Helical strands

The double-helical strand of a DNA molecule. The diagram at the left shows the hydrogen bonding between base pairs adenine-thymine and cystosine-guanine that hold the strands together. 

Resilin-like polypeptide and sequence motif Technique Helices (%) Strands (%) Turns (%) Unordered (%) (or random coil) Beta sheet (%) PPII (%)... 

This presented a more difficult problem How do the double-helical strands separate during DNA synthesis In a rapidly growing cell such as E. coli it has been calculated that if the strands separate by untwisting, the molecule would have to rotate at 10,000 rpm, a rate that is highly improbable. The answer to this problem lies in an understanding of the mechanism of DNA replication at the enzyme level. We will return to this subject after first considering the enzymes involved in DNA synthesis. 

Figure 12.5 Hypothetical protein with four parallel helical strands, viewed from the end looking down the axis. Each circle represents a cross section through a hehx. Black regions are hydrophihc, gray areas are hydrophobic. Left protein in an aqueous environment such as body fluid or aqueous fixative. Right protein in hydrophobic solvent such as alcohol or clearing agent. Each helix has rotated around its own axis to bring hydrophobic realms outward.

There are two levels of self-assembly in the formation of tetra-, penta-and hexa-nuclear products from the poly-bipyridyls (L) 20 and 21 and iron(II) salts FeCl2, FeBr2 or FeS04 - the products are anion-dependent. The coordination of three bpy units, from different ligand molecules, to the Fe2+ centers produces a helical structure interaction of these helical strands with anions results in further molecular organization to form the final toroidal product. The discussion draws parallels between the helical and toroidal structures here and secondary and tertiary structure in biological systems (482). Thermodynamic and kinetic intermediates have been characterized in the self-assembly of a di-iron triple stranded helicate with bis(2,2/-bipyridyl) ligands (483). 

Binds to DNA and prevents separation of the helical strands Affects neuronal transmissions Binds to opiate receptors and blocks pain pathway Acts as central nervous system depressant Inhibits Na/K/ATPase, increases intracellular calcium, and increases ventricular contractibility Blocks the actions of histamine on Hi receptor Blocks ai-adrenergic receptor, resulting in decreased blood pressure Inhibits reuptake of 5-hydroxytryptamine (serotonin) into central nervous system neurons Inhibits cyclooxygenase, inhibition of inflammatory mediators Inhibits replication of viruses or tumor cells Inhibits HIV reverse transcriptase and DNA polymerase Antagonizes histamine effects... 

Tian SF, Toda S, Higashimo H and Matsumara S (1996) Glycation decreases the stability of the triple-helical strands of fibrous collagen against proteolytic degradation by pepsin in a specific temperature range. J Biochem 120, 1153-1162. 

In the case of DNA, Troisi and Orlandi [26] have completed an integrated molecular dynamics/electronic structure study that examines precisely the issue of the dependence of the matrix element on geometry. These investigators studied a ten-base-pair double helical strand, whose interior contained two GC base pairs separated by four AT base pairs. They placed... 

The bradykinin receptor is a member of a family of receptors for which an intracellular interaction with a G-protein is a critical part of the signal transduction pathway following agonist binding. Structurally, these G-protein-coupled receptors extend from beyond the extracellular boundary of the cell membrane into the cytoplasm. The tertiary structure is such that the protein crosses the bilayer of the cell membrane seven times, thus forming three intracellular loops, three extracellular loops, and giving rise to cytoplasmic C-terminal and extra-cellular N-terminal strands. It is generally presumed that the transmembrane domains of these receptors exist as a bundle of helical strands. This assumption is derived primarily from the known structure of the trans-membrane portions of a structurally related protein, bacteriorhodopsin [40]. 

Figure 13 illustrates the use of sedimentation equilibrium analysis to assess, in a complementary manner to SEC (see Section 13.2.5.3, Figures 11 and 12), whether the oligomerization state of a model coiled coil was responsive to single amino acid substitutions at one a position along the amphipathic a-helical strands. 

Fig. 23. Schematic representation of different possible types of ion channel structures (from left to right) stack, string, rack, pipe of macrocycles, helical strand, two half-channel units, self-aggregated and macrocycle core bearing bundles of chains.

Fig. 41. Schematic representation of the columnar triple-helical superstructure derived from the X-ray data for (LP2, LU2) each spot represents a PU or UP base pair spots of the same type belong to the same supramolecular strand the dimensions are compatible with an arrangement of the PTP and UTU components along the strands indicated (see also text) the aliphatic chains stick out of the cylinder, more or less perpendicularly to its axis a single helical strand and the full triple helix are respectively represented at the bottom and at the top of the column [9.152].

These considerations also apply to systems where binding involves interactions other than metal coordination, such as hydrogen bonding or donor-acceptor forces. Such is the case for the chiral selection occurring in the course of the self-assembly of homochiral helical strands (Section 9.4.2) and ribbons (Section 9.4.4) through hydrogen bonding. 

Fig. 1. Schematic diagram of (a) an intermediate filament heterodimer with coiled-coil domains 1A, IB, 2A, and 2B, and noncoiled-coil connecting linkers LI, L12, and L2. A stutter occurs in the heptad substructure at a point close to the center of segment 2B. The N-terminal globular domains (green for Type I and brown for Type II chains) are termed the heads, and the C-terminal domains (red for Type I and orange for Type II chains) are designated the tails. In (b), the heads are shown folded back over the rod domain, where it is believed that this will stabilize segment 1A. In (c), the heads are shown away from the body of the rod domain and in a position where they can interact more easily with other cellular entities. As a consequence, segment 1A may become destabilized and hence unwind to form two separate a-helical strands.

In many respects, the linker LI can be likened to a flexible hinge, a role consistent with a swinging head model proposed for IFs. In this model, segment 1A can (under appropriate conditions) split into two separate Q-helical strands, thereby maximizing the range of movement of the head domains and hence increasing their capacity to interact with various other cellular entities (Parry et al, 2002). 

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