Polypeptide random-coil region

It is important to appreciate that nmr cannot be used to determine the amino acid sequence (primary structure) of a protein. However, provided that the amino acid sequence is known, 2D nmr techniques can be used to deduce the secondary and tertiary structure of a protein (i.e. the way in which the polypeptide chain is coiled to give a-helical, -stranded or random coil regions and the way in which these re-... 

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

Chapter E is devoted to the mean-square dipole moment and mean rotational relaxation time derived from dielectric dispersion measurements. Typical data, both in helieogenic solvents and in the helix-coil transition region, are presented and interpreted in terms of existing theories. At thermodynamic equilibrium, helical and randomly coiled sequences in a polypeptide chain are fluctuating from moment to moment about certain averages. These fluctuations involve local interconversions of helix and random-coil residues. Recently, it has been shown that certain mean relaxation times of such local processes can be estimated by dielectric dispersion experiment. Chapter E also discusses the underlying theory of this possibility. 

The curve drawn in Fig. 19 looks somewhat more like the theoretical curves in Fig. 11, but still exhibits no detectable minimum. It can be observed that the curve shows a strikingly steep rise in the region of high helical fractions, but the highest point reached is still far below the value which would be obtained if the sample assumed intact and rigid a-helical conformation. This fact indicates what great difficulty we encounter in experimental investigations of the dimensions of polypeptides in the vicinity of perfect helix. Furthermore, it indicates how sensitively the presence of even a small fraction of random-coil portions affects the overall shape of helical polypeptide molecules. 

The question arises as to whether or how closely Eq. (D-8) is obeyed by non-randomly coiled macromolecules, especially, by polypeptides in the helix-coil transition region. An answer has been given by a recent work by Norisuye (S3), who measured [fj] and for two high-molecular-weight samples of PBLG... 

Wada et al. (120) studied dielectrically the normal transition of two PBLA samples in m-cresol and observed that the higher-molecular-weight sample exhibited a secondary dispersion at frequencies above the region which could be associated with orientation polarization of the polypeptide. Their contribution will be discussed in the next section, in which such a dispersion is attributed to a relaxational alternation of helix and random-coil units. 

The fold of a protein is the way in which the regions of helix, strand and random-coil structure within its polypeptide chain are arranged in three dimensions to form its tertiary structure (see Sect. 2.1.3). This is the simplest, and yet often a very revealing, level at which the three-dimensional structures of different proteins can be compared with one another as is indicated below, such similarities may be indicators of remote evolutionary relationships, give clues to functional analogies, or insights into the processes of protein folding. 

As shown in Fig. 16, artifactual deflections are also observed at wavelengths at which the lamp fails to emit light, in this case the region of resonance absorption by the mercury itself between 255 and 260 m/t, a situation identical with absorption by a chromophore in the optical path. A second deflection is obtained with poly-L-glutamic acid in the random coil as the peptide absorption band below 250 mu is entered. Since this deceptive effect, which will be more marked in the steeper dispersions characteristic of helices, can at lower wavelengths obscure the authentic Cotton effect feature observed at 233 m/t by Simmons et al. (1961) in helical polypeptides and proteins (Fig. 4), and since these authors propose the amplitude of this... 

The folding of polypeptide chains into ordered structures maintained by repetitive hydrogen bonding is called secondary structure. The chemical nature and structures of proteins were first described by Linus Pauling and Robert Corey who used both fundamental chemical principles and experimental observations to elucidate the secondary structures. The most common types of secondary structure are the right-handed cx-helix, parallel and antiparallel /3-pleated sheets, and (3-turns. The absence of repetitive hydrogen-bonded regions (sometimes erroneously called random coil ) may also be part of secondary structure. A protein may possess predominantly one kind of secondary structure (a-keratin of hair and fibroin of silk contain... 

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