Model of structural changes

MATHEMATICAL MODELS OF STRUCTURAL CHANGE 4.2 be transformed, by a smooth reversible coordinate change, into a Morse-/... 

Fig. 6.14. Densities of states and free energies associated with Einstein model of structural change.

Dayhoff M 01978. A Model of Evolutionary Change. In Dayhoff M O (Editor) Proteins in A Has of F Sequence and Structure Volume 5 Supplement 3. Georgetown University Medical Center, Na Biomedical Research Foundation, pp. 345-358. 

This concerted model assumes furthermore that the symmetry of the molecule is conserved so that the activity of all its subunits is either equally low or equally high, that is, all structural changes are concerted. Subsequently Daniel Koshland, University of California, Berkeley, postulated a sequential model in which each subunit is allowed independently to change its tertiary structure on substrate binding. In this model tertiary structural changes in the subunit with bound ligand alter the interactions of this... 

In this model (Fay et al., 2005), portions of the N- and C-terminal regions, specifically residues 6 and 137, are in close proximity in the fibril, and the C-terminal domain retains a native-like structure. There is evidence that this non-amyloid-like fibril can convert to the cross-/ -containing filament with heat treatment, incubation at low pH (Bousset et al., 2003), or extensive drying (Fay et al., 2005), but it is unclear what sort of structural change might link the two fibril types. 

Physiochemical parameters are used to model the effects of structural changes on the electronic, hydrophobic, and steric effects for organic molecules, Examples of physiochemical parameters include, among others ... 

The choice of model often depends on the experiments involved. Workers in the area of, say, the effects of structural changes on the oxygen affinity and Hill constant for hemoglobin prefer the MWC model because it is essentially a structural theory. It provides a simple framework for the prediction and interpretation of experiments. Application of the theory to the Hill constant and other equilibrium measurements gives very acceptable results. Kineticists prefer the KNF model, since the kinetic measurements are more sensitive to the presence of intermediates. There are more variables in the KNF theory and there is more flexibility in fitting data. 

We have described several properties of aqueous solutions, some of which appear anomalous. It is now appropriate to discuss briefly what bearing these observations have on the degree and nature of involvement of the water structure in ion hydration. Specifically, are the observed concentration-dependent anomalies determined by the nature of the hydrated structures or are they manifestations of structural changes, induced by the ions, in the pure solvent The information which we have discussed also bears on the question of which model of hydration is most likely to be correct—the Frank-Wen (48) model or that of Samoilov (115). Some anomalies are amazingly abrupt. Vaslows occur over rather narrow concentration ranges, and those observed by Zagorets, Ermakov and Grunau are even sharper. Sharp transitions could be ex-... 

This review focuses on the use and limitations of the model-free methods in axial paramagnetic supramolecular mono- and polymetallic lanthanide-containing complexes. A comprehensive survey of the systems with three- and fourfold symmetry for which these techniques have been applied is proposed together with a detailed discussion of the limitations of Bleaney s approach for the modeling of paramagnetic anisotropies and the detection of structural changes along the lanthanide series. 

Gel structures are ubiquitous in foods and responsible for many of their physical properties. The space-filling network of polymers or aggregates provides solidlike properties in the presence of an enormous amormt of water. They are a form of solid water at ambient temperature and in fact they are used to immobilize free water in dietetic products. Gels have been extensively used as model systems to study strue-ture-property relationships due to their simple biphasic nature and the faet that the kinetics of structural changes can be continuously followed by oseiUatory rheometry. 

By modifying the classical theory and using a quantum-mechanical model for the critically activated complex it is possible to extend the detailed theory [Eqs. (XI.8.3) and (XI.8.3a)] in such a way as to include consideration of structural changes on the internal frequencies. In Eq. (XI.8.3) V represents a weighted average of the internal fre(i[uencies of a species that has the configuration of the transition state and represents the equilibrium constant for the equilibrium between this transition state and normal molecules. and respectively represent the standard... 

---