Hi Sebastiano,

I have had some experience with protein:protein complexes with KD ~ 10-1 uM, kinetic characterization and trying to purify a complex of these proteins using SEC. While I would say that if you have reliable evidence from SPR that you have a fast on (high Kon), then you must have a fast off (high Koff) because by definition KD = 10 E-6 = Koff/Kon. However, I have observed several systems where you have a KD ~ 10-1 uM, but the kinetics are not fast on/fast off. In my experience, I have never seen anything in the crystal structures of the weak affinity complexes I have solved that would coorelate B-factors to Kon/Koff, and while it might be tempting for you to draw this comparison in your structure, I would warn that this is too large a leap without further (non-anecdotal) evidence.

As a further note, during SEC purification of complexes, I have observed that you generally have to have the complexes at at least 5 to 10-fold higher initial concentration if you want to purify the complex, which you are only pushing with your 80-100 uM high end concentration. A colleague of mine once told me this is due to a 5 to 10-fold dilution effect upon addition to the column, but I have never verified this nor read any primary source that validated this so I cannot supply a reference (others might be able to help here). Good luck and cheers~


Quoting Sebastiano Pasqualato <sebastiano.pasqual...@ifom-ieo-campus.it>:

Hi all,
I have a crystallographical/biochemical problem, and maybe some of you guys can help me out.

We have recently crystallized a protein:protein complex, whose Kd has been measured being ca. 10 uM (both by fluorescence polarization and surface plasmon resonance). Despite the 'decent' affinity, we couldn't purify an homogeneous complex in size exclusion chromatography, even mixing the protein at concentrations up to 80-100 uM each. We explained this behavior by assuming that extremely high Kon/Koff values combine to give this 10 uM affinity, and the high Koff value would account for the dissociation going on during size exclusion chromatography. We have partial evidence for this from the SPR curves, although we haven't actually measured the Kon/Koff values.

We eventually managed to solve the crystal structure of the complex by mixing the two proteins (we had to add an excess of one of them to get good diffraction data). Once solved the structure (which makes perfect biological sense and has been validated), we get mean B factors for one of the component (the larger) much lower than those of the other component (the smaller one, which we had in excess). We're talking about 48 Å^2 vs. 75 Å^2.

I was wondering if anybody has had some similar cases, or has any hint on the possible relationship it might (or might not) exist between high a Koff value and high B factors (a relationship we are tempted to draw).

Thanks in advance,
best regards,

Sebastiano Pasqualato, PhD
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano

tel +39 02 9437 5094
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