Table 6.

Comparison of the measured binding parameters of the representative BAFs with orange G by NMR titrations

DOI: http://dx.doi.org/10.7554/eLife.00857.023

Compound	Predicted binding energy (kcal/mol)	fmax	Kd (µM)
BAF1	−8	0.47 ± 0.04	12 ± 7
BAF8	−12	0.82 ± 0.04	24 ± 5
Orange-G	−8	0.46 ± 0.06	43 ± 21

The second column lists the predicted binding energy for each top docked model of BAF compounds with KLVFFA fiber, and the binding energy of Orange-G with KLVFFA fiber were also calculated for comparison. Our computational method identified the BAF with better fit to the binding interface than Orange-G. We then used NMR titration to determine the binding affinity. Our previous mass spectrometric analyses of the crystal of the Orange-G with KLVFFA fibers have suggested a binding ratio of compound:fiber with the range of 1:1 to 1:10 (Landau et al., 2011). Together with our structural models and single binding site assumption, we estimated the binding ratio to be 1:3. Accordingly, calculated NMR binding parameters are listed in the table. The third column f_max is the maximum fraction of NMR signal decrease of compound upon binding saturation (‘Materials and methods’).