Domain type

Maximum coercive force, HJmT Shape Stress Crystal 

For all three types of anisotropy the coercivity can be calculated (Tab. 7.7). For SD magnetite and maghemite, shape anisotropy, dominates over strain and crystal anisotropy, whereas for hematite and goethite, morphology has little influence on coer-civity. 

Whether a phase displays SD, PSD orMD behaviour, can be determined from the shape of its hysteresis loop. In MD particles the Bloch walls can be moved by lower energies than the directions of magnetization in SD particles. The hysteresis loops of MD particles, therefore, are much narrower than those of SD particles (Fig. 7.12). For ferrimagnetic phases, the ratios Jrs/Js and Har/Hc (Fig. 7.9) (Day et al., 1977) can be used to distinguish between SD, PSD, and MD particles (Fig. 7.12, right). It should be kept in mind, however, that the coercive forces also depend on particle morphology. Calculations by Butler and Banerjee (1975) show that deviations from the rounded isometric shape towards elongated needles stabilize the SD behaviour and even SP particles may become SD (Fig. 7.13). 

An alternative way of identifying the domain state of magnetite utilizes the dependence of both the crystal and strain anisotropy constants on temperature. Kj of eq. (7.2) is negative at RTand becomes positive at -118 K, which is the so-called Ver-wey transition at which the crystal anisotropy vanishes and any original remanence, which is controlled by this anisotropy, is lost. This provides an easy test for the do- 

90 600 (xm particles in Fig. 7.14). Since the Verwey transition is unique for magnetite, it can be used for distinguishing magnetite from maghemite or greigite, neither of which shows such a transition. 

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Chemical dimensions (dimensions in the sample domain) type (Q), number (n) and amount (x) of analytes, i.e. distinct chemical species see Fig. 2.12 (left)... 

The loss of phase complexity in both systems may be attributed to an increase of the PS/PEO and PI/PEO interaction parameters. Because LiClC is selectively located in the PEO domains, the interaction parameters (/ps-peo and xpi-peo ) must increase, leading to variations in domain type and dimension. As the lithium salt increases the polarity (and presumably the solubility parameters) of the PEO domains, the interfacial tensions between PEO and PI, and PEO and PS are elevated. Thus, a reduction in the overall PEO interfacial area is required, which necessitates additional chain stretching. In consequence, the CSC structure becomes dominant when comparing doped and non-doped samples [171] (Figs. 54 and 55b). 

Domain Types, actions, Attributes, associations, refinements,... 

Although domains are often mobile and occur in many different modular architectures, it is notable that the co-occurrence of domains within single polypeptides is far from random, since a domain is usually found to co-occur only with a small subset of all domain types. When two domain types are not observed within the same molecule, it is likely that their activities are antagonistic, thereby effectively neutralizing the overall function of the molecule. Such an example is provided by protein kinase and phosphatase domains that are not currently known to cooccur within the same molecule. However, the reasons that functionally distinct and otherwise widespread domains have never yet been found together, such as signaling PDZ and SH2 domains, remains elusive. 

The CUE domain s propensity to bind ubiquitin was a quite recent discovery, and relatively little is known about its physiological role. Nevertheless, structural work done on this domain type has been instrumental for our understanding of ubiquitin recognition in general. Two independently solved structures of different CUE domains have been reported, both in isolation and in complex with ubiquitin [64, 65]. The NMR structure of the first CUE domain of the uncharacterized budding yeast protein Cue2 shows a three-helix bundle fold resembling that of the... 

In this respect, the CUE domain is not a isolated case. There are a number of other domain families, each of them only defined in the bioinformatical sense, that have significant matches within established UBA or CUE domain regions. Based on this similarity and on secondary-structure predictions, it can be expected that all of those domain types assume the typical UBA-like three-helix bundle fold. However, it is not clear if all of those domains also bind to ubiquitin, or if they have evolved to different binding properties. Many of the UBA-like domain classes are unpublished. Nevertheless, they should be briefly discussed here, as they are a logical extension of the UBA/CUE paradigm. 

Type XVI collagen is composed of 10 collagenous domains (COLI-COLIO) flanked by 11 NC domains. Type XVI collagen localizes near the dermal-epidermal junction. From immunoelectron microscopy of the papillary dermis, type XVI collagen associates with a fibrillin-1-containing matrix but not on collagen fibrils. ... 

