Helical array

Figure 14.6 A model of intermediate filament construction. The monomer shown in (a) pairs with an identical monomer to form a coiled-coil dimer (b). The dimers then line up to form an antiparallel tetramer (c). Within each tetramer the dimers are staggered with respect to one another, allowing it to associate with another tetramer (d). In the final 10-nm rope-like intermediate filament, tetramers are packed together in a helical array (e).

FIGURE 10.31 The umbrella model of membrane chamiel protein insertion. Hydrophobic helices insert directly into the core of the membrane, with amphipathic helices arrayed on the surface like an open umbrella. A trigger signal (low pH or a voltage gradient) draws some of the amphipathic helices into and across the membrane, causing the pore to open. 

Proteins that cross-link actin filaments bind to their sides to produce bundles or three-dimensional networks (Otto, 1994). In microvilli, approximately 20 actin filaments of the core are cross-linked by villin (95 kD) and fimbrin (68 kD) in helical array to form a compact bundle (Figure 5). Filamin (2 x 250 kD) induces the formation of an actin network with gel formation. By immunofluorescence microscopy, this ABP is found in the ruffled, motile edge of cultured cells, where only actin filaments are abundant. 

Some virus particles have their protein subunits symmetrically packed in a helical array, forming hollow cylinders. The tobacco mosaic virus (TMV) is the classic example. X-ray diffraction data and electron micrographs have revealed that 16 subunits per turn of the helix project from a central axial hole that runs the length of the particle. The nucleic acid does not lie in this hole, but is embedded into ridges on the inside of each subunit and describes its own helix from one end of the particle to the other. 

Crystals of another pure hydrocarbon host 48 are formed in dimethyl sulfoxide 74. Constituents of this structure are also arranged into helical arrays (Fig. 16). 

Electron microscopy was utilised by Henderson and Unwin 2301 to determine the arrangement of protein in the purple membrane. It was found to comprise seven, closely packed a-helical arrays roughly perpendicular to the plane of the membrane with bilayer regions occupying the remaining space. The seven helices were all 10-12 A apart and approximately 35-40 A long, the membrane itself being 45 A thick. These helices made up about 75 % of the polypeptide but the connectivity between them was not resolved. 

It appears probable that other transmembrane proteins function by providing related channels between helical arrays of polypeptide chains 238 240). 

Figure 6.10 Chiral hexakis-porphyrinato benzene compound 66, which possesses propellerlike structure and can self-assemble to form helical arrays.

Inouye, H., Bond, J. E., Deverin, S. P., Lim, A., Costello, C. E., and Kirschner, D. A. (2002). Molecular organization of amyloid protofilament-like assembly of betabellin 15D Helical array of beta-sandwiches. Biophys.J. 83, 1716-1727. 

While a polar-zipper model was initially proposed for Asp2Glni3Lys2 (Perutz et ah, 1994), more recently a water-filled nanotube was proposed in which the homopolymer in the / -conformation forms a helical array having 20 residues per turn (Perutz et ah, 2002a,b). (In the earlier work, the diffraction pattern had been interpreted as a fiber pattern—that is, with the 4.8-A reflection in the fibril direction.) Rather than being attributed to intersheet stacking, the 8.4-A reflection was not accounted for. Further,... 

With the demise of the uniform fiber model in 1974, it became necessary to devise other models to account for the early electron micrographs of chromatin fibers and the X-ray diffraction studies (see Ref. [1], Chapter 1). Two models appeared in 1976, and were the major contenders for consideration in 1978. The superbead model of Franke et al. [36] envisioned the chromatin fiber as a compaction of multi-nucleosome superbeads . The solenoid model of Finch and Klug [37] postulated a regular helical array of nucleosomes, with approximately six nucleosomes per turn and a pitch of 10 nm. Although a number of competing helical models appeared in the 1980s (see Ref. [1], Chapter 7) the solenoid model remains a serious contender to this day. Structural details of this model, such as the precise disposition of linker DNA, are still lacking. 

