A-helix structure

Neutral salt-soluble collagen as well as add-soluble collagen show a CD spectrum (Fig. 8) having bands at 198 nm, 0 = -53 (MX) (deg cm2 dmol-1), and at 223 nm, 0 = 7500 (deg cm2 dmol-1), the ratio between both being 7 1. Pysh has calculated the CD spectra of a-helix, -structure, polyproline I and II127 ... 

Hydrogen bonding (red dotted lines) in the a-helix structure of proteins. 

An investigation of lithium diisopropyl amide (LDA) by solid state NMR led to the observation of dramatic differences between the spectra of the solid polymer and the complex crystallized from THF. Li as well as "C and "N MAS spectra showed large sideband patterns in the former case and only a few sidebands in the latter. For both materials X-ray data are available and establish a helix structure for the polymeric material, which is insoluble in hydrocarbon or ethereal solvents, and a dimer structure of the THF complex (25, 26, Scheme 4). The obvious difference between both structures, apart from the solvent coordination in the THF complex, is the magnitude of the structural N-Li-N angle, which is close to 180° in the first case and close to 90° in the second (176° and 107°, respectively). Thus, a large difference for the electric field gradient around the Li cation is expected for the different bonding situations. 

In the mid-seventies. Law et al. studying ACTH-(1-39) and fragments, found a transition from random coil to a helix structure when the solvent water was gradually replaced by trifluoroethanol (TFE) (43). This latter solvent had been shown to favour the establishment of ordered structures ( 3-sheet or a-helix) like a membrane-receptor environment ("membrane-receptor mimetic" properties) (47). Subsequent work of the groups of Low and Fermandjian on ACTH-(1-39) and several large fragments and... 

Studies of the effect of a-helix inducing solvents such as trifluoroethanol (TFE) on the product distribution of oxidative folding of endothelin-1 (6) (0.01 mM peptide concentration in 80% TFE, pH 9.5) clearly revealed that induction of the a-helical conformation favors the onset of the cystine-stabilized a-helix structural motif with concomitant enhancement of isomer 1 (88 12 vs 75 25) (Table 1)J491 A similar enhancement of the correctly folded 6 by the addition of TFE has also been observed under other conditions. [5°1... 

The a helix structure is a right-handed helix, meaning that the chain spirals clockwise as it is viewed down the peptide chain. Because of the limited rotation around either side of the peptide bond, only a... 

Watson and Crick were the first to appreciate the significance of strong 3.4-A and 34-A spacings and the central crosslike pattern, which reflects a helix structure in the x-ray diffraction pattern of DNA. They interpreted this as arising from the hydrogen-bonded antiparallel double-helix structure. 

Pauling and Corey proposed the a-helix structure for a-keratins. 

Baldwin and co-workers [4] have made a pioneering contribution in this area. They demonstrated that short (11-15 residues) alanine-rich peptides (such as 1), having several glu-lys salt bridges adopt a stable monomeric a-helix structure in solution. 

A porphyrin template has also been used by DeGrado and coworkers [35] for developing a well-defined four a-helix structure (41) that has proton channel activity (see Sect. 3.2). Following modeling studies, they used a tetraphenyl porphyrin with four carboxylic acids at the meta positions as attachment points for the peptide segments. 

The ortho- and para carboxylic acid substituted tetraphenyl porphyrins were used by Nishino and coworkers [36] to prepare the well defined 4-a-helix structures 42 and 43, which are soluble in lipid bilayer membranes. The rigid template of 42 provides some stability to the bundle structure (as measured by... 

Fig. 16. Schematic representation of a four a-helix structure (40) showing the metalloporphyrin and the hydrophobic pocket where a small aromatic substrate can be complexed [34], (Reproduced with the permission of Ref. 34b)...

Finally, Sherman and co-workers [39] recently reported the preparation of a four a-helix structure 46 by attaching the peptide units onto a synthetic bowl... 

They showed that Cu(II) was bound in that position and that the binding process did not influence the tertiary structure. Moreover, the binding of Cu(II) further enhances the structural stability by 1.5 Kcal/mol. In a similar way, the group of Ghadiri [43] has succeeded in preparing a well defined four a-helix structure 50 by forming a Ru(II) complex with four pyridine-modified peptide units 51. 

