X-ray diffraction, electron microscopy, infrared spectroscopy and circular dichroism20-2S has shown that the structure is always lamellar and can be described as follows the lamellar structure consists of plane, parallel, and equidistant sheets of thickness d each sheet results from the superposition of two layers one of thickness dA formed by the polyvinyl chains in a more or less random coil conformation, the other with a thickness dB formed by the polypeptide chains in an a helix conformation, oriented perpendicular to the plane of the layers, arranged in a bidimensional hexagonal array, and generally folded. 

The major casein monomer subunits have random coil conformation that facilitates strong protein-protein interaction via hydrophobic and ionic bonding. The unique amphiphilic structure, which arises from separately clustered hydrophobic and negatively charged (acidic and ester phosphate) amino acid residues along the polypeptide chain, makes them susceptible to pH and Ca ion concentration effects. This amphiphilic nature is probably responsible for the excellent surfactant properties of commercial caseinate in a variety of food applications. 

Most polypeptide chains devoid of cross-links assume a random-coil conformation in 8 M urea or 6 M guanidinium chloride, as evidenced by physical properties such as viscosity and optical activity. When ribonuclease was treated with P-mercaptoethanol in 8 M urea, the product was a fully reduced, randomly coiled polypeptide chain devoid of enzymatic activity. In other words, ribonuclease was denatured by this treatment (Figure 3.53). 

Studies by Anfinsen of the reversible denaturation of the pancreatic enzyme ribonuclease prompted the hypothesis that secondary and tertiary structures are derived inclusively from the primary structure of a protein (Figures 4-11 and 4-12). RNase A, which consists of a single polypeptide chain of 124 amino acid residues, has four disulfide bonds. Treatment of the enzyme with 8 M urea, which disrupts noncovalent bonds, and j8-mercaptoethanol, which reduces disulfide linkages to cysteinyl residues, yields a random coil conformation. 

Most polypeptide chains devoid of cross-links assume a random-coil conformation in 8 M urea or 6 M guanidinium chloride. When ribonuclease was... 

The spiropyran-modified poly(L-glutamic acid) PGA-2 undergoes a coil helix transition upon exposure to visible light in hexafluoro-2-propanol solution. In the dark, the polypeptide, containing 30-80 mol% chromophore units in the open charged form, adopts a random coil conformation. Irradiation causes isomerization in the side chains, as indicated by complete bleaching of the colored solution (see Scheme 5.4). The formation of the colorless and uncharged spiropyran form induces spiralization of the polypeptide chain. The coil helix transition can be followed with the aid of CD spectra, as shown in Fig. 5.4. 

The secondary structure describes the overall conformation or shape of the protein molecule. Typical types of secondary structure are helices (cf Sections 4.2 and 4.6) and pleated sheets (j5 structures). Secondary structure results from main-chain hydrogen-bonded interactions. In pleated sheets, the a-amino acid chains can be arranged parallel or antiparallel to each other, with the antiparallel structure being thermodynamically more stable. a-Amino acids that yield helical homopolymers usually (but not inevitably) form helical sequences in proteins and polypeptides. The random coil that results from the rupture or lack of stabilizing hydrogens is not considered a secondary structure. Segments of a-helix, pleated sheet, and random coil are possible in the same molecule. 

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