Topology orientability

Q. Zhu, P. von Dippe, W. Xing, D. Levy, Membrane Topology and Cell Surface Targeting of Microsomal Epoxide Hydrolase. Evidence for Multiple Topological Orientations , J. Biol. Chem. 1999, 274, 27898 - 27904. 

A comparison of the photobehavior of two crystals, 7-methoxycoumarin (19) and methyl m-bromo-cinnamate (20), exemplifies the importance of the need for the existence of free volume close to the reaction site [133-135]. Neither of these molecules is topologically oriented for efficient reaction in the crystal, meaning that the reactive pairs need to undergo some inter-molecular realignment before they can dimerize. 

Levy, D., Membrane proteins which exhibit multiple topological orientations. Essays Biochem 31 (1996) 49-60. 

Zhu, Q., von Dippe, P., Xing, W. and Levy, D., Membrane topology and cell surface targeting of microsomal epoxide hydrolase. Evidence for multiple topological orientations, J Biol Chem 274 (1999) 27898-27904. 

Schittny, J.C., Timpl, R. and Engel, J. (1988) High resolution immunoelectron microscopic localization of functional domains of laminin, nidogen, and heparan sulfate proteoglycan in epithelial basement membrane of mouse cornea reveals different topological orientations. J. Cell Biol. 107 1599-1610. 

Zamoon J, Mascioni A, Thomas DD, Veglia G (2003) NMR solution structure and topological orientation of monomeric phospholamban in dodecylphosphocholine micelles. Biophys J 85 2589-2598... 

Janas, T., and Troy, F. A., 1989, The Escherichia coli K1 poly-a-2,8-sialosyl sialytransferase is topologically oriented toward the cytoplasmic face of the inner membrane, in Proc. Xth International Symposium on Glycoconjugates, Vol. 142, (N. Sharon, H. Lis, D. Duksin, and I. Kahane, eds.), Organizing Committee Press, Jerusalem, pp. 207-208. 

The essential differences between sequential-modular and equation-oriented simulators are ia the stmcture of the computer programs (5) and ia the computer time that is required ia getting the solution to a problem. In sequential-modular simulators, at the top level, the executive program accepts iaput data, determines the dow-sheet topology, and derives and controls the calculation sequence for the unit operations ia the dow sheet. The executive then passes control to the unit operations level for the execution of each module. Here, specialized procedures for the unit operations Hbrary calculate mass and energy balances for a particular unit. FiaaHy, the executive and the unit operations level make frequent calls to the physical properties Hbrary level for the routine tasks, enthalpy calculations, and calculations of phase equiHbria and other stream properties. The bottom layer is usually transparent to the user, although it may take 60 to 80% of the calculation efforts. 

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

When topological strategies are used concurrently with other types of strategic guidance several benefits may result including (1) reduction of the time required to find excellent solutions (2) discovery of especially short or convergent synthetic routes (3) effective control of stereochemistry (4) orientational (regiochemical) selectivity (5) minimization of reactivity problems and (6) facilitation of crucial chemical steps. 

Two pictures of two spatial (three-dimensional) models can represent the same structural formula without representing the same stereoformula they describe the same structural formula if they exhibit the same relationships (if they are topologically congruent, i.e., they satisfy conditions (I), (II), (III)). In order to describe the same stereoformula they must display the same relationships and the same spatial orientation [they satisfy (I), (II), (III), and in addition (IV) (with A ), that is, be spatially congruent]. If two formulas viewed as stereoformulas are equal then they are certainly equal when they are treated as structural formulas. Consequently there are at least as many stereoisomers as there are structural isomers. This fact is reflected by (2.8). It is true particularly for paraffins and monosubstituted paraffins. 

Figure 46-8. Fusion of a vesicle with the plasma membrane preserves the orientation of any integral proteins embedded in the vesicle bilayer. Initially, the amino terminal of the protein faces the lumen, or inner cavity, of such a vesicle. After fusion, the amino terminal is on the exterior surface of the plasma membrane. That the orientation of the protein has not been reversed can be perceived by noting that the other end of the molecule, the carboxyl terminal, is always immersed in the cytoplasm. The lumen of a vesicle and the outside of the cell are topologically equivalent. (Re drawn and modified, with permission, from Lodish HF, Rothman JE The assembly of cell membranes. Sci Am [Jan] 1979 240 43.)...

Due to the Kohonen learning algorithm, the individual weight vectors in the Kohonen map are arranged and oriented in such a way that the structure of the input space, i.e. the topology is preserved as well as possible in the resulting... 

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