Imidazole does not typically interfere with downstream applications and therefore removal is optional. Boiling a sample containing imidazole prior to SDS–PAGE may cause acid-labile bonds to hydrolyze. It is instead recommended to incubate the sample at 70°C for 5 min in SDS loading buffer prior to analysis.

Does imidazole degrade protein?

In addition to competing with your His tagged protein in the metal affinity chromatography, imidazole also behaves just like any salt: means it may interfere with any protein-protein interactions that are mediated by polar or charged residues (ionic interactions).

What does imidazole do to proteins?

Imidazole is utilized as a competitive agent for elution of histidine-tagged proteins. In addition, imidazole can be added in low concentrations in the sample and binding buffer in order to reduce the binding of contaminant proteins, and thus increase the final purity.