Domain approximation

Figure 1. Coronin domain organization and protein structure. A) Schematic of coronin domain organization. The p-propeller domain is approximately 400 residues in length and comprised of seven repeats (5 WD repeats and 2 unconventional repeats numbered and colored) flanked by short N- and C-terminal extensions (open). This is followed by the unique region (highly variable in sequence and length) and coiled-coil domain (approximately 35-50 residues in length). B) Crystal structures of mouse Coronin lA p-propeller domain (Appleton et al 2006/ PDB accession number 2AQ5) and coiled-coil domain (Kammerer et al 2005, PDB accession number 2AKF). The blades of the p-propeller are color-coded to match the schematic in A. The C-terminal extension (dark grey) associates with the underside of the blades. The coiled-coil domain of Coronin 1A (shown) forms parallel trimers, whereas the coiled-coil domains of some other coronins form dimers. N, amino terminus.

Such a tunnel switching of the magnetization can be described by the so-called one-domain approximation, when the total magnetization vector M is taken as a main dynamic variable with fixed absolute value M. Then the total energy density, or the anisotropy energy E, is obtained from the spin-Hamiltonian H using a spin coherent state n) chosen along the direction n [332,333] ... 

Fig. 1. Domain structure of ICAM-1. Each Ig domain is represented schematically by a circle closed by one or two disulfide bonds. Amino acid numbers indicate the beginning and end of each domain. Approximate locations of relevant binding sites are shown. Lollipop-shaped structures indicate N-linked glycosylation sites.

In the Fc of IgG [9,23] the two CH3 domains are paired in a pattern similar to that found for the CH1-CL interaction (Fig. 6). The two CH2 domains show no close interaction but have interposed between them two branched N-linked carbohydrate chains which make little contact between one another in human Fc [23] but more extensive contact in rabbit Fc [30]. In the pairing of the CH3 domains, approximately 1000 A2 of surface per domain is involved in the interaction. In the Ch2 case the carbohydrate provides a substitute for the domain-domain contact and helps to stabilise the CH2 domain. However, the CH2-carbohydrate contact area is only about half that of, for example, the CH3-CH3 contact so that one might expect a lower inherent stability for the CH2 domain. Indeed the CH2 domain is more sensitive to proteolytic degradation than the other domains of IgG [24], Domain stability has also been related to the apparent softness of parts of the CH2 domain most remote from the CH2-CH3 interface as indicated by large temperature factors or missing electron density in the crystal analysis of human Fc [23]. A corresponding softness has not, however, been found for rabbit Fc (Sutton B.J., personal communication). Tables 1 and 2 show a comparison of known CH3 and CH2 sequences. 

Under the diffusion domain approximation [1, 14, 17, 18], the hexagonal unit cell is approximated as a cylindrical cell of the same base area as shown in Figure 10.3. 

Previous studies have demonstrated that the results of simulations using the diffusion domain approximation show very good agreement with experiments [19]. 

As with the isolated microdisc simulations in Chapter 9, we here consider the simulation of the cyclic voltammetry of a simple fully reversible one-electron reduction. For an array, since each unit cell is identical, the concentrations of the electroactive species will necessarily be the same on either side of the cell boundary and there can be no flux of electroactive material across the boundary. After using the diffusion domain approximation, this boundary is at a distance r = Vd, therefore... 

Voronoi cells (b) diffusion domain approximation used to transform a Voronoi cell into a cylindrical cell of equivalent base area. 

In the same maimer as for the regularly distributed array, we can use the diffusion domain approximation to transform each Voronoi cell into a cyhndrical cell of the same base area, A , and of radius rd , as illustrated in Figure 10.6(b), thus reducing the problem of simulating each cell from... 

The area of a polymer domain approximates the proportion of the polymer volume in the blend. 

Alpha-Actinin is a rod-like (3-4 nmx 30-40 nm) cytoskeletal protein belonging to the same family as spectrin, dystrophin and utrophin. a-Actinin is a homodimer with a subunit molecular weight of 94-103 kDa in which the subunits are antiparallel in orientation. The molecule can be devised into three domains, an N-terminal actin binding domain (approximately residues 1-245), four internal 120 residue repeats, and a C-terminal region containing two EF-hand Ca -binding motifs (Baron et al. 1987, Blanchard et al. 1989). Apart from actin, a-actinin has been reported to bind to the cytoskel-... 

Closely packed but nonoverlapped chains fiilly occupy a polymer solution at c, and so the concentration of segments inside any one chain domain approximately matches the solution s bulk segment concentration. The value of c thus can be estimated as the ratio of M to the average volume pervaded by a chain in dilute solution. Ignoring unimportant order unity geometric prefactors. 

The correctness of the edge plane activity model for HOPG electrode kinetics is best justified by the close correlation of experiment and two-dimensional simulated voltammetry, using the diffusion domain approximation. 

---