Domain of Representation

Rajan, Linking the Behavioral and Structural Domains of Representation , IEEE Trans, on CAD, pages 103-110, January 1987. 

Figure 2-1. The Workbench Model of Design Representation 2.1.1 Domains of Representation...

Figure 15.19 Schematic representation of the peptide-binding domain of a class I MHC protein. The al and a2 domains are viewed from the top of the molecule, showing the empty antigen-binding site as well as the surface that is contacted by a T-cell receptor. (Adapted from P.J. Bjdrkman et al.. Nature 329 506-512, 1987.)...

FIGURE 1.11 Three -dimensional spacefilling representation of part of a protein molecule, the antigen-binding domain of immunoglobulin G (IgG). Immunoglobulin G is a major type of circulating antibody. Each of the spheres represents an atom in the structure. 

A thonght experiment was inclnded earlier that illnstrated how the complexity of a representation may appear very different depending npon the relative expertise of the perceiver within the relevant domain of knowledge. Consider the following task Complete the following chemical eqnation ... 

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

Fig. 8. (a) Structure of the full-length Rieske protein from bovine heart mitochondrial bci complex. The catalytic domain is connected to the transmembrane helix by a flexible linker, (b) Superposition of the three positional states of the catalytic domain of the Rieske protein observed in different crystal forms. The ci state is shown in white, the intermediate state in gray, and the b state in black. Cytochrome b consists of eight transmembrane helices and contains two heme centers, heme and Sh-Cytochrome c i has a water-soluble catalytic domain containing heme c i and is anchored by a C-terminal transmembrane helix. The heme groups are shown as wireframes, the iron atoms as well as the Rieske cluster in the three states as space-filling representations. 

Figure 41-9. Diagrammatic representation of the structures of two ion channels. The Roman numerals indicate the four subunits of each channel and the Arabic numerals the a-helical transmembrane domains of each subunit. The actual pores through which the ions pass are not shown but are formed by apposition of the various subunits. The specific areas of the subunits involved in the opening and closing of the channels are also not indicated. (After WKCatterall. Modified and reproduced from Hall ZW An Introduction to Molecular Neurobiology. Sinauer, 1992.)...

Figure 48-3. Schematic representation of fibronectin. Seven functional domains of fibronectin are represented two different types of domain for heparin, cell-binding, and fibrin are shown. The domains are composed of various combinations of three structural motifs (I, II, and III), not depicted in the figure. Also not shown is the fact that fibronectin is a dimer joined by disulfide bridges near the carboxyl terminals of the monomers. The approximate location of the RGD sequence of fibronectin, which interacts with a variety of fibronectin integrin receptors on cell surfaces, is indicated by the arrow. (Redrawn after Yamada KM Adhesive recognition sequences.

To solve the problems of representation and control, we will employ the framework of the branch-and-bound algorithm, which has been used to solve many types of combinatorial optimization problems, in chemical engineering, other domains of engineering, and a broad range of management problems. Specifically, we will use the framework proposed by Ibaraki (1978), which is characterized by the following features ... 

Figure 11 Diagrammatic representation of the tomato Bsubunit gene family members and related cDNAs in Arabidopsis thaliana. The four domains of the respective precursor proteins are coded as in Figure 4. The large triangles represent introns. Y s represent the position of glycosylation consensus sequences. Tomato Gene 1 is the fruit Bsubunit cDNA. Percentages underneath each mature and carboxyl domain indicate the respective identity to the mature and carboxyl domains of Tomato Gene 1.

For any symmetry operator T = T 0) (rewritten r when operating on the domain of basis functions x)) for instance, the rotation-reflexion about the z-axis, with matrix representation... 

Figure 4.8 (a) Representation of a magnetic chain in its ordered state, (b) The creation of a domain of reversed spins costs four times the exchange interaction, assuming unitary length for the spins, (c) If the reverse domain... 

The Fourier transform allows the mathematical conversion between the time domain and the frequency domain of a spectrum. The names for these domains refer to the x-axis of their conventional graphical representations. Figure 5.21 illustrates how these are important in terms of conventional spectra. Importantly, the time and the frequency domains contain exactly the same information. 

