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Although the binding data for the gα8 - cells appeared to show a sigmoidal curve, F tests comparing binding with a Hill coefficient of 1 to binding models with a variable Hill coefficient indicated that a model with a Hill coefficient of 1 was preferred for all cell lines except for gα5 -, where a model with a Hill coefficient of 2.9 ± 0.9 (mean ± s.e.m, n = 3) was preferred.
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The data were described using a one-site ligand binding model, with a ligand concentration of 0.19 μmol site mg−1 C, and a log K′ of 6.2.
However, the amide cross-peak of Leu31 demonstrates a significant urea dependence that can be fitted to a two-state binding model with a dissociation constant of 0.95 ± 0.04 M.
Fortunately, the Kd value could be determined at a lower temperature; at 10°C, the heat exhausted could be fitted to a one-site binding model with a Kd value of 21.0 ± 2.1 µmol/L (Fig. 1C).
Both datasets could be fit well to a three-site binding model with a single affinity for Nck.
The data could only be reliably fit using a one-site binding model with a Kd = 23 ± 4 μM and a JAZ ZF1/RNA stoichiometric ratio of 2 1.
In addition, F tests to compare a one-site binding model with a two-site binding model indicated that a one-site binding model was the preferred fit for all cell lines.
The fraction of bound duplex with increasing concentrations of MBP-tagged protein was quantified by using ImageJ and fit to a one-site binding model with a Hill coefficient to estimate a Kd.
The data could be fitted with a one-site competition binding model with a Ki of 1.4 μM, showing that the USP4 insert competes with Ub for binding to USP4 D1D2.
Data analysis was performed as previously described by fitting the data to a 1 1 binding model with a correction for changes in fluorophore intensity due to protein binding (OriginPro 8 SRO).
The observed fluorescence anisotropy at increasing concentrations of protein was measured by using an EnVision Microplate Reader (Perkin Elmer, Waltham, MA) and was fit to a one-site binding model with a Hill coefficient to estimate the Kd of single-stranded nucleic acid in the presence of increasing nucleotide.
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