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TOPIC: small molcule binding

small molcule binding 24 Aug 2011 02:00 #1

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I'm not familiar with the T100 Evaluation software but have you tried analyzing the single curves (i.e. not a global fit with all 4 conc) ? I've gotten screwy nonsensical numbers in the past doing a global fit and it has turned out that only one of the concentrations was throwing the whole fit out of line. When I discovered which concentration was askew, I was able to adjust the region selected for fitting and get a more reasonable global fit.

ProfPlum

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small molcule binding 24 Aug 2011 02:00 #2

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Hi,

How did you analyze the curves? What was the ka, kd and KD?
If you simulate the curves with the found numbers, do you get the same curves as you measured?

Arnoud

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small molcule binding 24 Aug 2011 02:00 #3

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Hi Arnoud,
I analyzed the curves with 1:1 model with T100 evaluation software,
the ka is 13[1/M*s], the kd is 0,002471[1/s], KD 1,853E-4 and rmax 55, flow 20µl/min, Chi2=2,11. When I simulate the curves I get the similar curves.



The simulation is ok with the exception of the beginning and the end of the injection where the buffer jump is simulated insetad of a fast a- and desociation.

Thank you
Barbara
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small molcule binding 24 Aug 2011 02:00 #4

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Hi Barbara,

Why do you think the ka is not right (13 [1/M*s] is very slow)? On what basis do you think the KD is OK. Did you other types of experiments to determine this?

You can try to fit without the bufferjump, but it looks like the kinetics are not exactly 1:1.
Also you can try the fitting module of Scrubber when you have that and compare.
Try fitting the kd alone: is it the same?

Arnoud

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small molcule binding 24 Aug 2011 02:00 #5

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Hi Arnoud,

Yes, the KD ( the IC50 value for this inhibitor ) has been determined in enzyme activity assay to be in this range.
The ka is too low because: the Quality control of biacore T100 says: ka outside the limits that can be measured by the instrument! (I don´t really know what that means, beacause it is actually measured??)
And I think that so slow interaction couldnt cause fast enzyme inactivation?

I tried to fit without buffer jump, but i think now this is not really a problem, but the non-1:1 kinetics, or some unspecific binding on denatured protein part on the chip next to the actual binding.
When I fit kd alone i get values from 7,82e-4 for the highest concentration and 2,92e-3 for the lowest.

Barbara

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small molcule binding 24 Aug 2011 02:00 #6

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Hi Barbara,

I understand now the error message: The instrument software is not capable to measure this slow association. Although it will calculated mathematically, the value is outside the specifications of the machine. However it is hard to understand why, because the curves look not that bad and the simulation was ok. You can check the specification of the machine for ka and kd.

The difference in kd is almost a factor 4, which is not so much but can be an indication of some secondary binding or mass transport. It can help to perform the experiment again with a higher flow rate if possible or lower the amount of ligand on the sensor chip.

I hope this wil hepl you because otherwise I don't know.

Arnoud

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