Helicates right-handed

Polynucleotides fold into helices, right-handed A and or... 

Figure Bl.17.11. Reconstructed density of an a,p-tiibulin protein dimer as obtained from electron crystallography (Nogales etal 1997). Note the appearance of the p-sheets ((a), marked B) and the a-helices ((b), marked H) in the density. In particular the right-handed a-helix H6 is very clear. Pictures by courtesy of E Nogales and Academic Press.

An a helix can in theory be either right-handed or left-handed depending on the screw direction of the chain. A left-handed a helix is not, however, allowed for L-amino acids due to the close approach of the side chains and the CO group. Thus the a helix that is observed in proteins is almost always right-handed. Short regions of left-handed a helices (3-5 residues) occur only occasionally. 

Figure 4.2 A p-a-p motif is a right-handed structure. Two such motifs can be joined into a four-stranded parallel p sheet in two different ways. They can be aligned with the a helices either on the same side of the p sheet (a) or on opposite sides (b). In case (a) the last p strand of motif I (red) is adjacent to the first p strand of motif 2 (blue), giving the strand order 1 2 3 4. The motifs are aligned in this way in barrel structures (see Figure 4.1a) and in the horseshoe fold (see Figure 4.11). In case (b) the first p strands of both motifs are adjacent, giving the strand order 4 3 12. Open twisted sheets (see Figure 4.1b) contain at least one motif alignment of this kind. In both cases the motifs ate joined by an ct helix (green).

Each repeat forms a right-handed P-loop-a structure similar to those found in the two other classes of a/p structures described earlier. Sequential p-loop-a repeats are joined together in a similar way to those in the a/P-bar-rel stmctures. The P strands form a parallel p sheet, and all the a helices are on one side of the P sheet. However, the P strands do not form a closed barrel instead they form a curved open stmcture that resembles a horseshoe with a helices on the outside and a p sheet forming the inside wall of the horseshoe (Figure 4.11). One side of the P sheet faces the a helices and participates in a hydrophobic core between the a helices and the P sheet the other side of the P sheet is exposed to solvent, a characteristic other a/p structures do not have. 

Since the first bracket on the right-hand side is a constant and the second is an integer, it is evident that, for any particular /, some leeway must exist in the value of the ratio rj/G for the equality to be satisfied. Here too, the presence of screw helicity must affect either / , or G, or both. In view of the fairly small variations of G allowed if the hybridization of the C atoms is to remain sp, and since the deformation of the C orbitals decreases as the radius of the cylindrical sheets increases, the distance between successive cylinders must decrease and probably tend towards a value characteristic of turbostratic graphite. 

FIGURE 6.18 Poly(Gly-Pro-Pro), a collagen-like right-handed triple helix composed of three left-handed helical chains. (Adaptedfrom Miller Scheraga, H. A., 1976, Calculation of the... 

Another important parallel /3-array is the eight-stranded parallel j8-barrel, exemplified in the structures of triose phosphate isomerase and pyruvate kinase (Figure 6.30). Each /3-strand in the barrel is flanked by an antiparallel a-helix. The a-helices thus form a larger cylinder of parallel helices concentric with the /3-barrel. Both cylinders thus formed have a right-handed twist. Another parallel /3-structure consists of an internal twisted wall of parallel or mixed /3-sheet protected on both sides by helices or other substructures. This structure is called the doubly wound parallel j8-sbeet because the structure can be... 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Figure 15.9 The structure of right-handed and left-handed Sot helices in fibrous sulfur (see...

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