Preferential interaction analysis

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... 

To circumvent the above problems with mass action schemes, it is necessary to use a more general thermodynamic formalism based on parameters known as interaction coefficients, also called Donnan coefficients in some contexts (Record et al, 1998). This approach is completely general it requires no assumptions about the types of interactions the ions may make with the RNA or the kinds of environments the ions may occupy. Although interaction parameters are a fundamental concept in thermodynamics and have been widely applied to biophysical problems, the literature on this topic can be difficult to access for anyone not already familiar with the formalism, and the application of interaction coefficients to the mixed monovalent-divalent cation solutions commonly used for RNA studies has received only limited attention (Grilley et al, 2006 Misra and Draper, 1999). For these reasons, the following theory section sets out the main concepts of the preferential interaction formalism in some detail, and outlines derivations of formulas relevant to monovalent ion-RNA interactions. Section 3 presents example analyses of experimental data, and extends the preferential interaction formalism to solutions of mixed salts (i.e., KC1 and MgCl2). The section includes discussions of potential sources of error and practical considerations in data analysis for experiments with both mono- and divalent ions. 

Fig. 3. Two-dimensional analysis of PDZ proteins interacting with the 5-HT2A and the 5-HT2C receptors C-termini. (A) Proteins from mice brain that bind to the C-terminus of the last 14 residues of the receptors were separated on 2D gels and stained with silver. Proteins that interact specifically (directly or indirectly) with the PDZ ligand of the receptor (arrows) were detected comparing protein patterns obtained with the native peptides (see Fig. 1) and mutant peptides in which the last residue was replaced by alanine. The position of one protein retained in a PDZ-independent manner by the 5-HT2A receptor C-terminus is also indicated (arrowhead). (B) Molecular determinants in the C-terminus of 5-HT2A receptor involved in its preferential interaction with CIPP.

Since the preferential interaction coefficient T can be interpreted in terms of Donnan equilibrium [66, 74, 96, 97], a grand canonical Monte Carlo (GCMC) simulations could be used to determine it, from a knowledge of the slope of salt concentration c3 as a function of the polyion concentration cD [68, 73, 74]. Such an analysis was carried out by Olmsted and Hagerman for a tetrahedral four-arm DNA junction, based on the so-called primitive model of the electrolyte [74]. 

Polymers containing UV stabilisers or fluorescent additives are an obvious target for UV microscopy, but the potential range of applications is much wider, in that UV absorbers or fluorescers can be selectively bound to specific chemical entities in the polymer or will preferentially interact with, or dissolve in, parts of the structure. A variety of applications of the UV microscope to studies of polymers has been reported (Table 5.15). Many applications of UV microscopy require quantitative analysis. 

Inoculation of potato disks treated with P. infestans lipids containing radiolabelled EPA and AA resulted in a decline in the proportion of radioactivity recovered in the triglyceride fraction (TG) and increases in the free fatty acid (FFA) and polar lipid fractions (Fig. 1). The reactions proceeded similarly in both incompatible and compatible interactions. Analysis of the fatty acid methyl esters obtained by methanolysis of lipids recovered from potato disks indicated that the treatments had no effect on the levels of elicitor fatty acids relative to the other fatty acids (Table 1). This suggests that the eicosapolyenoic acids were not preferentially metabolized. Recoveries of radioactivity in the lipids were similar for all three treatments (data not shown). Acyl esterase activities were similar in both interactions and declined during the course of the experiments (Fig. 2). 

It follows from equations (119) and (120) that an analysis of light-scattering data on the three-component system that ignores the presence of two solvents and uses the conventional refractive increment for the polymer, measured at fixed 3, leads to an apparent molecular weight = Q M, which depends on the preferential interaction and the refractive increments of solute and one (either) of the solvents. It turns out, however, that the light-scattering relation can be formulated, within inconsequential error, in terms of a refractive increment of the polymer defined by osmotic equilibrium... 

M. T. Record, Jr., M. Olmsted, and C. F. Anderson, Theor. Biochem. Molec. Biophys., 285 (1990). Theoretical Studies of the Thermodynamic Consequences of Interaction of Ions with Polymeric and Oligomeric DNA The Preferential Interaction Coefficient and Its AppUcation to the Thermodynamic Analysis of Electrolyte Effects on Conformational StabiUty and Ligand Binding. 

With a three-component system, such as a polymer in an aqueous salt solution, preferential adsorption of one component to the polymer can affect the analysis of light-scattering data.199 Such interactions can affect the SRI. Therefore, measurements of the SRI must be made at constant chemical potential. Constant chemical potential is achieved experimentally by dialyzing the solvent and polymer solution to equilibrium through a membrane permeable to the solvent but impermeable to the polymer.199... 

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