Linker region four-residue linkers

Figure 1. Database of linkers of length two to eight residues flanked by different secondary structural regions. Note the large population of two to four residue linkers flanked by P-sheets.

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...

SNAP-25, a protein of 208 amino acids, deviates from the typical SNARE structure in that it has two SNARE motifs, joined by a flexible linker region, but lacks a transmembrane domain (Figure 1). The linker contains a cluster of four palmitoylated cysteine residues by which the protein is anchored at the plasma membrane. SNAP-25 can be phosphorylated at positions Thrl38 and Seri 87 by cAMP-dependent protein kinase (PKA) and protein kinase C (PKC), respectively. SNAP-25 represents a small subgroup of SNAREs with a similar structure, including SNAP-23, SNAP-29, and SNAP-47. In contrast to the neuron-specific SNAP-25 these SNAREs are ubiquitously expressed. 

Figure 11 Structural models of CNG channels in the closed and open states. The helix S6 and of the pore lumen of the transmembrane domain along with the N-term position of their C-linker are shown. Only the C alpha atoms of two opposite subunits (out of four) are shown forthe sake of clarity. Selected residues, for which experimental measurements were carried out, are shown, d is the shortest distance between opposite C alpha atoms in the pore. The blue box indentifies the narrowest region of the pore.

Figure 4.2 Self-assembling peptide amphiphiles (PA) used for biomimetic mineralization of HA/PA nanocomposite, (a) Chemical structure of the PA, comprising 5 regions (1) a hydrophobic alkyl tail (2) four cysteine residues that can form disulfide bonds to polymerize the self-assembled structure (3) a flexible linker region of three glycine residues (4) a single phosphorylated serine residue that was able to interact strongly with calcium ions and help direct mineralization of HA (5) the cell adhesion ligand ROD. (b) Molecular model of one single PA molecule, (c) Schematic showing the self-assembly of PA molecules into a cylindrical micelle.

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