Thank you for your help. By chance, do you know of any equations would be most appropriate for slow exchange?

 

Regards,

Robert

 

From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Ken Cameron
Sent: Tuesday, May 08, 2018 4:33 AM
To: [log in to unmask]
Subject: Re: Kd from chemical shift analysis

 

Hi Robert,

 

CCPN use the equations from the Vanderbilt website.

Use the 9th equation down form protein-ligand. The longest equation is for monomer-dimer binding.

 

Cheers,

Ken

 

 

Senior NMR Scientist

Drug Discovery Programme

CRUK Beatson Institute

Garscube Estate

Switchback Road

Bearsden

Scotland G61 1BD

 

[log in to unmask]

Tel: 0141 330 6410

 

[log in to unmask]" alt="cid:[log in to unmask]">

 

 

 

From: CcpNmr software mailing list [mailto:[log in to unmask]] On Behalf Of Brian Smith
Sent: 08 May 2018 09:58
To: [log in to unmask]
Subject: Re: Kd from chemical shift analysis

 

Hi Robert,

Yes CCPNmr Analysis v2.x can hep you do this easily. Before you try fitting the data, evaluate whether you have data that will actually be worth fitting - do the chemical shifts titrate with increasing ligand concentration and follow what appears to be a saturation process, i.e. do they initially shift a lot for small ligand additions, but then you reach a ligand concentration beyond which you see no further changes?

For the actual procedure, some of this is covered in the analysis beginners course tutorial part 2

https://www.ccpn.ac.uk/v2-software/software/tutorials/analysis-beginners/beginners-analysis-2

but not in much detail - partly because it's quite simple. In outline:


If everything works well, for your chosen peaks, you can get braver and pick more peaks and even try trusting Follow Shift Changes to propagate the assignments for you, but this can get messy, so be sure to Archive your project before attempting anything risky.

 

Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
          College of Medical, Veterinary & Life Sciences,
  Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401


From: CcpNmr software mailing list [[log in to unmask]] on behalf of Hammond, Robert Glenn [[log in to unmask]]
Sent: 07 May 2018 23:16
To: [log in to unmask]
Subject: Kd from chemical shift analysis

Hello,

 

I am trying to calculate dissociation constant (Kd) of a ligand when it binds to my protein. I have found that CCPNmr can use binding models to do this but I am unsure on the protocol. I already have my HSQC spectra overlaid in a window. Although, I do not have the backbone assigned, I want to get a grasp on how to pick peaks and make the calculation. If anyone has experience doing this, I would be grateful if you could clarify a few things for me.

 

Also, if anyone has any alternative suggestions, I am open to trying a different method. Thank you.

 

Regards,

Robert

 

 

 

 

Robert Hammond

PhD Candidate

Department of Chemistry

University of Alabama at Birmingham

[log in to unmask]

(775)453-6605

 

 

 

 

 



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