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formula to calculate CSPs? - Printable Version

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formula to calculate CSPs? - haitio - 10-14-2019

Hi!
Can you please tell me what is the formula used for calculating CSPs (Ddelta) in the Chemical shift mapping-section of V3?

Kind regards,
Helena


RE: formula to calculate CSPs? - VickyH - 10-14-2019

Hi Helena,

it should be the one given in the paper https://doi.org/10.1111/febs.14771

Not so easy to recreate without formatting...

CSP(i) = SQRT { (Dd(Hi)2 + 0.14(Dd(Ni)2 }

where Dd is the change in chemical shift of residue i in the H or N dimension.

Vicky


RE: formula to calculate CSPs? - haitio - 10-15-2019

Thank you Vicky,
How are the H, N relative contributions incorporated into the Ddelta formula?

From the Tstar tutorial, K75
free 122.260, 7.194
2:0eq 120.449, 6.801
SQRT{(7.194-6.801)^2 + 0.14*(122.260-120.449)^2} = 0.78
Is this right?

If I choose from "NmrAtoms settings" relative contributions of H=1.0, N=1.0, the Ddelta for K75 is 1.17.
With the tutorial default values H=6.5, N=1.0, Ddelta for K75 is 1.98. How can I reproduce Ddelta=0.78?

Kind regards, Helena


RE: formula to calculate CSPs? - LucaM - 10-16-2019

Hi Helena,

I just noticed there was an issue in one of the latest updates, preventing the relative contribution to be passed in the formula. We will send the correction this morning.

FYI, on the table you have the Deltadeltas of all perturbations. That means if you want see the 0.78, you need to select as input spectra only the tStar-free and tstar-2:0eq, in the settings panel. For the contributions, open the popup NmrAtoms Settings, type 1 for H and 0.14 for N. Ok, and update module.

I hope this helps.

Best
Luca


RE: formula to calculate CSPs? - haitio - 10-16-2019

Many thanks!
Kind regards,
Helena


RE: formula to calculate CSPs? - haitio - 10-23-2019

Hi again Vicky, Luca
A question related to the calculation of Ddelta, and Chemical Shift Mapping module:
What is the the equation to which the CSPs (and P, L concentrations) are fitted in order to obtain Kd?

I am trying to figure out why I obtain a significantly different value of Kd for an old titration study, previously obtained by fitting data using SigmaPlot.

Kind regards,
Helena


RE: formula to calculate CSPs? - LucaM - 10-24-2019

Hi,
kDs are estimated using a non-linear fitting routine as in the paper from Williamson: https://www.sciencedirect.com/science/article/pii/S0079656513000265?via%3Dihub

I hope this helps.


RE: formula to calculate CSPs? - Iona_Black - 02-18-2020

(10-24-2019, 04:29 PM)LucaM Wrote: Hi,
kDs are estimated using a non-linear fitting routine as in the paper from Williamson: https://www.sciencedirect.com/science/article/pii/S0079656513000265?via%3Dihub

I hope this helps.

Hi Luca,

Just wondering if equation 6 from this paper is used for the non-linear fitting for estimating Kd? If so, I understand that in the CSP module under Select input data - Concentration - Setup that you can input the ligand concentration (molar) for each spectra, but where do you input protein concentration?

Thanks in advance,
Iona