Tab. 7.7 Maximum coercive force for natural single domain phases with different types of anisotropy and their critical diameter, dcrit, for the transition from single domain to pseudo-single domain type (from Soffel, 1991 with permission)...

The textures in homeotropic lamellar phases of lecithin are studied in lecithin-water phases by polarizing microscopy and in dried phases by electron microscopy. In the former, we observe the La phase (the chains are liquid, the polar heads disordered)—the texture displays classical FriedeVs oily streaks, which we interpret as clusters of parallel dislocations whose core is split in two disclinations of opposite sign, with a transversal instability of the confocal domain type. In the latter case, the nature of the lamellar phase is less understood. However, the elementary defects (negative staining) are quenched from the La phase they are dislocations or Grandjean terraces, where the same transversal instability can occur. We also observed dislocations with an extended core these defects seem typical of the phase in the electron microscope. 

Domain.]Type.Mnemonic[.Derived].Description.Refinement[.Attributes],... 

The actual shape analysis can be carried out on the "isolated" fragment density contour G(a), where one additional domain type is introduced. These domains represent the connection of fragment A to the rest of the molecule within the actual AB system ... 

Fig. 24. Composite LEED pattern for the FeCrNi(lll) surface exposed to electrolytes and annealed. Type 1 integral-index beams due to alloy. Type 2 pattern-of-twelve beams due to square CrO mesh. Type 3 beams due to initial growth phase of oxide with (2 x 2) local structure in (11 x 11) domains. Type 4 beams due to Cr203(001) film. The alloy contained Fe (70at.%), Cr (18at.%), and Ni (12at.%). Reprinted from ref. 54.

The standard Shape Group Method is applicable for the analysis of the entire series of non-interacting RIDCOs, for a whole range of density thresholds a, with the provision of an additional domain type representing the connection of region R to the rest of the molecule within the actual RM system. This additional domain type D i is defined as... 

Using this approach, new local domain types appear at those locations of the molecular electron density where the region R connects to the rest M of the molecule RM = M ... 

Fig. 6.6 Cytokine receptors have on their extracellular side a variety of different structural domains. Type I receptors have fibronectin-like domains, type III receptors have cysteine-rich domains, and type IV receptors have immunoglobulin-like regions. Type I receptors have intracellular, membrane-proximal Box 1 and Box 2 regions, which are docking sites for the JAK2 tyrosine kinase with which type I receptors primarily associate. (Reproduced from Fig. lA. p. 252 of ref. 33, with permission of Professor Taniguchi and Science.)...

The struetures of eight flavoprotein electron transfer complexes will be examined (Table 1). Four of these involve flavin to heme electron transfer, three involve electron transfer between flavin and an iron-sulfur center and one involves flavin to flavin electron transfer. These eomplexes provide a variety of domain types and arrangements, cofactor types and interdomain interaetions that can help define the factors important for the electron... 

At this writing, the three-dimensional sttuctures of eight different naturally occurring type 1 copper proteins are known. These include the cupredoxins plastocyanin at 1.33 A resolution (pdb code 1 PTC), azurin at 1.8 A (pdb code 2AZA), pseudoazurin at 1.55 A (pdb code IPAZ), amicyanin at 1.3 A (pdb code lAAC), auracyanin at 1.55 A (pdb code IQHQ), rusticyanin at 1.9 A (pdb code IRCY), and the phytocyanins cucumber basic protein at 1.8 A (pdb code2CBP), and stellacyanin at 1.6 A (pdb code IJER) Atomic coordinates for these and all other single-domain type 1 copper proteins are available from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) and can be accessed online at www.rcsb.org/pdb/. 

The fold of the serine protease domain-type was described in Section V.C. SCP is more like o-lytic protease (Fujinaga et al, 1985) than a-chymotrypsin (Matthews et al, 1967), but with loops that are even shorter (Fig. 4 see Color Insert). Unlike the other proteases, there are no disulfide bonds. The structure of the C terminus is completely different from either of the other two proteases, and it leaves the final three amino acids in the active site. These superimpose on the structure of a peptide inhibitor determined as a complex with o-lytic protease (Bone et al, 1987). This indicates that the N-terminal product of the autocatalytic lysis of... 

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