A-helical structures

Amorphous or "plastic" sulfur is obtained by fast cooling of the crystalline form. X-ray studies indicate that amorphous sulfur may have a helical structure with eight atoms per spiral. Crystalline sulfur seems to be made of rings, each containing eight sulfur atoms, which fit together to give a normal X-ray pattern. 

A helical structure for DNA strands had been suggested in 1949 by Sven Furberg in his Ph D dissertation at the University of London... 

R = -CH2CH(CH3)2, there occurs a modest deviation from a strict 0°-120° alternation which characterizes the trans-gauche sequence. This produces a helical structure with seven repeat units occurring in two turns. Even bulkier substituents, for example, o-methyl phenyl, produce still more open helices... 

Poly(7-benzyl-L-glutamate) is known to possess a helical structure in certain solvents. As part of an investigationf of this molecule, a fractionated sample was examined in chloroform (CHCI3) and chloroform saturated ( 0.5%) with dimethyl formamide (DMF). The following results were obtained ... 

The polypeptide chain of the 92 N-terminal residues is folded into five a helices connected by loop regions (Figure 8.6). Again the helices are not packed against each other in the usual way for a-helical structures. Instead, a helices 2 and 3, residues 33-52, form a helix-turn-helix motif with a very similar structure to that found in Cro. 

They started from the sequence of a domain, Bl, from an IgG-binding protein called Protein G. This domain of 56 amino acid residues folds into a four-stranded p sheet and one a helix (Figure 17.16). Their aim was to convert this structure into an all a-helical structure similar to that of Rop (see Chapter 3). Each subunit of Rop is 63 amino acids long and folds into two a helices connected by a short loop. The last seven residues are unstructured and were not considered in the design procedure. Two subunits of Rop form a four-helix bundle (Figure 17.16). 

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen parrs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical stnrcture or double helix ). 

FIGURE 5.51 The cholesteric phase of a liquid crystal. In this phase, sheets of parallel molecules are rotated relative to their neighbors and form a helical structure. 

Early biochemical studies supported the hypothesis that the HRl and the HR2 peptides would interact to form a helical structure (Chen et al. 1995 Lu et al. 1995). This hypothesis was strengthened when X-ray structures were resolved for co-crystals of HRl and HR2 peptides (Chan et al. 1997 Tan et al. 1997 Weissenhom et al. 1997). The results showed that in the six-helix bundle, three HRl domains were packed tightly together in the center of the bundle, with the HR2 domains bound in an antiparallel manner in grooves formed along the HRl core. 

In the case of myelin proteolipid solubilized in water/tetraethylene glycol monodo-decyl ether/dodecane microemulsions, its a-helical structure is preserved [176,177],... 

Because of the conversion of orthorhombic sulfur to monoclinic form, the above values of melting points are difficult to observe, as the resulting allotropic mixture melts at only 115 C. Amorphous or plastic sulfur can be produced through the rapid cooling of molten sulfur. X-ray crystallographic studies show that the amorphous form may have a helical structure with eight atoms per turn. This form is metastable at room temperature and gradually reverts back to crystalline within hours to days but this conversion can be rapidly catalyzed. 

The conformational changes which have been described so far are probably all relatively small local changes in the structure of H,K-ATPase. This has been confirmed by Mitchell et al. [101] who demonstrated by Fourier transform infrared spectroscopy that a gross change in the protein secondary structure does not occur upon a conformational change from Ei to 3. Circular dichroism measurements, however [102,103], indicated an increase in a-helical structure upon addition of ATP to H,K-ATPase in the presence of Mg and... 

Polymerization of triphenylmethyl methacrylate in the presence of a chiral anion catalyst results in a polymer with a helical structure that can be coated onto macroporous silica [742,804). Enantioselectivity in this case results from insertion and fitting of the analyte into the helical cavity. Aromatic compounds and molecules with a rigid nonplanar structure are often well resolved on this phase. The triphenylmethyl methacrylate polymers are normally used with eluents containing methanol or mixtures of hexane and 2-propanol. The polymers are soluble in aromatic hydrocarbons, chlorinated hydrocarbons and tetrahydrofuran which, therefore, are not suitable eluents. 

FIGURE 3.1 Schematic representation of the transmembrane topology of the 4TM receptor family. Only TM2 show an a-helical structure in electron microscopic studies the remaining TM regions may fold in (5-sheet structures. Both the N-terminus (indicated by NH2) and the C-terminus are located extracellularly. The cytoplasmic loops between TM3 and TM4 are variable in size and contain putative phosphorylation sites. 

X-ray diffraction studies on gramicidin commenced as early as 1949 218-219> and this early work pointed to a helical structure 220). Recent work by Koeppe et al. 221) on gramicidin A crystallised from methanol (/%) and ethanol (.P212121) has shown that the helical channel has a diameter of about 5 A and a length of about 32 A in both cases. The inclusion complexes of gramicidin A with CsSCN and KSCN (P212121) have channels that are wider (6-8 A) and shorter (26 A) than the uncomplexed dimer 221 222). Furthermore there are two cation binding sites per channel situated either 2.5 A from either end of the channel or 2.5 A on each side of its centre 222) Unfortunately these data do not permit a choice to be made from the helical models (i)—(iv) and it is not certain if the helical canals studied are the same as those involved in membrane ion transport. 

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. 21. Calculated linear and 2D spectra for Ala -Ala-Ala using fi = 12.3 cm-1 and = 52°, which corresponds to an a-helical structure. Linear spectrum (a) and 2D scans for parallel (b) and perpendicular (c) polarizations of the pump and probe pulses. From Woutersen and Hamm (2001)./. Chem. Phys. 114, 2727-2737, 2001, Reprinted with permission from American Institute of Physics.

ABF was probed through the reversible unfolding of a short peptide, deca-L-alanine, in vacuo [52] (see Fig. 4.10). The reaction coordinate, , is the distance separating the first and the last Ca carbon atom of the peptide chain. was varied between 12 and 32 A, thereby allowing the peptide to sample the full range of conformations between the native a-helical structure and the extended structures. The force acting along was accrued in bins 0.1 A wide. 

DNA has a helical structure, and all naturally occurring DNA turns to the right. 

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