Helix twist

This polymer crystallizes in three polymorphs. The threefold helical structure packs in a trigonal unit-cell with a = 14.3 A (1.43 nm) and c = 28.7 A (2.87 nm). The 8-fold helical structure occurs in a tetragonal unit-cell with a = 13.8 A (1.38 nm) and c = 78.2 A (7.82 nm). Axial periodicity in both cases is similar [h = 9.6 A (960 pm) and 9.8 A (980 pm), respectively], but the helix twist-angle is different (120 and 45°, respectively). Distribution of the charged side-groups in these helices was discussed. An orthorhombic form, with a twofold helical structure, has a repeat of 18.6 A (1.86 nm). 

Fig. 3. Variation in helix twist seen in the three domains of peptide T3-785.

Taylor, Kaiser, and their co-workers (Taylor and Kaiser, 1986) prepared a series of model peptides that were designed to test the role of each of the postulated modules in /8-endorphin. Figure 13 illustrates a-helical net diagrams of the proposed helical auxiliary sequence of /3-endorphin. The hydrophobic residues in this structure cover half the surface of the helix, twisting around the structure in a clockwise manner. [It has also been noted that if this sequence were to form a tt helix rather than an a... 

Fig. 18.5. Correlation between observed helix-twist angles and sum function 1 (a) and correlation between observed roll angles and sum function (b) for the dodecamer [d(CGCGAATTCGCG)]2. A decrease in helical twist or an opening of the roll angle on the side of the base pair where a clash occurs will relieve the steric hindrance between adjacent purines of opposite strands. For example, the clash at the first G-C base pair step (R-Y, step 2) takes place in the major groove. To relieve the steric hindrance, the twist angle has to be decreased, and at the same time the twist at each of the two neighboring steps is increased by half that amount. Thus, the contributions to X) 1 for tbe three steps 1, 2 and 3 are +1, -2, -t-1. If the clash occurs in the minor groove (e.g. with the neighboring C-G step, step 3), each of the contributions has to be doubled. Thus, the contributions to 1 for the three steps 2, 3 and 4 are +2, -4, +2 etc. (for details, see [39, 40]). The correlation coefficients were 0.94 (a) and 0.92 (b). For the correlations, the contributions of terminal base-pair steps (1 and 11) were omitted to avoid the influence of end effects...

With respect to a DNA double helix, twist refers to the total number of times the two strands of the helix cross over each other, excluding writhing. Twist is a measure of how tightly the helix is wound. 

Hydrophobic moment profile is calculated as described by Eisenberg et al. [48] to collect information about possible amphipathic helices and strands. We used only the PRIFT scale ( 27 in Table 5) to find hydrophobic moments. Scales used for the calculation of hydrophobic moments were not normalized. The PRIFT scale produces high moments (sometimes higher than 2.0) for sequence segments known to be highly amphipathic. An ideal a-helix twist angle of 100 was used to associate a-helix hydrophobic moments with all... 

A third type of helix is observed in X-ray studies of DNA made under conditions of low (75 %) humidity. A-DNA is right-handed, like B-DNA, but it has nearly 11 base pairs per helix twist, and they are inclined by 13° with respect to the plane perpendicular to the helix axis. A-DNA has a very deep major groove, in contrast to the B form. Since the 2 OH of the ribose moieties of RNA prevent RNA from adopting a B conformation, it has been suggested that DNA-RNA hybrids must have the A conformation. 

Helix twist Right Right Left Right... 

The first known structure of a fibrous protein was that of keratin. It comes in two forms, a- and -keratin, and their structures are what their designations imply. a-Keratin is the major protein of hair, nails, feathers, and skin, and is entirely a-helical, but it also has a higher order structure, with three strands of a-helix twisted around each other like strands of spaghetti. This results in a filament of increased stiffness and tensile strength. Leather is practically all a-keratin. /3-Keratin, on the other hand, is largely made up of antiparallel /3-pleated sheets. It is the principal protein of birds beaks and claws and of silk. 

Feiastic is the free energy density in the steady state due to the splay, twist, and bend deformations, and the helix twist, as given in Eq. (67),... 

The dynamics of helix twisting has also been considered with equations for torsional rotation of the DNA being developed (Barkley and Zimm, 1979). Assuming that intercalated dyes reflect the motional properties of nucleic acids, indications are that this motion can account for most of the fluorescence depolarization decay of ethidium intercalated into DNA,... 

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