FruA-His6 alone failed to produce a distinct complex, but in combination with His10-MrpC2, a slow-migrating complex es) was produced more abundantly than could be accounted for by binding of each protein alone, suggestive of cooperative binding.
When His10-MrpC2 waddedded, a slow-migrating complex es) was produced more abundantly than could be accounted for by binding of each protein alone, providing evidence for cooperative binding.
The combination of FruA-His6 and His10-MrpC2 produced a slow-migrating complex es) more abundantly than could be accounted for by binding of each protein alone, providing evidence for cooperative binding.
In EMSAs, cooperative binding produced a slow-migrating complex more abundantly than could be accounted for by binding of each protein alone [ 46], and similar results provide evidence for cooperative binding of the two proteins in the fmgBC [ 47], fmgD [ 45], fmgE [ 48], and dev [ 53] promoter regions.
Addition of a 10-fold lower concentration of His10-MrpC2 thethe 2-fold lower concentration of FruA-His6 produced slightly more complex than could be accounted for by binding of each protein alone, consistent with cooperative binding, but surprisingly a novel, slow-migrating complex was observed only for the MXAN_6247 region.
A similar pattern of weak binding by FruA-His6 alone, and a slow-migrating complex es) produced more abundantly by the combination of FruA-His6 and His10-MrpC2 (only a high concentration was tested) than could be accounted for by binding of each protein alone (i.e., evidence for cooperative binding), was observed for the pktA1, MXAN_2902, MXAN_4360, and mrpA regions (Additional file 10, top row).
The normalization was based on the equation (V = V_{0} /left[ {left( {M_{text{L}} + M_{text{R}} } right)/2} right]), where (V_{0}) is the binding energy calculated by the scoring function for each protein ligand complex, (M_{text{L}}) is the average binding energy of each ligand with different proteins, and (M_{text{R}}) is the average binding energy of each protein with different ligands.
In Fig. 4a the binding of protein over protein input is shown.
In docking-based IVS, a given small molecule is docked to the binding site of each protein in a target database through a docking engine.
Despite the similarity in protein structures, the binding profiles of each protein varied significantly, suggesting that differential fluorescence responses would be generated for each FP upon interaction of the sensor with competing analytes such as mammalian cells.
Specificity in these interactions arises from slight variations in the consensus sequences of each SH3-domain, and the hydrophobic and charge interactions of the residues near the binding regions of each protein.
