Extended coiled-coil domain

Fi-ATPase has three a and three (I subunits arranged in alternation around the y subunit, which has a globular base and an extended coiled-coil domain (Fig. 1.10). All of the a and (1 subunits bind nucleotides, but only the three (1 subunits are catalytically active. The crystal structures of F1-ATPase provide views of distinct conformational states of the catalytic 3 subunits [30,35,36]. The centrally located and asymmetric y subunit forms a shaft, and it has been proposed that its orientation determines the conformations of the P subunits. The original crystal structure [30] of Fi-ATPase from bovine heart mitochondria led to the identification of three conformations of the P subunits Pg (empty), Prpp (ATP analog bound), and P p (ADP bound). In a more recent high-resolution crystal structure [35], the Prpp and Pqp subunits contain an ATP analog (ADP plus AIFJ) and the third catalytic... 

We saw in Chap. 1 that the random coil is characterized by a spherical domain for which the radius of gyration is a convenient size measure. As a tentative approach to extending the excluded volume concept to random coils, therefore, we write for the volume of the coil domain (subscript d) = (4/3) n r, and combining this result with Eq. (8.90), we obtain... 

While there is no structural information on coronin constructs that only contain the N-terminal WD repeat (propeller) domain, severe a tion has been reported for coronin 1 (lA) truncation mutants lacking the C-terminal extension and the coiled coil domain. The crystal structure of coronin 1 (1A) implies an eminendy important role of the C-terminal extension domain for the stability of the protein, especially for the residues direedy interactii with the p propeller. Appleton et aL have thus put forward the hypothesis that the region 1-392 of coronin 1 (lA), which comprises the WD repeat domain and the C-terminal extension, represents a folding unit, albeit this awaits experimental validation. Notably, a construct of coronin 3 (1C) extending from the last blade of the p propeller to the coiled coil domain (300-474), possesses secondary structure as predicted and thus appears to be folded. It still remains a matter of speculation, whether blade 7 adopts its native conformation within this construct because strand D is missing. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

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...

Taken together, these and other data indicate that the laminin molecule is composed of one A, one Bl, and one B2 chain (Fig. 9). The carboxyl terminus of each B chain extends down the long arm of laminin in a coiled-coil structure while the remainder of each chain forms a short arm. The A chain of laminin could also participate in such a coiled-coil structure, although this has not been shown and would require the alignment of a comparable a-helical domain in the A chain. However, the A chain is presumed to form one of the short arms and to extend through the molecule to form the globule at the end of the long arm of laminin. 

Figure 13. Model depicting the morphology at both (a) a long time and (b) following heat treatment. (A) partially extended soft segment (B) hard segment domain (C) hard segment (D) coiled or relaxedT soft segment (E) lower-order hard-segment domain (97).

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