Interaction surfaces footprinting

Codina A, et al. Identification of a novel co-regulator interaction surface on the ligand binding domain of Nurrl using NMR footprinting. J. Biol. Chem. 2004 279 53338-53345. 

There are several other techniques Uke the fluorescent dye displacement assays, footprinting, Fourier transform infrared spectroscopy. X-ray crystallography, electron microscopy, confocal microscopy, atomic force microscopy, surface plasmon resonance etc used for hgand-DNA interactions that are not discussed here. 

When a gel is formed in the presence of a dye, it seems likely that most of the combined dye will be situated on or near the surface, since such interactions should generate defects in the gel structure... It seems reasonable to suppose that in the process of methanol extraction, which follows gel formation and drying, dye molecules on or near the surface are removed leaving micropores ( footprints ) of geometry and properties characteristic of the dye. The number of such pores should increase with the basicity of the dyes." [33]... 

Interaction of the functionalized-monolaycr electrode with Fe(III)-protoporphyrin IX, (15), resulted in the reconstitution of the protein with the two heme units. The surface coverage of the reconstituted de novo hemoprotein was found to be 2.5x10 mole cm Assuming that the protein footprint area is ca. 25 A, the saturated surface coverage of the de novo protein corresponds to 3.5x 10" mole cm and thus the experimental value... 

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