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binding strength. The ability of a molecule to stick to a particular binding partner and stay stuck. It’s often measured/reported with a value called the equilibrium dissociation constant, Kd. Ultimately it’s the result of energetically-favorable interactions between the binding partners (you have a negatively-charged patch? cool! I’ve got a positively-charged one. And our shapes complement each other nicely!). The higher the affinity 2 molecules have for one another, the more likely they are to stick to one another if they collide and/or the less likely they are to come apart once they’ve stuck. Chances of colliding with one another depend on their concentrations: the higher the affinity, the lower the concentration you need to get lots of binding (because you bind and stay bound when you collide as opposed to falling off and having to find and rebind). This relationship is reflected in the dissociation constant, Kd, which tells you how much of one binding partner (in terms of concentration, often in some form of molarity) you need to add before half of the other parter is bound (at equilibrium). The most important thing to remember about Kd is that the higher the affinity, the lower the Kd.

This can be counterintuitive but this inverse relationship occurs because, in the binding situation [A] + [B] ⇌ [AB], Kd is defined as [A]{B]/[AB} (the multiplied concentrations of unbound over bound) at equilibrium. So a higher Kd means that when you go take a molecular census, there are more unbound molecules, whereas a lower Kd means that you find more bound molecules.

note: Equilibrium occurs when the forward and backward reaction rates equalize so that the amount of binding equals the amount of unbinding and the overall proportions of unbound and bound don’t change over time (even though bindings & unbindings still occur). If you leave any reaction be long enough it (with same temperature, etc.) it will eventually reach the same equilibrium (same proportion of bound/unbound) no matter what you start with because that equilibrium is determined by that inherent energetic interaction stuff. As an equilibrium constant, Kd is a sort of “end result” measurement and it tells you nothing about the rates of binding (kon) and unbinding (koff). For that you need to measure kinetics.

Kd is the inverse of the equilibrium association constant, Ka, (i.e Kd = 1/Ka). Ka is defined as [AB]/[A][B} so it *is* higher with higher affinity. But, it’s in inconvenient units (M⁻¹) so biochemists usually work with Kd which is in nicer units (M or mM or nM or μM or whatever). We don’t do it to confuse you!

In the strict sense, affinity is the strength of a single site partner-partner interaction, as opposed to the aggregate strength of multiple binding sites which gives you an “effective affinity” aka “apparent affinity” which includes affinity in the strict sense (the inherent affinity of the single sites) as well as the effects binding to one site has to another. The effective affinity for multivalent binders (where you have multiple binding sites binding) is often higher than the inherent affinity of any one site because binding to one site kinda tethers the others nearby making it easier for them to bind. This effect is called avidity and it comes into play with things like antibodies (which have multiple binding sites for antigens) and lectins (which have multiple binding sites for carbs).