Structural maps

In interphase, microtubules are stabilized by several kinds of proteins that are found all along microtubules and are called MAPs. They tend to have repeating domains, which allow each MAP molecule to associate with more than one tubulin dimer. This produces a doubly effective method of controlling assembly, in that the conformations of several tubulin dimers may be individually stabilized and the stabilized subunits are also cross-linked. The binding of these structural MAPs is in turn controlled by kinases and phosphatases (Cassimeris and Spittle, 2001). During mitosis they are phosphorylated and detach from tubulin, whose assembly and disassembly comes under the control of proteins that operate more at the ends of microtubules. Differentiated cells, such as neurons, do not divide. However, as microtubules and MAPs are slowly transported along axons (Baas and Buster, 2004), the MAPs maybe phosphorylated in particular places, at times when structural plasticity is required for making synapses or other contacts. 

Doublecortin is so named because its mutation leads to brain developmental disorders that can include the formation in the brain of a double cortex due to an additional band of aberrantly placed neurons. The 30-kD N-terminal domain of the protein binds to and stabilizes microtubules 

The structure of the N-terminal DCX domains has been solved to high resolution by NMR and X-ray crystallography (Fig. 7A). The domains have also been imaged bound to microtubules (Moores et aL, 2004), making doublecortin the only MAP, apart from tau and MAP2c (Al-Bassam et aL, 2002 Kar et aL, 2003a) to have been studied so far by 3D analysis of EM images. 

N-terminal domain binds only to microtubules, whereas the C-terminal domain binds to both microtubules and soluble tubulin dimers (Kim et al., 2003). The second domain might, therefore, be active only at a microtubule end. 

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The maps most frequently consulted in field development are structural maps and reservoir quality maps. Commonly a set of maps will be constructed for each drainage unit. 

Structural maps display the top (and sometimes the base) of the reservoir surface below the datum level. The depth values are always true vertical sub sea. One could say that the contours of structure maps provide a picture of the subsurface topography. They display the shape and extent of a hydrocarbon accumulation and indicate the dip and strike of the structure. The dip is defined as the angle of a plane with the horizontal, and Is perpendicular to the strike, which runs along the plane. 

Other information that can be obtained from such map is the location of faults, the status and location of wells and the location of the fluid contacts. Figure 5.45 shows some of the most frequently used map symbols. Structural maps are used in the planning of development activities such as well trajectories/targets and the estimation of reserves. 

Example of a structure map used to determine where oil is likely to be trapped. 

Specific applications of carbon-13 n.m.r. spectroscopy to the glycophorins, an important family of glycoproteins present in the human erythrocyte membrane, are discussed by K. Dill (Clemson), who demonstrates the value of C-n.m.r. spectra for the structural mapping of glycoproteins. 

Khoo, K.-H., Chatterjee, D., Caulfield, J.P., Morris, H.R. and Dell, A. (1997b) Structural mapping of the glycans from the egg glycoproteins of Schistosoma mansoni and Schistosoma japonicum. Identification of novel core structures and terminal sequences. Glycobiology 7, 663-677. 

Snyder, B., and Hammes, G.G. (1984) Structural mapping of chloroplast coupling factor. Biochemistry... 

Fig. 15 A molecular OR gate, whose chemical structure maps the electrical circuit diagram shown in Fig. 20a. Two Aviram-Ratner molecular rectifier chemical groups have been bonded to a central chemical node. This intramolecular circuit with one simple node can be easily designed, because the node Kirchoff node law is valid here. Note that the molecular orbital of each partner can be still identified on the 2 T(E) because of their weak interactions through the CH2 bridge. This is not always the case. The obtained logic surface demonstrates an OR function for well-selected values of the input voltage, but with two logical level 1 outputs which would have to be corrected using an additional output circuit...

