Kindly help me in interpreting the binding energy with its Ka, Kd and KD values. Using in silico methodology, I have computed the binding energy between the protein-ligand complex (-29.06 kJ/mol). Experimental reports showed the protein-ligand complex have values of Ka (M-1 s-1) =(1.0±0.4) * 10 (6); Kd (s-1) = (1.3±0.4) * 10 (-5) and KD = 20±9.
I tried a lot to correlate the results. But I wont able to understand how to interpret the experimental and computational results. The temperature for the calculation is 298K.
P.S. Kindly read 10 (6) as 10 to the power 6 and so on.
Dear Mr. sahoo
Kd refers to dissociation constant. see below link :
http://en.wikipedia.org/wiki/Binding_constant
According to your experimental results, experimental binding free energy in your system is -62 kj/mol
best,
HHA
Dear Dr. Hamed,
I have calculated it as ~ -61 kJ/mol. I understand you have considered ln Kd value multiplied by RT. But the KD value is 20±9 pM. If we will consider the Kd, then what will be the lower part. I think we I have to consider the LN of equilibrium dissociation constant multiplied by RT. I am very much thankful to you. Kindly inform me, if I am right. In case I will consider the Kd, i need to find the reference concentration value.
Thanking You
Sincerely
Bikash
Kon = 10^6 M^-1 s^-1
Koff = 1.3x10^-5 s_1
Then, Kd = Koff/Kon = 1.3x10^-11 M = 13 pM
deltaG = RTlnKd = -62 kJ/mol
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