On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote:
Dear Everyone,
I have two questions about the conversion of binding energy to binding
affinity.
I predicted the binding energy of a protein-membrane complex by umbrella
sampling (based on Justin's tutorial). After sampling, the binding energy
should be the substract of (min-max) PMF. I have repeated the simulation 12
times, and then I have done umbrella samplings also 12 times, then got 12
binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the
value vary too much? or is it reasonable since the simulation results can be
different? Are those values too huge?
Without an explanation of how long your windows are and what the error estimate
for each replicate is, it is impossible to answer this question.
When I tried to convert the binding energy to Kd by the formula
deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is
-100kcal/mol, the kd is calculated as 3.35e-59 μM. The kd is 1.77e-126 μM
when binding energy is -200kcal/mol. This is impossible. But what is going
wrong?
I think you are doing your calculations incorrectly (I obtain your values when
using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the
mismatch), but even when done properly, the values are still unreasonable.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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