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Radioligand competition curves were analyzed by nonlinear regression using the commercial Grafit curve-fitting software (Erithacus Software, Surrey, UK), by fitting the binding data to the mechanistic two-state dimer receptor model [18], [19].
The parameter Kd' was calculated by fitting the binding data (over a range of HA concentrations) using the Hill equation for multivalent binding [10].
This was concluded by fitting the binding curves from the affinity titration to models describing one monovalent ligand (125I-EGF) binding to either one or two independent receptors on the cell with different kinetic parameters.
Also by fitting the binding data to eq. 4 (Materials and Methods), the KD value obtained for the A1R antagonist (DPCPX) was 8.6±0.9 nM for the A1R cell clone and the KD value obtained for the D2R antagonist (YM-09151-2) was 0.23±0.08 nM for the D2R cell clone.
The dose-dependant glycan binding data of the described HAs were used to calculate Kd' and n values (n ∼1.3 for all the HAs) by fitting the binding data to the Hill equation (for multivalent binding) and this was then used to generate theoretical binding curves to clearly distinguish the relative binding affinities of WT and mutant H2 HAs to representative avian and human receptors (Figure 6).
KD values were again obtained by fitting the binding data to a one side specific binding plot using GraphPad Prism5.
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Kinetic analyses were performed by globally fitting the binding results for the entire concentration series using a standard 1 1 kinetic model with integrated mass transport-limited binding parameters as described previously.
The dissociation constants (Kd) were calculated by fitting the concentration-dependent binding curve using a quadratic ligand binding equation.
We proceeded with the detailed analysis on chemical shift by fitting the data against binding models like single site, two site sequential, multiple sites simultaneous and single site with allosteric contribution models to interpret the binding mechanism.
For that temperature, the DLTS amplitude was calculated as a function of reverse voltage, by fitting the average electron binding energies of the s- and p-levels and by using tunneling emission data from Ref. [2].
The Kd values were calculated by fitting the data from the equilibrium binding experiment to a non-linear regression saturation binding model (GraphPad Prism 5.0), whereas the koff data were estimated from the kinetics experiments by fitting the data with the built-in models of the BIAeval 3.1 software (BIAcore).
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