Conformational adaptation

Fig. 24. Calculation of the conformational energy of Valinomycin as a function of the size of the polar core which contains the ion. This uses the structure of Fig. 20. The verticle lines are the optimal core sizes for the indicated ions. Based on the conformational energy component, selectivity for K+ and Rb+ would be similar and Cs+ less favored. Na+ is off the curve suggesting that this conformation cannot form a polar core small enough to complex Na+ by means of this conformation. Adapted with permission from Ref.

The above results proved the potential viability of the adsorbed hydrophilic macromolecules as bonded phases in chromatography of biopolymers but it must be admitted that additional crosslinking of previously adsorbed macromolecules is usually needed in order to obtain stable composites. The cross-linked bonded polymeric phases, however, may suffer from the restricted flexibility of the chain segment and their steric repellency may be diminished. Moreover, the conformational adaptivity of cross-linked chains for binding with solutes is poorer than that of grafted or chemically bound macromolecules. 

The notion that the segment containing C3 and T3 is important for conformational adaptability of the protein is supported by mutations in yeast. Mutations of the genes of the H-ATPase of Saccharomyces cerevisiae resulted in a thermo-sensitive... 

Some forms of rings and chains of vertex-sharing tetrahedra in silicates. How the chain conformations adapt to the size of the cation octahedra is shown for two chains (the octahedron chain is a section of a layer)... 

Kellershohn N, Laurent M. Species barrier in prion diseases a kinetic interpretation based on the conformational adaptation of the prion protein. Biochem J 1998 334 539-545. 

When a penetrant diffuses into a polymer, the perturbation will cause the polymer molecules to rearrange to a new conformational state. The rate at which this conformational adaptation occurs depends on the mobility of the polymer chains. At temperatures well above the glass transition, this occurs quite rapidly and the diffusive process resembles that in the liquid state. At temperatures near or below the glass transition, the conformational change does not take place instantaneously. Instead, there is a finite rate of polymer relaxation induced by the... 

Fig. B9.1.1. Distance distribution of a triantennary glycopeptide reflecting the multiple conformations (adapted from Wu et al. ).

Figure 12.16 Our calculated Raman spectra of two conformers of the hexyl [C5CjIm]+ cation between 750 and 500 cm i (a) AAAA and (b) GAAA conformers. (Adapted from Berg, R. W., Deetlefs, M., Seddon, K. R., Shim, L, and Thompson, J. M., /. Phys. Chem. B, 109, 19018-19025, 2005. With permission.)...

These conclusions are still consistent with the finding that significant conformational differences between Pr and Pfr do in fact exist ([65,147] for reviews see [8c, 148]). They can be rationalized—albeit not with conclusive rigour—by a conformational adaptation of the apoprotein part located around the bilatriene-binding pocket, following the Z E photoisomerization of the chromophore. This local change then should suffice to determine through bilatriene chromophore-protein interactions the spectroscopic characteristics of the chromophore as well as stability and reactivity of the two photochromic forms of phytochrome. 

Fig. 17. At low solution concentration, the protein has no neighbors on the surface and thus can optimally adapt to the surface, maximizing the number of binding interactions. At high solution concentration, any one adsorbed protein is immediately surrounded by neighbors, minimizing the probability that it can conformationally adapt to the interface. This behavior leads to the differences in adsorbed amount and adsorbed protein thickness (determined by ellipsometry), as discussed in the text...

Recently, considerable progress has been made on the calculation of electrostatic and hydrophobic interactions in biochemical systems 189 19 >. We can expect such calculations to become common for protein-solid surface interactions. Thus we can expect approximate values for the adsorption energy in selected systems to appear in the near future. The problem of time-dependent conformational adaptation of the protein to the surface (and vice versa) will be much more difficult. Initially, we will have to resort to crude measures of the structural stability of a protein, such as the temperature at which thermal denaturation occurs, the urea molar concentration for solution denaturation, etc. One or more of the models given in Fig. 13 should apply. 