As a starting point in the description of the solid intermetallic phases it is useful to recall that their identification and classification requires information about their chemical composition and structure. To be consistent with other fields of descriptive chemistry, this information should be included in specific chemical and structural formulae built up according to well-defined rules. This task, however, in the specific domain of the intermetallic phases, or more generally in the area of solid-state chemistry, is much more complicated than for other chemical compounds. This complexity is related both to the chemical characteristics (formation of variable composition phases) and to the structural properties, since the intermetallic compounds are generally non-molecular in nature, while the conventional chemical symbolism has been mainly developed for the representation of molecular units. As a consequence there is no complete, or generally accepted, method of representing the formulae of intermetallic compounds. 

Fig. 12.4. CUE and UIM bind to the same site terminal UIM of Vps27 [79]. In both panels, on ubiquitin. Schematic representation of (A) ubiquitin is rendered in darker colour and the ubiquitin in complex with the CUE domain of position of Lys-48 is indicated.

Equation (18.4) is completely equivalent to Eq. (18.11) in the time domain. Equation 18.5 is equivalent to Eq. (18.12) in the Laplace domain. Equation (18.6) is equivalent to Eq. (18.13) in the frequency domain. We will use these alternative forms of representation in several ways later. 

Fig. 2. The P4-P6-domain of the group I intron of Tetrahymena thermophila. A Schematic representation of the secondary structure of the whole self-cleaving intron (modified after Cate et al. [34]). The labels for the paired regions P4 to P6 are indicated. The grey shaded region indicate the phylogenetically conserved catalytic core. The portion of the ribozyme that was crystallized is framed. B Three dimensional structure of the P4-P6 domain. Helices of the PSabc extension are packed against helices of the conserved core due to a bend of approximately 150° at one end of the molecule...

Fig. 9.17 Examples of self-assembly of nanoparticles by a) hydrophobic interactions via a shell of unfunctionalized n-alkanes. Depicted is a Schematic 2D Representation of the RS/ Au nanoparticle packing structure in the solid state. Domains or bundles of ordered al-kylthiolate chains on Au particles interdigitate into the chain domains of adjacent particles in order to compensate the free volume of the outer region of the alkyl shell (Reprinted with permission from [146] A. Badia, L. Cuc-cia, L. Demers, et al.,J. Am. Chem. Soc. 1997, 779, 2582-2592. Copyright 1997 American Chemical Society), b) Direct comparison of hydrophobic interactions and chemical bridg-...

Figure 12.2 is a graphic representation of a portion of two-dimensional factor space associated with the system shown in Figure 12.1. In this illustration, the domain of factor (the horizontal axis ) lies between 0 and +10 similarly, the domain of factor X2 (the vertical axis ) lies between 0 and +10. The response axis is not shown in this representation, although it might be imagined to rise perpendicularly from the intersection of the factor axes (at jCj = 0, X2 = 0). Figure 12.2 shows the location in factor space of a single experiment at jc, = +3, X21 = +7.

Fig. 13. Schematic representation of the overall NOS architecture and summary of work presented in 139). Heterodimers were generated to test if electron transfer from the FMN domain proceeds via an inter- or intrasubunit process. When holo-NOS containing an inactive heme domain was dimerized with an active heme domain, activity was observed. However, when active holo-NOS was dimerized with the inactive heme domain, no activity was observed. These results indicate that the flavin domain of monomer A transfers electrons to the heme domain of monomer B.

Figure 2.1 Structures of histone acetyltransferases (HATs). Ribbon representation of the structures of the HAT domains of (a) Tetrahymena thermophila CcnS (PDBcode Iqsr), (b) Saccharomyces cerevisiae Hatl (PDB code Ibob), (c) S. cerevisiae Esal (PDB code Imja),...

Figure 2.2 Structures of CcnS histone acetyltransferase (HAT) bound to coenzymeA and various peptides. Schematic representation of Tetrahymena thermophiia CcnS HAT domain (ribbon representation) bound to coenzymeA and 19mers (both shown as ball and sticks) from (a) histone H3 (PDB code lpu9),...

Figure 2.3 Structures of mammalian classic histone deacetylases. Ribbon representation of the conserved catalytic domain of (a) class I human HDAC8 in complex with trichostatin A (TSA PDB code lt64), (b) human HDAC8 Tyr306Phe inactive mutant in complex with a peptidic acetyl-lysine substrate (PDB code 2v5w), (c) class I la human...

Figure 2.4 Structures of histone deacetylases from the sirtuin family. Ribbon representation of the structures of the conserved catalytic domain of histone deacetylases (a) Homo sapiens SirT2 (PDB code IjSf) and (b) Thermotoga maritima Sir2 bound to NAD and an acetylated p53 peptide (PDB code 2h4f).

---