Hello,
I hope this is not a trivial question, but I can`t work out where to input the protein concentration in the CSP module.
I can see in Chemical shift mapping / edit spectrum group series the concentration settings for what apprears ligand concentrations, but nothing on the protein concentration.
I would also be happy to specify everything in molar ratios rather than concentrations in which case the issue of sperately input of the protein concentration would be obsolete.
Also where can I find the exact equation that is being used for fitting.
Many thanks
best wishes,
Joern Werner
Hi Joern,
not a trivial question and this has changed over time, so I`m not quite sure if the documentation has kept up with this. Basically, you need to double-click on your SpectrumGroup in the sidebar, and then there should be a tab called `Series`. Here you can enter concentrations etc. The other way to get there is to click on `Edit Series...` in the Settings of the Chemical Shift Mapping module.
As regards equations - it is not the one from Williamson (2013), but based on a more simple one-site binding model:
y = Bmax*x/(Kd + x)
where Bmax is the maximum binding, so the protein concentration isn`t actually used.
Best wishes,
Vicky
Hi Vicky,
many thanks.
This may explain whay I get differnt results to what I thought I should get.
I think the model used is for the limit of fast excess of ligand over protein which is not quite right in many nmr titrations.
is there are possibilty to code up the use the eq6 from the Willisamson 2013 paper? and include what is done in the documentation?
Ddobs 1⁄4Ddmax ð1⁄2P?t þ1⁄2L?t þKdÞ?1⁄2ð1⁄2P?t þ1⁄2L?t þKdÞ ?41⁄2P?t1⁄2L?t? 21⁄2P?t
I am happy to have a look at the code, if I understand how is does the fitting I may have a go.
bw Joern