Helix lying

Fig. 3. (a) Helix-turn-helix motif of a DNA-binding protein (b) binding of the helix-tum-helix to target DNA showing the recognition helix lying in the major groove of the DNA. 

Answer A helical wheel is a two-dimensional representation of a helix obtained by projecting the helix down its central axis. An a helix contains 3.6 residues per turn, so each amino acid in the helix lies 100° around the axis from the previous residue (360°/turn)/(3.6 residues/tum) = 100° per residue. For the 18 amino acid helix considered here, the 18 vertices are separated by 20° increments. If there were a 19th residue, it would lie under the first residue on the projection, but five turns down the helix 5 turns X 0.54 nm/tum (pitch for an a helix) = 2.70 nm behind residue 1. To complete the diagram, follow the lines from residue 1 to residue 2, and so on, numbering the residues. Then, using the sequence given, label each residue with its one-letter abbreviation and a characterization of its R group properties—P for polar, and N for nonpolar. 

How does oxygen binding lead to the structural transition from the T state to the R state When the iron ion moves into the plane of the porphyrin, the histidine residue bound in the fifth coordination site moves with it. This histidine residue is part of an a helix, which also moves (Figure 10.22). The carboxyl terminal end of this a helix lies in the interface between the two a P dimers. Consequently, the structural transition at the iron ion is directly transmitted to the other subunits. The rearrangement of the dimer interface provides a pathway for communication between subunits, enabling the cooperative binding of oxygen. 

Figure 18.34. Components of the Proton-Conducting Unit of ATP Synthase. The c subunit consists of two a helices that span the membrane. An aspartic acid residue in the second helix lies on the center of the membrane. The structure of the a subunit has not yet been directly observed, but it appears to include two half-channels that allow protons to enter and pass partway but not completely through the membrane.

The L and M subunits form the structural and functional core of the bacterial photosynthetic reaction center (see Figure 19.9). Each of these homologous subunits contains five transmembrane helices. The H subunit, which has only one transmembrane helix, lies on the cytoplasmic side of the membrane. The cytochrome subunit, which contains four c-type hemes, lies on the opposite periplasmic side. Four bacteriochlorophyll b (BChl-Z>) molecules, two bacteriopheophytin b (BPh) molecules, two quinones (Q and Qg), and a ferrous ion are associated with the L and M subunits. 

Each base pair in the double helix lies in a plane that is perpendicular to the axis of the helix (Figure 23-6b). Adjacent pairs of bases in DNA are separated by 0.34 nm and rotated with respect to one another so that 10 base pairs occupy each turn of the helix, which repeats every 3.4 nm. 

In addition to the zinc-finger proteins, two other major classes of transcriptional factors are recognized, and these are depicted schematically in Figure 28.23. In the helix-tum-helix proteins, one helix (called the recognition helix) lies in the major groove of the DNA, its side chains making specific contacts with the DNA bases. 

The problem of the interaction of circularly polarized light with an a-helix lying flat on a surface is depicted in Figure 3. 

The situation is entirely different if the side chains adopt a p-sheet structure. Here, the AFM-pictures in the dry state and measured in solution reveal a helical conformation of the cylinder (Fig. 21). The pitch of the helix lies in the regime of 15-25 nm, which cannot be explained by helix formation on a molecular (i.e.. 

---