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Linker region clustering

DNA-binding site specificity among the C -zinc cluster family of transcription factors is achieved by the linker regions... [Pg.190]

Subsequently Stephen Harrison s group determined the x-ray structure of a PPRl-DNA complex and showed that the zinc cluster domain of PPRl and its mode of binding to DNA was very similar to that of GAL4, and that PPRl also dimerized through a coiled-coil region. However, the linker region... [Pg.190]

When the second-site revertants were segregated from the original mutations, the bci complexes carrying a single mutation in the linker region of the Rieske protein had steady-state activities of 70-100% of wild-type levels and cytochrome b reduction rates that were approximately half that of the wild type. In all these mutants, the redox potential of the Rieske cluster was increased by about 70 mV compared to the wild type (51). Since the mutations are in residues that are in the flexible linker, at least 27 A away from the cluster, it is extremely unlikely that any of the mutations would have a direct effect on the redox potential of the cluster that would be observed in the water-soluble fragments. However, the mutations in the flexible linker will affect the mobility of the Rieske protein. Therefore, the effect of the mutations described is due to the interaction between the positional state of the Rieske protein and its electrochemical properties (i.e., the redox potential of the cluster). [Pg.112]

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. [Pg.111]

The other sub-cluster of H-L5-H exhibits a folded turn conformation with CO(i) to N-H(i+3) hydrogen bond in the linker region, quite different from the first sub-cluster. A third distinct sub-cluster has a helical conformation in the linker region. The E-L5-E linker has one large cluster and the second and third residues of the linker prefer mostly Or and the fourth residue conformations. The linker H-L5-E has a preference for main chain conformation to be cu for both the second and third residues and is non-specific for the other linker resicuies. Pro is found more often at the second position. The E-L5-H linker has no specific preference for main chain torsions at the first and fourth positions. However, L2 to L4 positions prefer Pe r r respectively. Our analyses on other linkers of less than eight residues are found to form similar clusters in the backbone conformational space. [Pg.676]

Our method of clustering based on a-carbon distances and in turn backbone and side chain torsions has demonstrated the existence of possible structural motifs within well defined linker regions. The method is not quite exhaustive to account for data outside the clusters and its limitadons arise due to non-standard way of defining limits of the clusters. Nevertheless, the method does seem to bring out the stmctural differences among various linkers. Our analyses on mainly -a proteins fiom the CATH database (results not shown here) has resulted in two major clusters of three residue linkers between helices (H-L3-H) and few of the helical proteins have same angle of orientation of helices within a cluster. We are yet to extend this observation to the unique data set of protein chains discussed in this paper. [Pg.677]

The conserved linker between repeats III and IV is critical for fast inactivation. Cleavage of the III-IV linkage causes a strong reduction in the rate of inactivation. A cluster of three hydrophobic residues (IFM) in the linker is an essential component, probably serving as a hydrophobic latch to stabilize the inactivated state. Other parts of the a subunit are also involved in fast inactivation. Conformational changes in the P region contribute to the slow inactivation process. [Pg.1306]

Structural Alignment of the Switch-1 and Switch-2 Regions of Kinesin Motor Domains with Secondary Structure Assignments and Classification of the Switch-2 Cluster and Neck/Neck Linker Conformations... [Pg.306]

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... 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...

See other pages where Linker region clustering is mentioned: [Pg.187]    [Pg.187]    [Pg.190]    [Pg.191]    [Pg.305]    [Pg.721]    [Pg.214]    [Pg.408]    [Pg.416]    [Pg.369]    [Pg.115]    [Pg.569]    [Pg.51]    [Pg.667]    [Pg.408]    [Pg.220]    [Pg.115]    [Pg.218]    [Pg.324]    [Pg.720]    [Pg.338]    [Pg.309]    [Pg.191]    [Pg.87]    [Pg.403]    [Pg.13]    [Pg.88]    [Pg.41]    [Pg.223]    [Pg.294]    [Pg.323]    [Pg.241]    [Pg.147]    [Pg.277]    [Pg.313]    [Pg.313]    [Pg.315]    [Pg.318]    [Pg.318]   
See also in sourсe #XX -- [ Pg.669 , Pg.677 ]




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Linker regions

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