Three nearest neighbors, indexed as 0, 6, and 11, are indicated. The axial slab shown represents 1% of the total length of the virion. From Marvin.31a (B) A 2.0 nm section through the virus coat with the helices shown as curved cylinders. The view is down the axis from the N-terminal ends of the rods. The rods extend upward and outward. The rods with indices 0 to -4 start at the same level, forming a five-start helical array. The rods with more negative indices start at lower levels and are therefore further out when they are cut in this section. (C) The same view but with "wire models" of the atomic structure of the rods. From Marvin et al 2... 

This volume focuses on extensions of peptide chemistry into the novel areas of template-conjugated peptides, helical arrays of polypeptides, dendrimers, and C-terminally modified peptides. The volume concludes with an overview of the classic syntheses of representative peptide natural products. 

Main, E. R., Xiong, Y., Cocco, M. J., D Andrea, L., and Regan, L. (2003). Design of stable a-helical arrays from an idealized TPR motif. Structure 11, 497-508. 

Fig. 8. Generation of the form of the helical diffraction pattern. (A) shows that a continuous helical wire can be considered as a convolution of one turn of the helix and a set of points (actually three-dimensional delta-functions) aligned along the helix axis and separated axially by the pitch P. (B) shows that a discontinuous helix (i.e., a helical array of subunits) can be thought of as a product of the continuous helix in (A) and a set of horizontal density planes spaced h apart, where h is the subunit axial translation as in Fig. 7. This discontinuous set of points can then be convoluted with an atom (or a more complicated motif) to give a helical polymer. (C)-(F) represent helical objects and their computed diffraction patterns. (C) is half a turn of a helical wire. Its transform is a cross of intensity (high intensity is shown as white). (D) A full turn gives a similar cross with some substructure. A continuous helical wire has the transform of a complete helical turn, multiplied by the transform of the array of points in the middle of (A), namely, a set of planes of intensity a distance n/P apart (see Fig. 7). This means that in the transform in (E) the helix cross in (D) is only seen on the intensity planes, which are n/P apart. (F) shows the effect of making the helix in (E) discontinuous. The broken helix cross in (E) is now convoluted with the transform of the set of planes in (B), which are h apart. This transform is a set of points along the meridian of the diffraction pattern and separated by m/h. The resulting transform in (F) is therefore a series of helix crosses as in (E) but placed with their centers at the positions m/h from the pattern center. (Transforms calculated using MusLabel or FIELIX.)...

Harding, L. P., Jeffery, J. C., Riis-Johannessen, T., Rice, C. R., Zeng, Z. T., Anion control of the formation of geometric isomers in a triple helical array. Dalton Trans. 2004, 2396-2397. 

Figure 10.27 The structure of [Cd12(10.20)18](BF4)24 showing (a) polyhedral metal cage and the four encapsulated BF4 anions (b) view down one of the Cd6 pseudohexagonai faces, emphasising the cyclic helical array of ligands and the presence of an anion in the centre of the face (reproduced with permission from [22] 2006 American Chemical Society).

A central backbone of straight tubular structures formed by the self-assembly of biotinylated lipids was used as a scaffold in order to construct functionalized three-dimensional, highly ordered helical arrays of streptavidin (Figure 7.38).259 260,261 Using these structures... 

Microtubule filaments are hollow cylinders made of the protein tubulin. The wall of the microtubule is made up of a helical array of alternating a- and 13-tubulin subunits. The mitotic spindle involved in separating the chromosomes during cell division is made of microtubules. Colchicine inhibits microtubule formation, whereas the anticancer agent, taxol, stabilizes microtubules and interferes with mitosis. 

The product of gene 8 is the major capsid protein of the filamentous phage. The protein is synthesized as a precursor with an N-terminal extension of 23 amino acids, which is necessary for the insertion of the protein into the bacterial cytoplasmic membrane where the leader peptide is cleaved. During the process of phage assembly, about 2700 copies aggregate around the virus DNA to form a helical array with the amino terminus exposed to the... 

The myosin protomers can self-associate to form a thick filament by the assembly of some 400 myosin tails in a staggered side-by-side packing with the myosin heads projecting at regular intervals in a helical array (Fig. 5-32). The thick filament is bipolar with a 150 nm bare zone in the center where two oppositely oriented sets of myosin tails come together. The center of this region is called the M line. This thick filament forms part of a myofibril. 

---