Conformation extended

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Fischer projection formulas can be used to represent molecules with several stereogenic centers and are commonly used for caibohydrates. For other types of structures, a more common practice is to draw the molecule in an extended conformation witii the main chain horizontal. In this arrangement, each tetrahedral caibon has two additional substituents, one facing out and one in. The orientation is specified widi solid wedged bonds for substituents facing out and with dashed bonds for substituents that point in. 

Free rotation around each of the carbon-carbon bonds makes saturated fatty acids extremely flexible molecules. Owing to steric constraints, however, the fully extended conformation (Figure 8.1) is the most stable for saturated fatty acids. Nonetheless, the degree of stabilization is slight, and (as will be seen) saturated fatty acid chains adopt a variety of conformations. 

The amino acid compositions and sequences of the /3-strands in porin proteins are novel. Polar and nonpolar residues alternate along the /3-strands, with polar residues facing the central pore or cavity of the barrel and nonpolar residues facing out from the barrel where they can interact with the hydrophobic lipid milieu of the membrane. The smallest diameter of the porin channel is about 5 A. Thus, a maltodextrin polymer (composed of two or more glucose units) must pass through the porin in an extended conformation (like a spaghetti strand). 

FIGURE 9.27 The O-Unked saccharides of glycoproteins appear in many cases to adopt extended conformations that serve to extend the functional domains of these proteins above the membrane surface. (Adaptedfrom Jentofi, N., 1990, Trends in Biochemical Sciences 15 291-294.)... 

The conformation of bovine myelin basic protein (MBP) in AOT/isooctane/water reversed micellar systems was studied by Waks et al. 67). This MBP is an extrinsic water soluble protein which attains an extended conformation in aqueous solution 68 but is more density packed at the membrane surface. The solubilization of MBP in the AOT reversed micelles depends on the water/AOT-ratio w0 68). The maximum of solubilization was observed at a w0-value as low as 5.56. The same value was obtained for another major protein component of myelin, the Folch-Pi proteolipid 69). According to fluorescence emission spectra of MBP, accessibility of the single tryptophane residue seems to be decreased in AOT reversed micelles. From CD-spectra one can conclude that there is a higher conformational rigidity in reversed micelles and a more ordered aqueous environment. 

Several years ago Makino et al. 86) studied the influence of anions on the conformation of poly-[L-methionine-S-methylsulfonium] salts in solution. They found that especially perchlorate will induce a-helix formation whereas Cl- and Br do not. Since then several authors 87 92) have found a similar a-helix inducing effect in the case of poly-L-lysine (Lys) and other BPAA at low pH-values where the polymer molecules usually attain an extended conformation due to the electrostatic repulsion of the ammonium groups. Therefore, the a-helix inducing effect is obviously an... 

The heterogeneity of the reaction medium is also important in determining the molecular weight and in solution polymerization of maeromonomers. The magnitude of the effect varies according to the solvent quality. PS macromonomer chains in good solvents (e.g. toluene) have au extended conformation whereas in poor solvents (e.g. melhylcyclohexane) chains are tightly coiled.89 As a consequence, the radical center may see ail environment that is medium dependent (see also Sections 7.6.5 and 8.3.7). 

Fairly recently, another method for obtaining polymer materials with uniaxial orientation has been developed. It is the directed polymerization i.e. the synthesis of polymers under conditions at which the material attains instanteneously the oriented structure. The formation of crystals from the macromolecules in an extended conformation occurs in those polymerizing systems simultaneously with polymerization22. ... 

The crystallization of polymer melts at high pressure (several thousand of atmospheres), just as the crystallization in flowing melts and stirred solutions, leads to the formation of ECC in which the molecules assume almost completely extended conformations. This suprising feet (the crystallization was carried out at hydrostatic compression) was first extablished experimentally by Wunderlich30 and then confirmed by other authors31 33. However, diverse opinions exist about the mechanism of ECC formation. 

The thermodynamic analysis of conformational and structural transformations in the melt at high pressures34 showed that the free volume and free energy minimum required for hydrostatic compression is attained as a result of the transition of the molecules in the melt into a more extended conformation (gauche —> trans transitions) since the extended molecules ensure a more compact packing of the chains at compression. Chain uncoiling leads to a decrease in their flexibility parameter f with increasing pressure p ... 

A polymorphic behavior involving packing of chains having completely different conformations has been found also for isotactic polymers. For instance, isotactic polystyrene, under suitable experimental conditions, can produce crystalline gels in which the chains assume a nearly fully extended conformation [11,12], very close to a truns-planar, rather than the classical conformation of three-fold helix [13]. The two possible conformations proposed for the two crystalline forms of i-PS are shown in Fig. 2. 

Recently, a / -dodecapeptide was found to display a CD spectrum in water which was very similar to that assigned to the 12/10-helix, with a single maximum near 200 nm. Careful NMR analysis however, revealed a predominantely extended conformation without regular secondary structure elements [174]. This result stresses that the CD signature assigned to the 12/10-structure might not be unique and again (see Section 2.2.3.1) that CD spectra must be interpreted with caution. 

While conformation II (Fig. 2.34) of Uke-y -amino acids is found in the 2.614-helical structure, conformation I, which similarly does not suffer from sy -pen-tane interaction, should be an appropriate alternative for the construction of sheet-like structures. However, sheet-like arrangement have not been reported so far for y-peptides composed of acyclic y " -amino acid residues. Nevertheless, other conformational biases (such as a,/9-unsaturation, cyclization between C(a) and C(y)) have been introduced into the y-amino acid backbone to restrict rotation around ethylene bonds and to promote extended conformation with formation of sheets in model peptides. Examples of such short chain y-peptides forming antiparallel (e.g. 152 [208]) and parallel (e.g. 153-155 [205, 208]) sheet-hke structures are shown in Fig. 2.38. 

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