NaCl could destroy the electrostatic interactions.
HAc could damage the hydrogen bond between proteins.
Is this right?
How to destroy non-covalent interactions between proteins?
If you speak of a complex, then you can try to increase the ionic strength of the solution in a controlled manner, in order to weaken the electrostatic interactions, or change the pH. You can also use urea or guanidine, always under controlled conditions, for the non-electrostatic interactions. The check is to use an instrumental observable (UV CD, fluorescence, etc.), structure sensitive, which can ensure the permanence of the structural organization of the various proteins released from the complex. But if you mean the total elimination of these interactions in the context of a single protein, then the recipe is 50 years old: put your protein in a solution of 6 M guanidinium hydrochloride and all non-covalent interactions, of any nature, will be lost. If you need a more powerful denaturant, you can use guanidinium thiocyanate. Alternatively, urea 12 M does more or less the same things.
Giovanni, thanks for you kind suggestions.
Urea is so severe that it can destroy all protein structure. What I need is separate protein from others by destroying weak interactions to get one protein or protein complexes.
Is it scientifically imprecise that "NaCl could destroy the electrostatic interactions, HAc could damage the hydrogen bond between proteins"?
Not NaCl, but the increase of ionic strength of any salt (electrolyte) destabilizes the electrostatic interactions (Coulomb law), including hydrogen bonding between subunits. The effect that you will have with acetic acid, will be that of decreasing the pH of the solution (if not buffered). Upon this condition, some acid-base residues may result protonated. This might have an effect on the interactions at the interface but also on the structure itself. Guanidine is more severe. Urea can be better graded because of its wider concentration range (up to 12 M). At low concentrations, it is very likely that you will denature the complex rather than to unfold its subunits.
If the interaction between the two proteins is relatively weak, diluting the complex below the dissociation constant (Kd) will cause dissociation of the complex. The Kd can be affected by pH, ionic strength, and temperature. A combination of high ionic strength and low temperature may dissociate a complex held together by predominantly hydrophobic interactions.
I have one more question.
According to what you said, acid, salt and denaturant can all be used as elution agents in affinity-enrichment experiments. Why acid and salt are not usually used? The most common is SDS-loading buffer. Too weak to get a good result?
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