Axial rise

DNA conformation Occurrence Axial rise per base (nm) Base pair turn Base pair repeat unit... 

A computer-built model, having an axial rise per disaccharide of 0.84 nm and possible stabilization by an 0-3-H 0-5, intramolecular hydrogen-bond from a hexosamine to a uronic acid residue, is a rather extended, two-fold helix (see Fig. 8),346 with each fold approximately corresponding341,346 to the disaccharide repeat in Fig. 7a. A substantially similar model was obtained by use of calculations also taking into consid-... 

The molecules are helices having a twofold screw-axis, with an axial rise per disaccharide residue of 9.45 A (945 pm). The axes of the chains are parallel, and about equally spaced, but are not further organized into crystalline arrays. A hydrogen bond was proposed between the OH-3 group of the 2-acetamido-2-deoxy-D-glucose residues and 0-5 of the D-galactose 6-sulfate residues. 

All the above-mentioned proteins have single-stranded folds based on solenoidal windings of one polypeptide chain. Recently, however, several triple-stranded /1-helices (alternatively, triple-stranded /l-solenoids ) have been described in bacteriophage tail proteins (Kanamaru et al., 2002 Smith et al., 2005 Stummeyer et al., 2005 van Raaij et al, 2001). In these structures, three identical chains wind around a common axis and their coils have an axial rise of 14.5 A, that is, 3 x 4.83 A (for details see Sections IV and V.D). In this chapter, triple-stranded /l-solenoids will be abbreviated as TS /l-solenoids, while the term /1-solenoid, if not otherwise qualified, will apply to the predominant group of single-stranded /l-solenoids. 

The arcs most typical of TS /1-solenoids differ in conformation and consensus sequence from those of single-stranded /1-solenoids (Hennetin et al., 2006). This difference may originate in the fact that each chain of a TS /1-solenoid has an axial rise of 14.5 A as opposed to 4.8 A. On the other hand, the inverted arcs of the TS /1-solenoid from hyaluronidase HylPl (Smith et al., 2005) have ( -conformations, like those found in single-stranded /1-solenoids (Hennetin et al., 2006). Neither the /1-strands nor the /1-arcs of TS /l-solenoids contain proline, while the long loops frequently contain this residue. 

We infer that the spread of repeat lengths appears to be determined primarily by the region from residue 1 to 65. Although the linker between that region and the appended GFP moiety has some influence, it is not the principal structural determinant. With an axial rise per subunit of 0.47 nm (see above), these repeats translate into twist angles per subunit for short repeats of about 40 nm, 4—5° per subunit for the longest repeats of about 150 nm, -1.0° per subunit. The commonest repeat of —100 nm corresponds to a twist angle of -1.8° per subunit. 

Figure 19. Contour diagram for the conformational energy of the terminal residue of a hexasaccharide segment of the a-(1 2)-L-fucan constrained to satisfy the helical condition. Contours of axial rise per residue and residues per hehcal turn are superimposed - see text for details. Contours are drawn at absolute energies 2,4,10,25, and 50 kcal/mol.

Using the formula of Fraser and McRae (1973), the pitch P can be calculated from the supercoil radius r0, the axial rise per amino acid h (1.495 A for polyalanine Arnott and Dover, 1967), and the twist differential At. 

The bold contours indicate nonbonded conformational energy in kcal/mol, the thin lines indicate the number of residues per turn (n), and the dashed lines indicate the axial rise per residue (h), in Angstroms. The position of the conformation of the KOH-amylose is shown in the map by a filled circle (l l). 

Molecular models of polynucleotide helices consistent with the observed axial rise per nucleotide (7z) and its turn angle ( ), which are accurately measurable from the fibre... 

Figure 2.20. Models of collagen structure. (A) Model of three parallel left-handed helixes of collagen showing the location of Coc (C) for chains A, B, and C. Note all glycines are found in C-l position because this is the only amino acid residue that can be accommodated at the center of the triple helix. Later studies by Ramachan-dran and co-workers indicated that the three chains are wrapped around each other (B) in a right-handed superhelix. The axial rise per residue is 0.29 nm, and the axial displacement of different Coc atoms is shown in parentheses in angstroms.

Figure 6.3. Stress-strain curve for silk. The ultimate strength of dragline silk is about 800 MPa, with a modulus of about 7 GPa and strain at failure of 30%. Note that these values are higher than those for collagen, reflecting the higher axial rise per residue along the molecule.

Our last example of the mechanical properties of a protein is that of keratin found in the top layer of skin. The stratum corneum in skin is almost exclusively made up of different keratins that have an a-helical structure. The helices do not run continuously along the molecule so the structure is not ideal. However, the stress-strain characteristics are shown in Figure 6.4 and demonstrate that at low moisture content the stress-strain curve for keratins in skin is approximately linear with a UTS of about 1.8 GPa and a modulus of about 120 MPa. These values are between the values reported for elastin and silk, which is consistent with the axial rise per amino acid being 0.15 nm for the a helix. Thus the a helix with an intermediate value of the axial rise per amino acid residue has an intermediate value of the... 

Structure type Pitch (A) Base-pair tilt (°) Number of nucleotides per pitch Axial rise h and turn angle t per nucleotide Groove widthb (A) Groove depthb (A) ... 

A large number of stable conformations of both natural and synthetic DNA have been observed. They may be characterized in terms of gross structural parameters such as N, the number of molecular asymmetric units in K turns of the helix h, the axial rise per residue and r, the axial rotation per residue. Both right- and left-handed helices have been observed [13, 43]. In typical cases the molecular asymmetric unit is a mononucleotide but dinucleotide asymmetric units have been found in molecules in which the chemical repeat consists of two nucleotides [11]. The nucleotide conformations can be related to the different helical parameters both in terms of the backbone and conformational angles and features such as the sugar pucker and the base-pair displacement and orientation with respect to the helix axis. 

Figure 4.2. Representation of the DNA double helix with some average structural parameters. The ribbons represent the sugar-phosphate backbone, and the lines represent the A-T or G-C base pairs. Adjacent base pairs are separated by 3.4 A ( axial rise ) one full twist of the double helix occurs over 10.5 base pairs, which is equal to 35.7 A ( helical pitch ). The base pair tilt angle (see text) is too small to be readily observable here, and thus the base pairs appear to stack parallel with each other. Shown in the inset is the 34.3° twist angle, not evident in the representation. [Adapted from Fig. 1.12 of Ref. 7, with permission.]...

Axial rise is the distance between adjacent planar bases in the DNA double helix. In B-form DNA there are about 3.4 A between adjacent base pairs. 

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