Hydrophobic interactions models

Moelbert, S. De Los Rios, P. 2003, Hydrophobic interaction model for upper and lower critical solution temperatures . Macromolecules, vol. 36, no. 15, pp. 5845-5853. 

Hummer G, Garde S, Garcia A E, Pohorille A and Pratt L R 1996 An information theory model of hydrophobic interactions Proc. Natl Acad. Sc/. 93 8951... 

Simplified models for proteins are being used to predict their stmcture and the folding process. One is the lattice model where proteins are represented as self-avoiding flexible chains on lattices, and the lattice sites are occupied by the different residues (29). When only hydrophobic interactions are considered and the residues are either hydrophobic or hydrophilic, simulations have shown that, as in proteins, the stmctures with optimum energy are compact and few in number. An additional component, hydrogen bonding, has to be invoked to obtain stmctures similar to the secondary stmctures observed in nature (30). 

Fig. 20 Vertical model of complementary assembly of peptide mixtures. Hydrophobic interactions are represented by the interlocking of raised sections and holes. The axis is indicated by dots. Reproduced from Takahashi et al. [57] with permission. Copyright Wiley-VCH. Numbers refer to the peptide entries in Fig. 18. Positively charged residues are dark shaded in contrast with the negatively charged residues which are light shaded...

Ghose, A. K., Crippen, G. M. Atomic physicochemical parameters for three-dimensional strucmre directed quantitative structure-activity relationships. II. modeling dispersive and hydrophobic interactions. 7. Chem. Inf. Comp. Sci. 1987, 27, 21-35. 

Separations in hydrophobic interaction chromatography have been modeled as a function of the ionic strength of the buffer and of the hydrophobicity of the column, and tested using the elution of lysozyme and ovalbumin from octyl-, butyl- and phenyl-Sepharose phases.2 The theoretical framework used preferential interaction analysis, a theory competitive to solvophobic theory. Solvophobic theory views protein-surface interaction as a two-step process. In this model, the protein appears in a cavity in the water formed above the adsorption site and then adsorbs to the phase, with the free energy change... 

Perkins, T.W., Mak, D.S., Root, T.W., and Lightfoot, E.N., Protein retention in hydrophobic interaction chromatography modeling variation with buffer ionic strength and column hydrophobicity, J. Chromatogr. A, 766, 1, 1997. 

The number of binding sites can be determined in this model by a plot of d Ink /dlnm at constant temperature, pH, and ion valency. To do that, it may be assumed that dlny /dlnm is approximately zero. The actual value is -0.04 for 0.1 to 0.5 M sodium chloride and less at lower concentrations. To a first approximation, the stoichiometry of water molecules released by binding protein could be determined from the slope of the plot of dink /dlnm vs. m. However, especially at low salt concentration and near the isoelectric point, the slope of such plots is nonlinear. The nonlinearity may be due to hydrophobic interaction between stationary phase and protein or a large change of ionic hydration on binding.34... 

Liposomes are formed due to the amphiphilic character of lipids which assemble into bilayers by the force of hydrophobic interaction. Similar assemblies of lipids form microspheres when neutral lipids, such as triglycerides, are dispersed with phospholipids. Liposomes are conventionally classified into three groups by their morphology, i.e., multilamellar vesicle (MLV), small unilamellar vesicle (SUV), and large unilamellar vesicle (LUV). This classification of liposomes is useful when liposomes are used as models for biomembranes. However, when liposomes are used as capsules for drugs, size and homogeneity of the liposomes are more important than the number of lamellars in a liposome. Therefore, "sized" liposomes are preferred. These are prepared by extrusion through a polycarbonate... 

This simple three-state model of protein folding, shown schematically in Figure 7, ascribes a separate force to shaping the structure of each state. Local steric interactions trap the protein chain in a large ensemble of conformations with the correct topology hydrophobic interactions drive the chain to a smaller, more compact subset of conformations then dispersion forces supply the enthalpy loss required to achieve a relatively fixed and rigid ensemble of native conformations. 

Hummer, G., Garde, S., Garcia, A. E., Paulaitis, M. E., and Pratt, L. R. (1998b). The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc. Natl. Acad. Sci. USA 95, 1552-1555. Hummer, G., Garde, S., Garcia, A. E., Pohorille, A., and Pratt, L. R. (1996). An information theory model of hydrophobic interactions. Proc. Natl. Acad. Sci. USA 93, 8951-8955. 

The squaraine probe 9g was tested for its sensitivity to trace the formation of protein-lipid complexes [57]. The binding of dye 9g to model membranes composed of zwitter-ionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin (CL) in different molar ratios was found to be controlled mainly by hydrophobic interactions. Lysozyme (Lz) and ribonuclease A (RNase) influenced the association of 9g with lipid vesicles. The magnitude of this effect was much higher... 

The reactions of the cycloamyloses may also be useful in achieving stereoselective organic synthesis or they may serve as models for hydrophobic interactions in aqueous solution. As the scope of cycloamylose catalysis is extended to include other reaction types and other cycloamylose derivatives, additional applications will undoubtedly be revealed for the cycloamyloses as catalysts. 

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