4- linker, rotational

The organic linkers can rotate freely in the solid MOF at ambient conditions. The energy barrier of a linker rotation along the connection axis is AE ai 0.35 eV (IRMOF-1). The rotation can, therefore, be thermally activated, which we also observed in MD simulations. These we have performed within NVT ensembles at 300 K and 1200 K. The nearly free rotation of the linker was already observed at 300 K. These simulations indicate also good thermal stability of the MOFs even at 1200 K. 

Fig. 7. Cross-linker model for nucleosome arrangement in the chromatin fiber superstructure in the presence (a) or absence (b) of H1/H5, based on data in the literature (see text) and H5-containing mono-nucleosome stem structure in Fig. 3(c). In 3D, the plane of the nucleosomes is expected to rotate more or less regularly around the fiber axis, forming a solenoid-like superstructure. Nucleosomes 1, 2 and 5 are in the open conformation of Fig. 3(a), nucleosomes 4 and 7 in the open conformation of Fig. 2(b), and other nucleosomes in the closed negative (Fig. 2(c)) or positive conformations. Nucleosomes are expected to thermally fiuctuate between the different conformations, within an overall dynamic equilibrium of (ALkn) -l (see text). -I- and - refer to node polarities. (From Fig. 5 in Ref. [28].)...

Since the linker DNA is assumed straight and the nucleosome non-deformable, the fiber geometry of the two-angle model is completely determined by the entry-exit angle of the linker DNA at each nucleosome and by the rotational angle... 

TV-acylpyrrolidine ring in S2 by a single methylene linker. This is a novel design and the candidate ligand appears to be more rigid than NAPAP, since it has a smaller number of rotatable bonds. Hence, the penalty paid for the loss in entropy upon binding should be smaller for this CCLD hit than for NAPAP. 

Figure 10.19 ATP-fueled rotation of fluorescently labeled actin that is attached to the y subunit of the F,-ATPase by a streptavidin-biotin linker. The /3 subunits are immobilized on a microscope slide. [Modified from H. Noji, R. Yasuda, M. Yoshida, and K. Kinosita, Nature 386,299 (1997).]...

N-terminals of the /3 subunits. At the other end, a cysteine residue was introduced into the exposed tip of the y subunit, which was coupled to biotin, and then attached to a fluorescently labeled actin filament via a streptavidin linker. The ATP-dependent anticlockwise rotation of the 1- to 3-p.m-long actin filaments was seen in a fluorescence microscope.94 Smaller probes show that the rotation is consistent with the turnover of ATP by the FrATPase, which is consistent with a three-step motor.95,96 This implies that ATP synthesis requires that the y subunit be cranked in a clockwise direction by a rotary motor in F,. 

The flexibility of the linker group was found to be responsible for the much lower effective rotational correlation time, consequently lower relaxivity of many different types of macromolecular agents. For dendrimers loaded with... 

Gd(III) chelates, the relatively low relaxivity is the consequence of the flexibility of the linker group between the Gd(III) chelate and the rigid dendrimer molecule (slow water exchange is also limitative). Internal flexibility has been also proved for certain non-covalently bound Gd(III) chelate - protein adducts. The tr value determined for MP-2269 bound to bovine serum albumin is 1.0 ns, one order of magnitude lower than the rotational correlation time of the protein molecule [50]. 

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...

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