In a helix

There are two broad kinds of polyion conformation the random coil and the ordered helix. In a helix there are regularly repeated structures along the coil there are none in the case of a random coil. In this book we are concerned with the latter where there are often several conformations with approximately equal free energies and, thus, conformational changes occur readily. 

Half-pipe jackets are formed by welding sections of pipe, cut in half along the longitudinal axis, to the vessel wall. The pipe is usually wound round the vessel in a helix Figure 12.72c. 

A typical virus with helical symmetry is the tobacco mosaic virus (TMV). This is an RNA virus in which the 2130 identical protein subunits (each 158 amino acids in length) are arranged in a helix. In TMV, the helix has 16 1/2 subunits per turn and the overall dimensions of the virus particle are 18 X 300 nm. The lengths of helical viruses are determined by the length of the nucleic acid, but the width of the helical virus particle is determined by the size and packing of the protein subunits. 

Secondary structural predictions about NPAs, and direct biophysical measurements, have demonstrated that the NPAs are rich in a-helix, with no p-structure either predicted from secondary structure prediction algorithms, or detected by circular dichroism (Kennedy et al, 1995b). In this they are the antithesis of the similarly sized cLBPs and lipocalins. The predictions are that each individual NPA unit protein will fold into four main regions of helix, and it has been speculated that the tertiary structure is as a four-bundle helix protein, similar to other invertebrate carrier proteins (Sheriff et al., 1987). 

The LBP-20 proteins were predicted to be rich in a-helix, and with very little, if any, (i/extended structure, and this has been confirmed by circular... 

The membrane establishes in and out. The membrane is asymmetric because the inner and outer leaflets can have a different lipid composition and contain different proteins (Fig. 3-3). Proteins can be associated with either side of the membrane, or they can pass through the membrane using membrane-spanning segments. The functional part of the protein can be on the cytosolic side, the external side, or even in the membrane itself. A common structure for spanning a membrane is an a-helix (but there are examples of sheets spanning a membrane). It takes about 20 amino acid residues arranged in a helix to span to a 30 A hydrophobic interior of the bilayer. 

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

The /(-helix is a well-authenticated fold, having been observed in more than 20 crystal structures, mostly of secreted bacterial proteins (Jenkins and Pickersgill, 2001 Yoder and Jurnak, 1995 see also Kajava and Steven, this volume). In a /(-helix, the polypeptide chain winds around the molecular axis, each coil consisting of three short /(-strands with connecting turns (Fig. 11). Corresponding strands in successive turns are stacked, generating narrow parallel /(-sheets that are aligned with the... 

Fig. 15. Coherence transfer efficiencies as a function of delay 2TC for the residues in a-helix and ffisheet in the sequential HNCA-TROSY scheme. Equation (8) is plotted using the following parameters T2 un-trosy = 50 ms, T2 o = 25 ms, 2Ta = 25 ms,...

Fig. 17. Efficiencies of coherence transfer for the residues in a-helix and P-sheet, as a function of delay 4Ta in the iHNCA-TROSY experiment. Equation (9) is plotted...

Ida and Pingala are, respectively, the microcosmic active and passive (lunar and solar) currents of the One Force flowing through the human being, on all levels. They weave about the central column in a helix, similar to the DNA helix of which they are the prematerial prototype. There is a rabbinic parable that says that the Creator—blessed be He— when fashioning the universe took a spiral of flame (fire) and a spiral of ice (water) and wove them together. 

Strand DNA normally exists in the bacterial nucleus in a helix, in which two strands are coiled together. [NIH]... 

With 3.6 residues per turn, side chains protrude from the a-helix at about every 100° in azimuth. Since the commonest location for a helix is along the outside of the protein, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues (Schiffer and Edmundson, 1967). This trend can sometimes be seen in the sequence, but it is not strong enough for reliable prediction by itself. Different residues have weak but definite preferences either for or against being in a-helix Ala, Glu, Leu,... 

CD studies have recently been made on urea-isolated and renatured individual proteins from the small ribosomal subunit (Venyaminov and Gogia, 1982). In another study (Dijk et al., 1983a), many proteins obtained from both the small and large ribosomal subunits by a gentler salt extraction method were measured with the CD technique. It was found that, in general, the 30 S proteins are rich in a helix and contain a rather small amount of /3 sheet, whereas the 50 S proteins are more diverse, especially in their a helix content, and most are relatively rich in /3 sheet (Dijk et al., 1983a). 

Most recently, Baltzer and co-workers have incorporated a lysine-bound nicotinamide into a more complex peptide scaffold [75]. This approach takes advantage of the augmented reactivity of a lysine residue contained in a helix-turn-helix scaffold (as described previously [76]). An adjacent histidine is able to selectively catalyze the formation of an amide bond between activated esters and the lysine c-amino group under aqueous conditions. Thus, reaction of the 42-residue peptide LA-42 withp-nitrophenyl hT-methylnicotinate in an aqueous solution at pH 5.9 yields the nicotinoyl-functionalized peptide (Fig. 27). 

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