Topological determinant

Internal Stop-Transfer and Signal-Anchor Sequences Determine Topology of Single-Pass Proteins... 

Lipid-Protein Interactions that Determine Topology... 

Schleiff, E., Tien, R., Salomon, M. and Soil, J., Lipid composition of outer leaflet of chloroplast outer envelope determines topology of OEP7, Molecular Biology of the Cell 12 (2001) 4090 102. 

As noted earlier (compare Table I), studies made using small prochiral substrates gave the first concrete indications that product configuration in some glycosylase-catalyzed reactions does not depend on that of the substrate but is determined topologically by protein structures which determine how incoming cosubstrates approach the catalytic center.26,32,36,45 4S... 

Since the Hiickel determinant contains only information about the number of unsaturated carbons and how they are connected together, it is sometimes referred to as a topological determinant. (Topology refers to properties that are due to the connectedness of a figure, but are unaffected by twisting, bending, etc.)... 

In the held of protein similarity May and Johnson have devised a GA for protein structure comparison.Their binary string GA encodes three translations and three rigid body rotations. On decoding an individual a transformation is generated to superimpose one protein on top of another. The htness function uses a dynamic programming technique to determine topological equivalences. 

The detailed consideration of these equations is due largely to Kozeny [50] the reader is also referred to Collins [51]. However, it is apparent that, subject to assumptions concerning the topology of the porous system, the determination of K provides an estimate of Ao- It should be remembered that Ao will be the external area of the particles and will not include internal area due to pores (note Ref. 52). Somewhat similar equations apply in the case of gas flow the reader is referred to Barrer [53] and Kraus and co-workers [54]. 

For states of different symmetry, to first order the terms AW and W[2 are independent. When they both go to zero, there is a conical intersection. To connect this to Section III.C, take Qq to be at the conical intersection. The gradient difference vector in Eq. f75) is then a linear combination of the symmetric modes, while the non-adiabatic coupling vector inEq. (76) is a linear combination of the appropriate nonsymmetric modes. States of the same symmetry may also foiiti a conical intersection. In this case it is, however, not possible to say a priori which modes are responsible for the coupling. All totally symmetric modes may couple on- or off-diagonal, and the magnitudes of the coupling determine the topology. 

Gelemter and Rose [25] used machine learning techniques Chapter IX, Section 1.1 of the Handbook) to analyze the reaction center. Based on the functionalities attached to the reaction center, the method of conceptual clustering derived the features a reaction needed to possess for it to be assigned to a certain reaction type. A drawback of this approach was that it only used topological features, the functional groups at the reaction center, and its immediate environment, and did not consider the physicochemical effects which are so important for determining a reaction mechanism and thus a reaction type. 

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

In this chapter the symmetry properties of atomie, hybrid, and moleeular orbitals are treated. It is important to keep in mind that both symmetry and eharaeteristies of orbital energetics and bonding "topology", as embodied in the orbital energies themselyes and the interaetions (i.e., hj yalues) among the orbitals, are inyolyed in determining the pattern of moleeular orbitals that arise in a partieular moleeule. 

Molecular descriptors must then be computed. Any numerical value that describes the molecule could be used. Many descriptors are obtained from molecular mechanics or semiempirical calculations. Energies, population analysis, and vibrational frequency analysis with its associated thermodynamic quantities are often obtained this way. Ah initio results can be used reliably, but are often avoided due to the large amount of computation necessary. The largest percentage of descriptors are easily determined values, such as molecular weights, topological indexes, moments of inertia, and so on. Table 30.1 lists some of the descriptors that have been found to be useful in previous studies. These are discussed in more detail in the review articles listed in the bibliography. 

Earhest simulators determined the sequence of the calculations for the vatious unit operations from the expHcit iaput from the engineer or from the sequeace ia which the topological information about unit operations was entered. AH simulators today analyze the topology automatically and determine the sequence. Most of them, however, allow the user to alter this sequence through various techniques of creating hypothetical calculation units of convergence, recycle, and control blocks or units. 

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 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

The structures of many different plant, insect, and animal spherical viruses have now been determined to high resolution, and in most of them the subunit structures have the same jelly roll topology. However, a very different fold of the subunit was found in bacteriophage MS2, whose structure was determined to 3 A resolution by Karin Valegard in the laboratory of Lars Liljas, Uppsala. 

The major factors that determine the optimum choice of topology are ... 

This is eompletely determined by the topology previously ehosen. 

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