Circular polypeptide structures

A photochromic polymer containing azobenzene units has also been prepared by modification of a naturally occurring microbial poly(E-L-lysine) (Scheme 5, Structure IX), and investigated by means of absorption and circular dichroism spectroscopy.1431 The structure of this polymer, however, does not correspond to those of polypeptides, which are poly(amide)s of a-amino acids, and therefore the results cannot be discussed in terms of the typical polypeptide structures (a-helix, P-structure, random coil) and their standard CD spectra. 

Fig. 5.3 Standard circular dichroism (CD) spectra of common polypeptide structures (1) a-helix, (2) -structure, and (3) random coil. Adapted from Pieroni et al. [14] with permission from Elsevier.

Amino acid sequences of eleven homologous sea anemone polypeptides have been elucidated. All possess three disulfide bonds. The six half-cysteine residues always occur in the same positions (7,8). Initial studies concerning the toxin secondary and tertiary structures relied upon circular dichroism, laser Raman, and, to a lesser extent, fluorescence spectral measurements (15—18). The circular dichroism spectra of the four toxins so far examined are essentially superimpos-able and thus indicate a common secondary structure. The only peak observed, a negative ellipticity at 203 nm, largely results from a non-regular ("random")... 

The influence of adsorption on the structure of a -chymotrypsin is shown in Fig. 10, where the circular dichroism (CD) spectrum of the protein in solution is compared with that of the protein adsorbed on Teflon and silica. Because of absorbance in the far UV by the aromatic styrene, it is impossible to obtain reliable CD spectra of proteins adsorbed on PS and PS- (EO)8. The CD spectrum of a protein reflects its composition of secondary structural elements (a -helices, / -sheets). The spectrum of dissolved a-chymotrypsin is indicative of a low content of or-helices and a high content of //-sheets. After adsorption at the silica surface, the CD spectrum is shifted, but the shift is much more pronounced when the protein was adsorbed at the Teflon surface. The shifts are in opposite directions for the hydrophobic and hydrophilic surfaces, respectively. The spectrum of the protein on the hydrophilic surface of silica indicates a decrease in ordered secondary structure, i.e., the polypeptide chain in the protein has an increased random structure and, hence, a larger conformational entropy. Adsorption on the hydrophobic Teflon surface induces the formation of ordered structural elements, notably an increase in the content of O -helices (cfi, the discussion in Sect. 3.1.4). 

A prime example of a Refolding model is that of the insulin protofilament (Jimenez et al., 2002). Insulin is a polypeptide hormone composed of two peptide chains of mainly o -helical secondary structure (Fig. 3A Adams et al., 1969). Its chains (21- and 30-amino acids long) are held together by 3 disulfide bonds, 2 interchain and 1 intrachain (Sanger, 1959). These bonds remain intact in the insulin amyloid fibrils of patients with injection amyloidosis (Dische et al., 1988). Fourier transform infrared (FTIR) and circular dichroic (CD) spectroscopy indicate that a conversion to jS-structure accompanies insulin fibril formation (Bouchard et al., 2000). The fibrils also give a cross-jS diffraction pattern (Burke and Rougvie, 1972). 

Photochemically Triggered Induced Circular Dichroism in Liposomes When an optically inactive chromophore is subject to the effect of optically active environment, optical activity may be induced at the absorption wavelength of the optically inactive chromophore. This phenomenon of induced circular dichroism(ICD) is often observed in polypeptides bearing various achiral chromophores on the side chain( ). The strong chiral environment caused by the peptide helix structure is responsible for this. Distance from, and orientation to, the chiral field decide the degree of ICD appearing on the achiral chromophore. 

Nuclease behaves like a typical globular protein in aqueous solution when examined by classic hydrodynamic methods (40) or by measurements of rotational relaxation times for the dimethylaminonaphth-alene sulfonyl derivative (48)- Its intrinsic viscosity, approximately 0.025 dl/g is also consistent with such a conformation. Measurements of its optical rotatory properties, either by estimation of the Moffitt parameter b , or the mean residue rotation at 233 nin, indicate that approximately 15-18% of the polypeptide backbone is in the -helical conformation (47, 48). A similar value is calculated from circular dichroism measurements (48). These estimations agree very closely with the amount of helix actually observed in the electron density map of nuclease, which is discussed in Chapter 7 by Cotton and Hazen, this volume, and Arnone et al. (49). One can state with some assurance, therefore, that the structure of the average molecule of nuclease in neutral, aqueous solution is at least grossly similar to that in the crystalline state. As will be discussed below, this similarity extends to the unique sensitivity to tryptic digestion of a region of the sequence in the presence of ligands (47, 48), which can easily be seen in the solid state as a rather anomalous protrusion from the body of the molecule (19, 49). 

S S CONTENTS Preface, C. Allen Bush. Methods in Macromo-lecular Crystallography, Andrew J. Howard and Thomas L. Poulos. Circular Dichroism and Conformation of Unordered Polypeptides, Robert W. Woody. Luminescence Studies with Horse Liver Dehydrogenase Information on the Structure, Dynamics, Transitions and Interactions of this Enzyme, Maurice R. Eftink. Surface-Enhanced Resonance Raman Scattering (SERRS) Spectroscopy A Probe of Biomolecular Structure and Bonding at Surfaces, Therese M. Cotton, Jae-Ho Kim and Randall E. Holt. Three-Dimensional Conformations of Complex Carbohydrates, C. Allen Bush and Perse-veranda Cagas. Index. 

Numerous studies have been undertaken to elucidate the secondary structure of soluble elastin. These studies have been performed on elastin, elastin solubilized by oxalic acid (a-elastin) or potassium hydroxide (/, -elastin). synthetic polypeptide models of elastin, and tropoelastin. Techniques used include circular dichroism, FT-Raman, and electron microscopy. No consensus has been reached on the overall structure of elastin. 

The detection of ordered structures such as a-helix or p-structurcs, and quantitative measurements of their populations, are essential aspects of structural investigation in polypeptides. The most sensitive technique for such investigation is certainly circular dichroism (CD) spectroscopy, because the various structures are characterized by typical and standard CD spectra. 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

A number of techniques can be used to monitor the growth of amyloid fibrils and provide information on the kinetics of fibril assembly or disassembly. These techniques include light scattering or dye binding assays where Thioflavin T binds to the emerging fibril structure resulting in an increase in fluorescence (Krebs et al., 2005). Fourier transform infrared spectroscopy and circular dichroism can be used to monitor a change in secondary structure as the polypeptide adopts a (3-sheet-rich confirmation (Nilsson, 2004) and a quartz crystal oscillator used to follow an increase in fibril mass as a function of time (Knowles et al., 2007). 

Database searches aimed at identifying related proteins found that the closest structural relative to bacteriocin AS-48 is the effector polypeptide from porcine lymphocytes, NK-lysin.63 Similar to AS-48, this 76-residue protein adopts a globular fold with five helices surrounding a hydrophobic core but lacks a circular backbone.64 Instead, NK-lysin comprises three cross-bracing disulphide bonds that stabilise the structure. Despite the linear backbone of NK-lysin creating differences in the orientation of helix 5 in relation to the one in AS-48, and despite no significant sequence homology between them, the backbone... 

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. 

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