Hi,
I think inside a protein crystal, it is a macromolecular crowding
environment. According to what I read, it seems that in a crowding
environment, the KD of proteins to ligands may change - often gets tighter.
As we know, 20-80% of the total volume in a protein crystal is occupied by
the protein molecules, which leaves less volume for the solvent. Also
instead of having all directions to diffuse, a small molecule's movement in
a protein crystal's solvent channel is restricted by the geometry of the
channel: the protein molecules form a static mesh, and the ligands cannot
penetrate the protein molecules. I suspect that under such conditions some
of the presumptions upon which the KD is defined would not hold true. As I
understand, essentially the KD definition is a probabilistic collision model
of tiny, spherical, free moving points in a continuous space with dimensions
considerably larger than that of the reactants. If the volume for the
molecules to move around is reduced and the movements are also restricted by
geometric factors, I would imagine that more collision will occur thus more
binding will take place.
Zhijie
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From: "Jacob Keller" <[email protected]>
Sent: Friday, June 24, 2011 6:58 PM
To: <[email protected]>
Subject: [ccp4bb] Kd's in Crystals
Dear Crystallographers,
what is the dogma with regard to affinities in crystals? For example,
if I soak three crystals in 1pM, 1nM, and 1uM compound X, and they all
show equivalent density, does that mean that the affinity is really
better than 1pM, or is the crystal of such a high local concentration
(~600mg/mL) that it will be fully occupied at nearly any
concentration, provided external ligand concentration does not change
due to binding in the crystal? I guess there is also the problem that
the crystallization solutions are very non-physiological, but
neglecting that, is there any straightforward way to think of this, or
is there a good reference?
Jacob Keller
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [email protected]
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