Neck helix

The neck helix is roughly perpendicular to the central //-sheet. The construct ends with helix a6. 

Fig. 3. Conformation of the switch-2 cluster and neck linker/neck region in various members of the kinesin superfamily. The upper four panels (A, B, E, F) show crystal structures of N-type kinesins with their motor domain at the N-terminus and the neck at the C-terminus. (C), (D), (G), and (H) show C- and M-type kinesins with their neck N-terminal to the motor domain, except for PoKCBP (G) where the C-terminal neck mimic is shown instead of the N-terminal neck (which is not included in the crystal structure). Each structure is shown in two orientations that differ by a rotation of 90 degrees. Rat conventional kinesin (RnKHC [A]) has been chosen to define standard orientations with the neck helix a7 parallel/perpendicular to the drawing area. Orientations for the other structures have been determined by least-squares superposition of their P-loop regions with that of RnKHC (using 11 Ca-atoms of residues F83-T93 in RnKHC). (B), (C), and (D) show the structures of dimeric constructs with the second motor domain in pale colors. The Ned structure in (C) is 180-degree symmetric the symmetry axis is oblique to the drawing plane and coincides with the axis of the coiled-coil that is formed by the two neck helices. In the asymmetric structure of the Ned N600K mutant (D), the second motor domain (pale) is rotated by about 75 degrees around an axis perpendicular to the coiled-coil. The structures shown in (A), (B), (F), and (G) have their switch-2 cluster in permissive conformation, whereas the conformation of structures (C), (D), (E), and (H) is obstructive, as can be told by observing the slope of the extended switch-2 helix a4. Color code red, switch-2 cluster including the extended...

The structure of the kinesin monomer is classified into the three subdomains—head, neck-linker, and tail (see Figure I.IA). The head domain (residue 1-323) contains a nucleotide-binding pocket, a catalytic site, which controls the conformational state of the neck-linker (residue 324-338) made of 15 amino acids. The neck-helix domain (residues from 339 to the C-terminus), extended from the neck-linker, forms an alpha-helical structure dimeric kinesins are made via coiled-coil interactions between the neck-helices from two monomers (see Figure I.IA). 

FIGURE 1.1 (See color insert following page 172.) Kinesin and microtubule. (A) Conventional kinesins are homodimer, each of the monomer is made of head, neck-linker, and neck-helix domain. The neck-linkers of two heads are colored in green and yellow, respectively. The neck-helices from the two monomers associate the two subunits. (B) A microtubule with 13 protofilaments, each of which is made of an 8nm periodic head-to-taU alignment of the tubulin dimer subunits. A single protofilament that is used as a track for kinesin is colored in red. Kinesins take steps hand-over-hand along the protofilament. 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

The monomeric rat kinesin construct (amino acids 1-354) comprises the head domain (including the core motor domain, amino acids 2-325, and the neck linker, amino acids 326-338) and the first half of the neck domain. In the crystal structure, the neck linker consists of two strands, /19 and /110, that form hydrogen bonds with strands />8 and fJ7 of the core /1-sheet (Fig. 2E). The neck linker ends close to loop L10 at the tip of the core domain where the (a-helical neck domain (helix a7) is attached to the core motor domain. Its orientation is roughly in the plane of the core /1-sheet and perpendicular to the strands. 

C-type kinesins have a class-specific neck at the N-terminal side of their motor domain. In the case of DmNcd, the neck forms a continuous a-helix with the less conserved stalk. Constructs of the motor domain with a sufficiently long part of the neck dimerize by formation of a coiled-coil. 

Figure 34.26. Structure of Ned. The head domain of ned is quite similar to that of conventional kinesin, including the presence of a P-loop NTPase domain (shaded in purple). In the ADP form of ned (shovm), the amino-terminal part of this fragment forms an a-helix that docks into the site occupied by the neck linker in the ATP form of conventional kinesin.

A 500-ml. two-necked round-bottomed flask is attached to a distillation column (25 X 2 cm.) packed with Fenske helixes and fitted with a slow variable-reflux-ratio distillation head. One hundred milliliters of dry ethanol is placed in the flask, and 7.7 g. (0.335 mol) of sodium is added slowly. Then 31.5 g. (0.355 mol) of phenol dissolved in 50 ml. of ethanol is added and the mixture is boiled. The ethanol is... 

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