Domain rotation

Cobalt—chromium films (20 at. % Cr) exhibiting strong perpendicular anisotropy, ie, hexagonal i -axis normal to the substrate surface, have been studied (53). Fifty nanometer films are composed of columnar crystaUites and the domain size was found to be a few stmctural columns in diameter. Magnetization reversal was shown to occur by domain rotation in thick films. Thinner (ca 10-nm thick) films do not show the columnar crystaUite... 

The EO behavior is also clearly chiral a clockwise response to a force applied perpendicular to the clock face, with a counterclockwise response to a force of opposite orientation. Furthermore, domains of opposite handedness can also be seen in these LC cells. That is, while the brushes in some domains rotate counterclockwise in response to an applied field of positive sign, other domains rotate clockwise in response to the same field. The EO behavior of a pair of such domains is enantiomorphous, implying that the domains themselves are heterochiral. 

Phosphoryl transfer to asp351 allows dissociation of ADP, and then the N and P domain interface opens. The A domain rotates so that the TGES loop closes into the gap left by the loss of ADP. The A domain rotation, in turn, causes marked rearrangement in transmembrane hehces, opening the lumenal gate and releasing Ca " ions into the lumen. 

Figure 20.1. The magnetization process (a) demagnetized state (b) unsaturated state (c) saturated state. When an external magnetic field is applied, domain rotation and domain wall motion occur simultaneously or sequentially. Domain configuration can be found by minimizing the total energy related to magnetization. (From Ref 1, with permission from Elsevier.)...

The active-site cleft has a less open arrangement in renins than in the other aspartic proteinases. Many loops as well as the helix hc (residues 224-236) belonging to the C-domain (residues 190-302) are significantly closer to the active site in the renin structures compared to those of endothiapepsin-inhibitor complexes. This is partly due to a difference in relative position of the rigid body comprising the C-domain. For instance, there is a domain rotation of 4° and translation of 0.1 A in the human renin complex with respect to the endothiapepsin-difluorostatone complex. 

High resolution crystallographic studies have demonstrated that AspAT has open and closed conformations. Upon the binding of a substrate which favors the closed conformation, the small domain rotates so that the active site residues are brought closer to the substrate moiety. This movement of the small domain is important for initiation of the catalytic reaction. Therefore, the closed conformation is believed to represent the functional states of the enzyme.291 Three distinct crystal forms of mAspAT were analyzed, namely triclinic crystal for open conformation, monoclinic and orthorhombic crystals for closed conformation. The enzymes cocrystallized with substrate analogs seemed to have a tendency to assume the closed conformation.28 291 The order of this tendency was shown to be apoenzyme1 > PLP form of the enzyme > PMP form of the enzyme. 

This extrinsic domain movement is explained using a combination of two rotations (i) whole domain rotations against the rest of the complex and (ii) the relative rotations within the domain between base and cluster binding folds. Between these, the rotation of the whole domain is more prominent than the rotation within the domain. Therefore, as a first approximation, the conformational change of ISP is well described by rotation of the whole extrinsic domain. 

The conformational change in the N-lobe involves an opening of the binding cleft through relative movement of the two domains the N2 domain rotates 54° relative to Nl, about an axis passing through the... 

Stewart etal., FIg. 12. The interaction between the integrin proximal domain and the Adl2 penton base protein. (A) The integrin density is shown extracted along estimated boundaries to model the proximal domain of one integrin heterodimer and shown with the penton base and fiber. (B) The modeled proximal domain rotated to showtheinteractionwithasingle penton base protrusion. (G) The same view as in (B),but with the protrusion removed to reveal the RGD-binding cleft. The color scheme is the same as in Fig. 11. Scale bars 25 A. [Reproduced with permission from Chiu etal. (1999).]... 

Fig. 17.7 (a) STM image (40 nm x40 nm) and LEED pattern, and (b) top and side view structural model of the Nb Oj oxide film grown on Cu AuflOO). The STM image in (a) shows two domains rotated by 90°. The rhombic j3x-j3 R30° nit cell the niobia layer and the (2x7) super structure between oxygen and metal atoms are indicated. Adapted in part from [44] with permission. Copyright (2005) Elsevier... 

Domain rotation brings the protein into the closed form, excluding all the residual water molecules from the active site the combined effect of the metal positive charge and of the unshielded positive charge of the nicotinamide ring lowers the pAT of the coordinated alcohol below 7. A proton is expelled from the cavity, possibly via a hydrogen-bond network of protein residues. 

Figure 5. Schematic representation of the possible reaction mechanism of LdAdK Ado-induced domain rotation around the flexible diglycine motif (GIy-61-Gly-62) places the enzyme in precatalytic conformation. ATP binding causes further conformational changes, resulting in the initiation of a series of events in which Asp-299 first withdraws a proton from the 5 hydroxy group of Ado (solid line) followed by a direct nucleophilic attack on the y-phosphate of ATP (broken line). The resulting quinquivalent transition state is stabilized by Arg-131. Arg-131 also increases the electrophilicity (6+) of the y-phosphorus group. Reproduced with permission from Datta R et al, Biochem J 2005 387 591-600 2005 The Biochemical Society. ...

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