Conserved mode

Tong L, Qian C, Massariol MJ, Deziel R, Yoakim C, Lagace L (1998) Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease. Nat Struct Biol 5 819-826... 

The same process is then followed for the H2S section and in a somewhat conservative mode we simply add the bed requirements together to establish the design. There are occasionally requirements to remove mercaptans and even then some rather large ones. Type 5A can be chosen for some service and in the rare cases we may choose to us a NaX for large sulfur species. 

The complete W(E, J) is obtained by convolution of the contributions of conserved modes and transitional modes. For the charge-dipole potential, the transitional modes are the free-rotor modes of the ion and two perturbed rotor modes of the linear neutral fragment, only the latter being governed by... 

The role of cells residing within skeletal tissues is to maintain a balance between the processes of resorption and formation. When these two processes are essentially equal, a conservation-mode of remodeling exists... 

In addition to the specific recognition of a particular receptor peptide by TRAFs, a diverse set of receptor sequences may be recognized in a conserved mode of interaction by TRAFs. This ability of TRAFs to recognize diverse receptor sequences forms the basis for the wide spectrum of biological effects that TRAFs mediate. The molecular basis of this recognition resides on the conserved interaction of TRAFs with a few conserved key residues of receptor sequences rather than structural plasticity. 

Falck J, Coates J, Jackson SP. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage. Nature 2005 434(7033) 605-611. 

Each reactant state correlates with some state of the products along the potential. Vibrations and rotations that are similar in the reactant and product (conserved modes), remain in the same quantum state throughout the channel, in the sense that their quantum numbers remain the same throughout. Other modes that change between reactants and products (transitional modes), are subject to correlation rules. Channels with the same angular momentum are not permitted to cross, similar to the non-crossing rule in diatomic molecules. 

In the absence of a current precise knowledge of the potential energy surface, interpolations were used to obtain approximate normal mode frequencies for the conserved modes and methyl radical moments of inertia at intermediate R values, as described in Ref. 1 lc, using the interpolation g(R) specified by Eq. (2.13). The number of quantum states for the conserved modes [Nk in Eq. (2.10)] was obtained at each value of R by a direct count of the approximately harmonic levels. Calculations were made for two values of a in Ref. 1 lc, as reported below. The potential energy and structural parameters that determine V the conserved mode frequencies, and the moments of inertia are given in tables in Ref. 11c. 

For the calculation using Variflex, the number of a variational transition q uantum s tates, N ej, w as given b y t he v ariationally d etermined minimum in Nej (R), as a function of the bond length along the reaction coordinate R, which was calculated by the method developed by Wardlaw-Marcus [6, 7] and Klippenstein [8]. The basis of their methods involves a separation of modes into conserved and transitional modes. With this separation, one can evaluate the number of states by Monte Carlo integration for the convolution of the sum of vibrational quantum states for the conserved modes with the classical phase space density of states for the transitional modes. 

Under some circumstances (to be discussed in Part 12), vertebrate genomes evolve, however, according to a transitional, or shifting, mode, in which nucleotide substitutions are accompanied by compositional changes. Fig. 11.1 presents a scheme of the conservative mode of evolution and of the three kinds of eompositional transitions, or shifts, that we have observed. In Fig. 11.1 the distribution of DNA molecules is approximated by the... 

Figure 11.1. A schematic representation of A the major , B the minor , and C the whole-genome , or horizontal , compositional transitions, or shifts, in the genomes of vertebrates. This scheme displays the CsCI profiles (which are good approximations of the compositional distributions of DNA molecules) along with the changes that follow the compositional shift under consideration (broken lines). A refers to the transitions between cold- and warm-blooded vertebrates B to the transition between the general mammalian pattern and the murid pattern C to the transitions among cold-blooded vertebrates D to the conservative mode of evolution. (Modified from Bernardi et al., 1997).

Figure 12,2. A. Scheme of negative selection in the conservative mode of evolution. Isochores (solid lines) that drift beyond the GC thresholds indicated by the broken lines are counterselected. B. Scheme of negative and positive selection in the transitional or shifting mode of genomes evolution. Isochores (solid lines) with decreasing GC levels are counterselected, whereas those with increasing GC levels are selected for. (From...

Figure 12..1. A. scheme of Lhe conservative mode of compositional evoiulion of a GC-rich noncoding imergenie region from a warm-blooded vertebrate. The compositional optimum of the region is set at 55 Xi GC, The arbitrary ibresholds of the tolerated range are indicated by horizontal broken lines. Red and blue arrows lefei- to changes towards GC or AT. respectively. Thick arrows refer to critical changes (see...

In this version of VTST, there is no need to distinguish between transitional modes and conserved modes. All modes of the molecule can be treated as transitional, some changing toward product vibrations, others toward rotations. 

In the more complex dissociation of ethane into two methyl radicals, there are 12 conserved and 6 transitional modes. The conserved modes are associated with the CH stretch and bending motions of the two methyl fragments. The fate of the conserved and disappearing vibrational modes is shown in table 7.4. The 6 transitional modes for... 

The interaction potential V is anisotropic and depends on the relative orientation of the two fragments as well as their separation, R. The frequencies for the fragments, that is, the conserved modes, versus R have been determined by either interpolation between reactant and products frequencies (Wardlaw and Marcus, 1984, 1985, 1988), or by reaction path following (Aubanel and Wardlaw, 1989). 

CH3CH3 Modes Conserved Modes Attr. CHj Modes ... 

The transitional mode Hamiltonian is given by the last four terms in equation (7.36). In the work of Wardlaw and Marcus, the phase space volume for the transitional modes was calculated versus the center of mass separation R, so that R is assumed to be the reaction coordinate. In recent work, Klippenstein (1990, 1991) has considered a more complex reaction coordinate. The multidimensional phase space volume for the transitional modes can not be determined analytically, but must be evaluated numerically, for example, by a Monte Carlo method of integration (Wardlaw and Marcus, 1984). The density of states is then obtained by dividing the phase space volume by h", where n is the dimensionality of the integral, and differentiating with respect to the energy. The total sum of states of the transition state is obtained by convoluting the density of the transitional modes with the sum of the conserved modes, N(E,J) so that... 

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