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QUESTION

I am investigating the strength of binding of a small peptide to a protein by isolating the bound version and subjecting it to collisions with gas molecules (CID mass spectrometry) to dissociate the complex. When I plot the collision energy against the proportion of bound and unbound proteins I get a curve that looks like a Kd curve. However, as the interaction isn't in equilibria (i.e. it is in the gas phase) calculating the Kd value wouldn't be correct.

So is there another value I could calculate to describe the strength of the interaction?

{ asked by Anake }

ANSWER

You should be looking at the interactions in terms of kinetics and not thermodynamics. k_on and k_off should do the trick.

{ answered by bobthejoe }
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