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To obtain the details of substrate binding, we performed a co-crystallization of WbnH with UDP-GalNAC.
Because it is not possible to extract useful binding parameters using a direct ITC titration for a low Mg2+ binding, we performed a competitive ITC binding experiment by titrating Ca2 + to a solution containing the protein plus 20 mM Mg2+.
To enhance the analytical signal and minimize the background signal resulting from nonspecific binding, we performed a series of experiments to evaluate the effects of various parameters (the concentration of the capture probe; the time required for hybridization; the number of washings required to eliminate nonspecific binding) on the oligonucleotide detection.
To determine the specificity of 99mTc binding, we performed a metal competition assay using increasing concentrations of CdCl2, CoCl2, CuCl2, or ZnCl2.
For additional independent confirmation of binding, we performed a bandshift assay using two oligos flanking the core OCT4 motif (Fig. 8A).
To test whether the N-terminal region of Foxp3 is involved in NFAT binding, we performed a mutational analysis of Foxp3 assessing the domains required for this interaction.
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To assess the regulatory properties of the CTCF binding site overlapping rs225014 and to test whether the rs225014 alleles directly affect the binding, we performed an EMSA.
In order to analyze the potential effects of the mutation on vemurafenib binding, we performed an in silico crystal structure analysis.
To identify the enzyme responsible for b-VAD-FMK binding, we performed an affinity pull-down of the 'enzyme biotin-VAD-FMK' complex using an avidin column followed by protein separation on a 1D gel.
To address the question whether SFA's inhibitory activity on chemokine expression is dependent on cyclophilin A binding, we performed competitive experiments with a 100-fold molar excess of CsA (10 µM).
To confirm that both signals were caused by SF1 binding, we performed supershifts, using an anti-FLAG antibody, which recognizes both the wild-type and mutant SF1 proteins (expressed via the pCMV6-Entry hNR5A1 vector, which contains C-terminal DDK and c-Myc tags).
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