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. 2004:384:212-32.
doi: 10.1016/S0076-6879(04)84013-8.

Analysis of heterogeneous interactions

James L Cole  1
Affiliations

Analysis of heterogeneous interactions

James L Cole. Methods Enzymol. 2004.
No abstract available

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Figures

Figure 1
Figure 1
Schematic illustraiton of specific and nonspecific hetero-interactions. A) Discrete binding with A+2B → AB2 model. B) Nonspecific binding of a large ligand to a finite, one-dimensional lattice. One of the 6 possible configurations for binding of two ligands of length 4 to a linear lattice of length 10. The open circles represent lattice sites. C) Overlapping ligand model for the nonspecific binding of two ligands of length 4 to a helical lattice of length 10 with a minimal offset of 2. The leftmost binding site on the ligand must contact a lattice site indicated by an open circle. Only one of the 15 possible configurations is shown.
Figure 2
Figure 2
Array designs used in global nonlinear least squares fitting of sedimentation equilibrium experiment. A) Design of the concatenated data arrays. Individual data sets are denoted A, B, C, with elements 0-k, 0-l, and 0-m, respectively. The index vector labels each point in the array with the source data file. B) Design of the parameter array for an A+2B → AB2 model with n data sets.
Figure 3
Figure 3
Multiwavelength sedimentation equilibrium of PKR dsRBD binding to 20 mer dsRNA. The data were obtained under the following conditions: rotor speed, 23,000 RPM; temperature, 20°C; RNA concentration, 0.5 µM and protein concentrations of 0.5 µM, 1 µM and 2 µM in 75 mM NaCl, 20 mM HEPES, 5 mM MgCl2, 0.1 mM EDTA, pH 7.5. Detection wavelengths are: 230 nm (o), 260 nm (formula image) and 280 nm (△). Solid lines are a global fit of the data to an unconstrained model of three ligands binding to the 20 mer RNA. The results of the fit are given in table I. Inset: residuals. Traces have been vertically offset for clarity.
Figure 4
Figure 4
Species distribution from sedimentation equilibrium analysis of PKR dsRBD binding to 20 mer dsRNA. Best fit parameters from the unconstrained analysis in Table 2 were used to generate radial concentration gradients for all the species present in solution. Species are RNA (formula image ), protein (formula image ), AB (formula image ), AB2 (formula image ), AB3 (formula image ). A) [RNA] = 0.5 µM, [Protein] = 0.5 µM. B) [RNA] = 0.5 µM, [Protein] = 1 µM. C) [RNA] = 0.5 µM, [Protein] = 2 µM.
See this image and copyright information in PMC

References

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