Conformation a-helical

Fig. 5.17 Histogram of the normal modes calculated for a polyalanine polypeptide in an a-helical conformation. The height of each bar indicates the number of normal modes in each 50cm section.

Compared to Ras, Gq subunits are extended at their N-termini by about 30 residues that in free Ga are disordered but, as we will see, obtain a helical conformation in association with Gpy. 

The conformation adopted by a molecule in the crystalline structure will also affect the density. Whereas polyethylene adopts a planar zigzag conformation, because of steric factors a polypropylene molecule adopts a helical conformation in the crystalline zone. This requires somewhat more space and isotactic polypropylene has a lower density than polyethylene. 

The ct-form which forms on rapid crystallisation from the melt and which has a helical conformation. 

FIGURE 7.22 Suspensions of amylose in water adopt a helical conformation. Iodine (b) can insert into the middle of the amylose helix to give a bine color that is characteristic and diagnostic for starch. 

As Fig. 16 shows, the preferential binding of DMSO, DMF and NMF from aqueous solution to (Lys HBr)n at low contents of the organic solvent x increases with its concentration. However, at approximately x3 = 0,2 a maximum is reached and then preferential hydration between x3 = 0,3 and 0,5 occurs. No preferential binding was observed for NMP, EG or 2 PrOH, however increasing hydration occured with x3. Only in 2 PrOH at x3 > 0,3 a-helix formation occured. Furthermore binding parameters for the systems NMP + DMSO, EG + DMSO and DMF + DMSO have been determined. An initial preferential binding of DMSO by (Lys HBr)n, a maximum and a subsequently inversion of the binding parameter was also observed in these mixtures. The order of relative affinity is DMSO > DMF > EG > NMP. In DMF/DMSO-mixtures (Lys HBr) attains an a-helical conformation above 20 vol.- % DMF and in 2-PrOH/water above 70 vol.- % 2 Pr-OH. 

Hydrophobicity plots of AQPs indicated that these proteins consist of six transmembrane a-helices (Hl-H6 in Fig. la) connected by five connecting loops (A-E), and flanked by cytosolic N- and C-termini. The second half of the molecule is an evolutionary duplicate and inverse orientation of the first half of the molecule. Loops B and E of the channel bend into the membrane with an a-helical conformation (HB, HE in Fig. lb) and meet and each other at their so-called Asn-Pro-Ala (NPA) boxes. These NPA motifs are the hallmark of AQPs and form the actual selective pore of the channel, as at this location, the diameter is of that of a water molecule (3 A Fig. la and b). Based on the narrowing of the channel from both membrane sides to this small... 

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

Peptoids based on a-chiral aliphatic side chains can form stable helices as well [43]. A crystal of a pentameric peptoid homooligomer composed of homochiral N-(1-cyclohexylethyl)glycine residues was grown by slow evaporation from methanol solution, and its structure determined by X-ray crystallographic methods. In the crystalline state, this pentamer adopts a helical conformation with repeating cis-... 

Fig. 2.16 Effect of electrostatic interactions on 3i4-helix formation in an aqueous environment [1 75 a, 175 b, 176]. y -Peptides 86 and 87 adopt a stable helical conformation mediated by salt bridges near neutral pH. While the propensity of these peptides to adopt a helical conformation is strongly de-...

A, these peptides are approximately 36 A long and thus compare well with ma-gainin II in a-helical conformation (23 residues, 34.5 A long). 

Figure 5-4. Hydrogen bonds (dotted lines) formed between H and 0 atoms stabilize a polypeptide in an a-helical conformation. (Reprinted, with permission,...

The classic disilene 1 is unusual in that it exists in at least three crystalline modifications orange and yellow unsolvated forms and a yellow toluene solvate (Fig. 2). The orange polymorph has a helical conformation in which all of the mesityl substituents are twisted in the same direction thus molecules of 1 in this form are chiral.51 The toluene solvate has an unusual conformation in which two mesityl rings cis to each other are nearly coplanar with the Si=Si bond, while the other two cis mesityl groups are nearly orthogonal.41 The structure of the yellow unsolvated form is not yet known. Because of the flat potential surface for the Si=Si... 

Crystalline samples of syndiotactic poly(methyl methacrylate) (st-PMMA) may be obtained from chloroacetone 178). This guest could be completely replaced by a variety of other guest molecules such as acetone, 1,3-dichloroacetone, bromoacetone, pinacolone, cyclohexanone, acetophenone and benzene. The X-ray diffraction patterns for these inclusion compounds were similar. These data indicate that the st-PMMA chains adopt a helical conformation of radius about 8 A and pitch 8.85 A. The guest molecules are located both inside the helical canals and in interhelix interstitial sites. 

Fig. 8. Theoretical simulation of VCD (top) and IR absorption (bottom) spectra of alanine dodecapeptides for the amide V bands for a fully a-helical conformation (left) and a fully left-handed 3i-helical conformation (right). The simulations are for the same three isotopically labeled (13C on the amide C=0 for four Ala residues selected in sequence) peptides as in Figure 7 N-terminal tetrad (4AL1), middle (4AL2), and C-terminal (4AL4). The 13C feature is the same for all sequences, confirming the experimentally found unfolding of the C-terminus. The agreement with the shapes in Figure 7 is near quantitative. Reprinted from Silva, R. A. G. D., Kubelka, J., Decatur, S. M., Bour, R, and Keiderling, T. A. (2000a). Proc. Natl. Acad. Sci. USA 97, 8318-8323. 2000 National Academy of Science, U.S.A.

For comparison, the calculated linear and 2D spectra using ft = 12.3 cm-1 and 6 = 52°, which correspond to an a-helical structure (see the contour plot Fig. 19) for the isotopomer Ala -Ala-Ala are shown in Figure 21. The observed spectra for Ala -Ala-Ala are strikingly different from the calculated spectra for a molecule in an a-helical conformation. We emphasize here an important point In contrast to the NMR results on oligo(Ala), in which averaging of different backbone conformations might be present because measurements are made on a time scale that is slow compared to that of conformational motions, these vibrational spectroscopy results are detected on a very fast time scale (Hamm et al, 1999 Woutersen and Hamm, 2000, 2001). This rules out conformational averaging. 

Fig. 7.9 In the a-helical conformation of the model dipeptide N-acetyl N -methyl glycineamide (left), the C-H bond lengths and H-C-X angles at the a-carbon are different (1.081 A and 1.078 A for C-H and 109.3° and 109.7° for H-C-N). Thus, the a-carbon is asymmetric. In contrast, in the C5 conformation of N-acetyl N -methyl glycineamide (right), bonds and angles at C(a) are identical, there is a molecular symmetry plane, and the a-carbon is symmetric. (All values from Schafer et al. 1984.)...

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