Analysis of heterogeneous interactions - PubMed (original) (raw)
Analysis of heterogeneous interactions
James L Cole. Methods Enzymol. 2004.
No abstract available
Figures
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
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
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 (
) 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
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 (
), protein (
), AB (
), AB2 (
), AB3 (
). 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.
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