The frequency of the amide I peak observed in the lens is sensitive to protein secondary structure. From its absolute position at 1672 cm-1, which is indicative for an antiparallel pleated 3-sheet structure, and the absence of lines in the 1630-1654 cm-1 region, which would be indicative of parallel (1-sheet and a-helix structures, the authors could conclude that the lens proteins are all organized in an antiparallel, pleated 3-sheet structure [3]. Schachar and Solin [4] reached the same conclusion for the protein structure by measuring the amide I band depolarization ratios of lens crystallins in excised bovine lenses. Later, the Raman-deduced protein structure findings of these two groups were confirmed by x-ray crystallography. 

In organic solvents such as trimethylphosphate or trifluoroethanol, the azo-mod-ified polymers show the CD pattern of the a-helix structure, with the two typical minima at 208 and 222 nm (Figure 5). In trimethylphosphate, the dark-adapted... 

The mechanism of the photoresponse was tentatively explained as follows. When azo units are in the planar, apolar, trans configuration, they merge into the hydrophobic core of the micelles, forcing the polypeptide chains to assume a coil conformation. Isomerization of the azo units to the skewed, polar, ds configuration inhibits hydrophobic interactions and causes the azo units to retreat from of the micelles, thus allowing the polypeptide chains to adopt the a-helix structure favored in the absence of micelles. In other words, the primary photochemical event is the trans-ds isomerization of the azobenzene... 

The different conformational behavior of the azobenzoyl- and the azobenzenesul-fonyl-L-lysine polymers was explained on the basis that the monomeric units VI may interact with HFP differently than units V do (Scheme 4). The strongly proto-nating solvent HFP (pKa = 9.30) 36 is known to form electrostatic complexes with various organic compounds, including amines and dimethylsulfoxide 1371 on the other hand, sulfonamides are significantly protonated in acid media 38 so it may be presumed that protonation and formation of electrostatic complexes can occur for azobenzenesulfonyl-L-lysine residues, as well. In HFP therefore, polypeptides of structure V can adopt the ordered a-helix structure, while polypeptides of structure VI should be forced by the electrostatic interactions arising from complexation with HFP to adopt a disordered conformation. 

A sample of poly(L-ornithine) containing 48 mol% azo units was found to adopt the a-helix structure in HFP/water = 1/1. In this solvent mixture, however, irradiation at 360 nm followed by irradiation at 460 nm produced the trans-cis photoisomerization of the azo moieties, but did not induce any change of the backbone conformation. When the surfactant sodium dodecyl sulfate was added to the HFP/water solvent mixture, the CD spectrum displayed an intense side chain CD couplet and a negative band at about 225 nm which was assigned to the presence of a P-structure. The CD bands were almost completely abolished upon trans-cis photoisomerization. 

In conclusion, it was found that complexes of poly(ethylene oxide)-h-poly(L-lysine) with retinoic acid with short poly(L-lysine) segments of 18 and 30 monomers form core shell micelles. The cores of the micelles contain a lamellar smectic A-like structure, formed by a poly(L-lysine) retinoate complex, which is surrounded by a corona of poly(ethylene oxide). Although the poly(L-lysine) chains are relatively short, they adopt an a-helical conformation to a pH as low as 9. This effective stabilization of the a-helix structure seems to be due to the formation of a protective surrounding coat of retinoate and a shell of poly(ethylene oxide). 

The characteristics of the isolated biopolymers depend on their structure. Cellulose and amylose are linear polymers, whereas amylopectin, pectin and hemicelluloses are branched polymers. Pectin and amylopectin contain carboxylic groups, which make interactions with water molecules very important. Amylose has a helix structure, whereas the cellulose molecule looks like a ribbon. The interactions with water and other neighbouring molecules are therefore different. 

These principles are best recognized when studying relatively simple molecular systems that have an ability to exploit weak interactions to create structure. Among many, peptides are the perfect choice for such studies considering their versatility in make up given the 20+ natural and synthetic amino acid residues, and their functional diversity. In addition, the amino acid sequence of the primary structure combined with the ability of forming secondary (3-sheet or a-helix structures provide substantial room for the creation of hierarchical structures based on weak intermolecular forces, mainly hydrogen bonds. A limited sequence of residues also prevents additional complication from tertiary and quaternary structures as seen with proteins. 

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