Altogether, the identification of the coordinating residues in the endogenous hDAT Zn2+ binding site followed by the engineering artificial sites have defined an important series of structural constraints in this transporter. This includes not only a series of proximity relationships in the tertiary structure, but also secondary structure relationships. The data also provided information about the orientation of TM7 relative to TM8. A model of the TM7/8 microdomain that incorporates all these structural constraints is shown in Fig. 4 (36). The model is an important example of how structural inferences derived from a series of Zn2+ binding sites can provide sufficient information for at least an initial structural mapping of a selected protein domain. 

Notice, however, that in more recent papers, on the basis of a progressive improvement of the structure maps, slightly different versions of the chemical scale were reported without however any substantial modification to its meaning and application. 

A quantum-mechanical interpretation of Miedema s parameters has already been proposed by Chelikowsky and Phillips (1978). Extensions of the model to complex alloy systems have been considered. As an interesting application we may mention the discussion on the stabilities of ternary compounds presented by de Boer et al. (1988). In the case of the Heusler-type alloys XY2Z, for instance, the stability conditions with respect to mechanical mixtures of the same nominal composition (XY2+Z, X+Y2Z, XY+YZ, etc.) have been systematically examined and presented by means of diagrams. The Miedema s parameters, A t>, A ws1/3, moreover, have been used as variables for the construction of structural maps of intermetallic phases (Zunger 1981, Rajasekharan and Girgis 1983). 

Pettifor s structure maps additional remarks. We have seen that in a phenomenological approach to the systematics of the crystal structures (and of other phase properties) several types of coordinates, derived from physical atomic properties, have been used for the preparation of (two-, three-dimensional) stability maps. Differences, sums, ratios of properties such as electronegativities, atomic radii and valence-electron numbers have been used. These variables, however, as stressed, for instance, by Villars et al. (1989) do not always clearly differentiate between chemically different atoms. 

An empirical relation between band gap and Zunger s orbital electronegativity in s/ -bonded compounds has been determined by Makino (1994a) using a formula derived from the bond orbital model. Based on the bond orbital model and Zunger s orbital electronegativity, new structural maps of AB, AB2 and AB3 compounds between transition metals have been successfully constructed (Makino 1994b). 

Pettifor, D.G.(1995) Structure mapping. In Intermetallic Compounds-Principles and Practice, eds. Westbrook, J.H. and Fleischer, R.L. (John Wiley Sons Ltd., Chichester), Vol. 1, pp. 419-438. 

Annan R.S. and Carr S.A. (1997), The essential role of mass spectrometry in characterizing protein structure mapping posttranslational modifications, J. Protein Chem. 16(5), 391-402. 

Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers. 

It is emphasized that the final result is the structure map of the examined crystal rather than a pseudo structure map. This is because the difftaction intensities have been pushed towards the corresponding kinematical values during the calculation of partial structure factor in each cycle of the correction. In addition, in the final step, structure refinement by Fourier synthesis modifies the peak heights towards the true values to some extent. It is obvious that all the missing structure information due to the CTF zero transfer is mended after phase extension. The amplitudes are provided by the electron diffraction data, and the phases are derived from the phase extension. As a result, the resolution of the structure analysis by this method is determined by the electron diffraction resolution limit. 

Electron energy calculations now offer a coherent explanation of trends observed both across and down the periodic table and the grouping and overlaps observed in structure maps. Of particular importance are the marked changes that occur on moving to elements of higher atomic number, which means that some of the earlier assumptions concerning similarities of behaviour for compounds of the 3d, 4d, and 5d elements (Kaufman and Bernstein 1970) have had to be revised. Quantum... 

The problem of validation has been of long-term interest to the author. Ribbons (Carson, 1997) was presented as a visual sanity check of a structure, mapping properties of crystallographic interest to the ribbon drawing (Carson and Bugg, 1988). Residues were colour-coded by main-chain and... 

An approach based on orbital radii of atoms effectively rationalizes the structures of 565 AB solids (Zunger, 1981). The orbital radii derived from hard-core pseudopotentials provide a measure of the effective size of atomic cores as felt by the valence electrons. Linear combinations of orbital radii, which correspond to the Phillips structural indices and have been used as coordinates in constructing structure maps for AB solids. 

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