Hey,
I know that this is an old thread, but I've started working with these
things again.
The equation y = A ((B+x)-sqrt((B+x)^2 - 4x))
where
y = ChemShiftChange
A = maxChemShiftChange/2
B = 1 + Kd/[protein]
Seems to be widely used in different forms, but is there any brackets
missing in the equation for B?
Is it B = (1 + Kd)/[protein]
or B = 1 + (Kd/[protein])?
Thanks a million
Conny
On Mon, 2 Jun 2008 09:15:41 +0100, Wayne Boucher <[log in to unmask]>
wrote:
>Hello,
>
>On the fitting equation front, in fact up until 7 August 2007 that was the
>formula we were fitting. But somehow I was convinced (and I can't
>remember why or how) that we should instead be using the formula that is
>in there now (which is similar to the below, but not the same). I think
>what I'll do is add the below in as well.
>
>Well, in the C world, this becomes simplified somewhat to:
>
> y = A ((B+x)-sqrt((B+x)^2 - 4x))
>
>where y = ChemShiftChange, A = maxChemShiftChange/2, B = 1 + Kd/[protein].
>Somehow in the Python world we'll have to allow these parameters to be
>converted to the form you want. (That probably won't be done until the
>next release, so once the above is in, for now it will require an Excel
>spreadsheet or similar to do the calculation converting A, B to
>maxChemShiftChange, Kd, given [protein].)
>
>I'll have to look into the other issues.
>
>Wayne
>
>On Sun, 1 Jun 2008, Lisa Rose Warner wrote:
>
>> Hello all,
>>
>> I am having the same issues as Conny. As an additional note, I ran into
this problem after I performed an update on Friday. I hadn't downloaded
updates since February and prior to updating, I had no problems grouping
peaks and fitting.
>>
>> As for the fitting equation, it would be very useful to have a prompt for
protein concentration and use the following equation to fit to a ligand
concentration titration series.
>>
>> ChemShiftChange= (Kd + [ligand] + [protein] - Sqrt[(Kd + [ligand] +
[protein])^2 - 4*[ligand]*[protein]])/(2*[protein]) *maxChemShiftChange
>>
>> (For an example, see PNAS 2008 vol. 105 (2) pp. 506-11)
>>
>> Thanks -- Lisa
>>
>> On Sun, Jun 1, 2008 at 10:21 AM, Conny Johanssin
>> <[log in to unmask]> wrote:
>> > I've been making some titrations lately and have run into some trouble
>> > analysing the data.
>> >
>> > 1) When I make histograms of resonance1 vs shift dist The resonances
are not
>> > displayed on the x axis, but they are for other people in the lab. Still we
>> > are all using the same installation of Analysis. See attachment for
screenshot.
>> >
>> > 2) When I try to fit my titration to the saturation curve function in
>> > analysis (the longest function, 2nd from bottom) and then press group peaks
>> > I get a error (see screen dump). The annoying thing is that I got it to
work
>> > with another titration 2 weeks ago, but not this time. I've tried both
>> > ligand ratio and ligand conc.
>> >
>> > 3) When I managed to fit the function 2 weeks ago I got a really nice
>> > fitting curve and equation (with the variable values). Theoretically, I
>> > should be able to derive the Kd from this function. It would be really nice
>> > to be able to do that right away in Analysis rather than using some other
>> > program. Anyhow, I don't recognize the equation and I find it strange that
>> > it doesn't need the protein concentration, just the ligand. Do you have
some
>> > kind of reference on this equation where I can read about it, or where does
>> > it come from? Do you know how I can get the Kd from the equation?
>> >
>> > Thanks
>> > Conny
>> >
>>
>>
>>
>> --
>> Lisa R. Warner
>> Graduate Student
>> Dept. of Biochemistry
>> University of Colorado, Boulder
>> 215 UCB
>> Boulder, CO 80309-0215
>> 303.492.8085
>>
>>
>>
>> --
>> Lisa R. Warner
>> Research Assistant
>> Dept. of Biochemistry
>> University of Colorado, Boulder
>> 215 UCB
>> Boulder, CO 80309-0215
>> 303.492.8085
>>
|