Despite the impressive catalytic properties of 29 (and its analogs), the conforma-tionally rigid N-spiro structure can also be a drawback, in particular with regard to conformational adaptation and the difficulty of modification. Addressing this issue,... 

The ladder-like structure, where complex formation takes place on a molecular level via conformational adaptation (zip mechanism),... 

Kiaholz, B.P., Renaud, J.P., Mitschler, A., Zusi, C., Chambon, P., Grone-MEYER, H., Moras, D. Conformational adaptation of agonists to the human nuclear receptor RAR gamma. Nat. Strutt. Biol. 1998, 5, 199-202. 

The origin of this entropic loss is the conformational adaptation the ligand undergoes during binding. 

The mechanism of the anomalous enhancement of the gauche population for short POE chains in water is not clear at present. Possible effects relevant to the specific interactions may be associated with the conformational adaptation of the POE chain to the water structure and/or the amphiphilic behavior of the POE chain in water. A clue to the elucidation of the anomalous conformational behavior probably lies in the observation of the more significant effect for shorter chains and in the particular composition of the binary system at the point of the maximum gauche population. 

The zeolite is rigid and ordered, and lacks conformational adaptability, in contrast to an enzyme, which can coil, uncoil, and twist around. Yet the zeolite can incorporate transition metal functions—these are of prime importance in enzyme catalysis—and it can effect redox reactions reactions over zeolites can be inhibited by competitive adsorption of reactants, products, solvents, or poisons—a phenomenon observed in biological and some other inorganic heterogeneous catalytic systems Rideal kinetics have been identified in some zeolite-catalyzed alkylations, a pattern which has its parallels in the enzyme field a few cases of stereospecificity (such as orfho-alkylation effects, unusual olefin isomer ratios), where a transition state not otherwise attainable intervenes, may exist. What better group of catalysts than zeolites might there have been to activate the evolutionary process in the dark, fermenting Pre-Cambrian seas some 1,000,000,000 years ago ... 

Another characteristic dress is molecular-structural detail. A. W. Weitkamp, in his study of the hydrogenation of polycyclic aromatic molecules, provides us with an excellent demonstration of the role of the finer points of stereochemical architecture and conformational adaptability. Incidentally, his introductory sentence ( Perhydro derivatives of monomethyl- and dimethylnaphthalenes should be among the very best candidates for components of.. . fuels for aviation turbine engines ) provides an interesting illustration for the strong motivating role of the industrial community in the expansion of catalytic research. 

FIGURE 12.5 Various conformations adapted by grafted polymer molecules sticking out in a liquid. Grafting is depicted by a dot. The local polymer segment density q> is indicated as a function of distance from the surface x. The approximate thickness of the polymer layer <5 is also indicated. 

Burkhardt C, Zacharias M. Modelling ion binding to AA platform motifs in RNA a continuum solvent study including conformational adaptation. Nucleic Acids Res 2001 29 3910-3918. 

A particularly good example of the power of preorganization combined with conformational adaptation is seen in the calix[4]spherands (142a), compounds in which a hemispherand moiety is affixed to the lower rim of a calix[4]arene. Although the hemispherand part of the molecule is... 

Investigation of the conformational adaptability of apolipoproteins during assembly with lipids and during metabolic transformations of lipoproteins in circulation. Elucidation of the conformational changes at the atomic level will be a major challenge dependent on the success of high-resolution analysis of apolipoprotein and lipoprotein structures. 

Figure 19 Free energy surfaces for correct (R, top) and incorrect (W, bottom) incorporations by T7 DNA Polymerase. TSC, TS1, and TS2 subscripts refer to transition states for conformational change, 03 -Pa bond formation, and pyrophosphate departure, respectively. Wjsic and Wts2c refer to transition states for mismatched incorporation in a fully closed conformation. Adapted with permission from J. Florian M. F. Goodman A. Warshel, Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6819-6824. Copyright 2005 National Academy of Sciences.

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