AMBER Archive (2009)

Subject: Re: [AMBER] Ki and G

Date: Mon Sep 14 2009 - 06:59:40 CDT

Hi Bill,

the binding (association) constant Ka of a ligand is connected to its free
enthalpy of binding via

dG = -RT ln(Ka)

Most often, its inverse, the dissociation constant Kd is given (just flip
the sign in the equation above). If the Ki you have is just the binding
constant of an inhibitor to a receptor:

E + I <-> EI

that is all you need. Be aware that in many ligand binding studies,
competitive inhibition is what's actually measured and the given constants
are IC50 values. In this case, you need to use the Cheng-Prussoff equation
for the conversion:

IC50 = Ki ( 1 + [L]/kD )

and the IC50 value depends on the used ligand concentration as well. See
Cheng et al. Biochem. Pharmacol. 22, 3099-3108 (1973). Also note that
binding constants are often determined with respect to ph7 and
physiological ion strength in biochemical systems, which makes a
difference if the binding involves proton uptake/release.

So you have to check the experimental data on what they actually measured
for any comparison.

Kind Regards,

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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