Hello, everyone.
In SPR or BLI, I wonder if apparent difference of KD (binding affinity) requires comparison.
I heard at least 10-fold comparison of KD means apparent difference.
Then, less 10-fold comparison of KD does not means difference?
Could I see the reference about this?
Differences in Kd values must be considered in, at least, two different ways.
If just the technical issue is of concern, a 3-fold to 5-fold factor in Kd may be technically relevant, which corresponds to 0.6-1 kcal/mol difference in Gibbs energy.
However, a 3-fold to 5-fold factor in Kd may not be physiologically relevant.
I would say that a 10-fold factor would be both technically and physiologically relevant.
If you want to know whether the Kds of two ligand-receptor pairs can be considered to be different, measure each of them multiple times (at least 3 times), calculate the averages and standard deviations, and perform a t-test. A P-value of 0.05 or less is usually considered to be statistically significant.
Adam B Shapiro I agree more or less with that, but very often statistically significant differences do not reflect significant "size effects".
For example, it may be possible for a 2-fold difference to be statistically significant after 10 replicates, but the 2-fold difference is not physiologically/practically relevant. The same size effect can be made to be statistically relevant just by increasing the number of replicates, and this is something that can be employed to magnify small differences. The abusive use of p-values has put them into question.
On the other hand, Kd's should be averaged employing the geometric average, not the arithmetic average, and, consequently, their geometric standard deviation should also be calculated. This derives from the logarithmic relationship between Kd's and ΔG's (equilibrium constants would follow a log-normal distribution and energies would follow a normal distribution).
has anyone found a reference in the literature for the 10-fold difference?
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry