[Messi]

Hi guys,

I am reading this article, and it isn't making too much sense. It is measuring the binding constant of a ligand with its target telomere.

The article shows K_D values and they are to the 10⁷ range. Doesn't this mean the ligand has VERY VERY low affinity for its target molecule? Usually K_D values are in the nanomolar range, no? And this is in the opposite direction!

I have posted a screen shot of the table below.

Any help would  be greatly appreciated!

[Yggdrasil]

This is quite odd.  The units for a dissociation constant (K_D) should be units of concentration (e.g. molar), not inverse concentration (M^-1).  Likely, they have two typos and the units for the measurements should be 10^-7 M.  The other possibility is that they are reporting association constants (1/K_D) in units of 10⁷ M, but since biochemistry papers almost always report dissociation constants, I'm inclined to go with the former possibility.  It is certainly not correct as written since I have no idea how one could measure a dissociation constant of 4x10⁷ M!.

Maybe you can e-mail the authors of the paper to clarify. 

[curiouscat]

Might you be misreading the table? What it might mean is the  values in each cell = 10⁷ × k_D

Hence the M^-1 units too.

I've often seen Table Headings written that way. Maybe they ought to have written K_D (x 10⁷)
That makes the number in each cell a pure number (no units).

Does that make sense?

[Messi]

Might you be misreading the table? What it might mean is the  values in each cell = 10⁷ × k_D

Hence the M^-1 units too.

I've often seen Table Headings written that way. Maybe they ought to have written K_D (x 10⁷)
That makes the number in each cell a pure number (no units).

Does that make sense?

Ok, valid point, but then why does the article state that compound 2d) experienced the highest degree of stabilization if it has the largest value in the table?

[curiouscat]

Ok, valid point, but then why does the article state that compound 2d) experienced the highest degree of stabilization if it has the largest value in the table?

Hard to say. Can you post more of the context? Yes, something's fishy.

[Babcock_Hall]

Is it possible that the table gives values of association constants, not dissociation constants?

[curiouscat]

Know what I think?

He made his tricky table and then later he mis-read it himself while concluding that "compound 2d) experienced the highest degree of stabilization" 

Wacky but possible! 

I bet the Table's right but the conclusion's wrong and Ligand 1a actually binds strongest. Like Yggdrasil says, an email might be called for.

[Messi]

Just sent an e-mail!

I am pretty sure, ligand 2d) is suppose to have the highest degree of stabilization. I believe you are probably correct Babcock, association constants are given. The author must have accidentally written K_D instead of K_A. It is however strange that he would use association constants rather than dissociation constants..

[Babcock_Hall]

I agree; dissociation constants, not association constants, are much more typical in the biochemistry/molecular biology literature.  If the paper needs to be corrected, then you are doing the authors a favor by pointing it out.

[jhonsmith]

Dear Likely, they have two typos and the units for the measurements should be 10-7 M.  The other possibility is that they are reporting association constants (1/KD) in units of 107 M, but since biochemistry papers almost always report dissociation constants, I'm inclined to go with the former possibility. Hence the M-1 units too. Can you post more of the context,...? pleas Thanks

    

[Messi]

I got in contact with the authors and they thanked me for correcting their mistake. The units were association constants, but they had written dissociation constants by accident.

They said they will update their paper ASAP.