Structure-first models

These models start from the most comprehensive structural information available. Since there is no X-ray diffraction structure yet, this comes principally from polypeptide linear sequence data and deductions therefrom. Two major structural proposals (see Chapter 11) are from Zuber and colleagues (B800-850, B875, B1015) [31] and from Loach and co-workers (B875) [33]. A proposal based on a mix of structural and spectroscopic information comes from Kraimer et al. [34]. 

The Zuber model of B850 consists of a cyclic unit structure of (here considering pigments only) BChl pairs in C6 symmetry or possibly groups of 4 BChl molecules in C3 symmetry. Pearlstein and Zuber [35] have considered the conse- 

It was pointed out some time ago that many effects in optical spectra of this complex can be explained if it is assumed that the 3 molecules of Chi b form an exciton-coupled trimer with C3 symmetry, while the Chi a molecules are not so 

Qn the other hand, there seem to be no serious objections to the C3-symmetry model of the Chi b chromophores in Chi alb- 2. Even so, because less structural information is available for these complexes than for the bacterial antennas, one must accept the model cautiously. 

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Evaluating the structural kinetic model, we first consider the possibility of sustained oscillations. Starting with the simplest scenario, all saturation parameters are set to unity, corresponding to bilinear mass-action kinetics and... 

The first model was very simple. It is symmetrical with respect to the reactants and products and it violates the so called cut-off rules of Wolfsberg and Stem which state that atoms positioned two bonds away from the isotopic site should be included in the calculations (Wolfsberg and Stem, 1964 Stem and Wolfsberg, 1966). Ibis model was chosen so that a large number of calculations could be made rapidly. The second, more realistic, model using the reactants shown in reaction (45) was used to calculate the KIEs for certain selected transition state structures suggested by the simpler model. 

As previously discussed, the binuclear Cu(I) haemocyanins constitute another important class of dioxygen carriers. The first model compound whose structure in the oxygenated form resembles most closely that of oxyhaemocyanin is the dicopper(II) complex with the tris(3,5-diisopro-pylpyrazolyl)borate ligand shown in Figure 26.29... 

Although the effects of y-H2AX foci are still poorly understood, two theories have been proposed that may not be mutually exclusive [17,18], The first model suggests that the post-translational modification may impart structural transitions to DSB domains, and the second implicates the histone variant as a signaling intermediate in the repair pathway. 

Two models for the mechanism of the isomerization have been proposed. The first model was originally proposed because of similarities between enzymes involved in the activation of C-H bonds next to a carbonyl function (Fig. la). Stereochemical considerations were used to suggest that the ring structure of the sugar is opened to... 

Hr was the first binuclear iron protein for which a three-dimensional structure was determined and is the most extensively studied. Thus, the protein has become the standard of comparison for other binuclear iron proteins, with the inherent hazards of defining a class on the basis of one example. Indeed, recent crystal structures for model compounds and the RNRB2 subunit indicate some surprises and substantial diversity in the class. Nonetheless, the structure of Hr is an appropriate place to begin. 

The relationship between the structure of the oligopeptide sequences and the rate of enzymatically catalyzed release of a drug or drug model was studied in detail. Over 50 different oligopeptide sequences were introduced into HPMA copolymers and their degradability by different enzymes studied. First, model enzymes, chymotrypsin [235, 238,239, 243,244], trypsin [245], and papain... 

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