binding affinity

what is binding affinity?

strength of non-covalent interaction between a receptor and ligand

determines how tightly two molecules bind together

how is binding affinity typically quantified?

typically quantified using equilibrium dissociation constant, K_d

what is the equilibrium dissociation constant, K_d?

the concentration of ligand required to occupy half of the available binding sites at equilibrium

measured in M (molar)

what do a low and high K_d represent

Low K_d = high affinity (tight binding), low concentration of ligand required

• ligand binds faster, RL complex lasts longer

High K_d = low affinity (loose binding), high concentration of ligand required

• ligand will bind slower and RL complex dissociates faster

how can K_d be calculated

• by using k_off and k_on

• by using concentration of receptor, ligand and receptor-ligand complex at equilibrium

what is k_on?

k_on is the kinetic rate constant that accounts for the forward binding reaction of receptor and ligand

measured in M^-1s^-1

R+L → RL

what is k_off?

k_off is the kinetic rate constant that accounts for the reverse unbinding (dissociation) of the R-L complex

measured in s^-1

RL → R+L

what is the equation for K_d using k_off/k_on?

what is the equation for K_d using concentrations at equilibrium?

what is the equation for K_a (reverse of K_d)?

why is binding affinity a useful?

can be used in drug design to identify drug candidates

a higher binding affinity means that a lower concentration of drug is required, reducing potential side effects

how is binding affinity determined?

in a lab through experimentation

• vary the concentration of ligand in a solution containing a low, fixed concentration of receptor

• at each concentration of ligand, measure the fraction of occupied binding sites, θ

what is the equation for θ?

what is the new equation when you make θ a function of [L]?

what is the range of θ?

0 to 1

• 0 when [L] = 0

• 1 when [L] = ∞

• when θ = 0.5, [L]=K_d