HELP! Protein Graphics!! Sorry, No help available on that

John Kuszewski johnk at spasm.niddk.nih.gov
Tue Jan 31 14:18:44 EST 1995


In article <1995Jan31.152912.3642 at alw.nih.gov>, phoebe at vger.niddk.nih.gov (Phoebe Rice) writes:
|> 
|> |> ...look at calmodulin for an example of
|> |> how precise but wildly inaccurate a crystal structure can be.
|> 
|> If my memory serves me right, the crystal structure of the calmodulin-
|> peptide complex looks pretty much like the NMR structure.  The
|> structure without the peptide looks different, of course, because there
|> is a flexible linker between the two halves of the molecule.  But its
|> still not "wildly inaccurate", its just seen in one of its zillion
|> possible conformations.  How about settling for "misleading"?  Even
|> then, isn't it rather naive to expect  one crystal structure of
|> something where allostery is involved to tell you everything?
|> 
|> Phoebe Rice
|> Phoebe at vger.niddk.nih.gov


By "inaccurate," I just meant that the RMSD between the (single) crystal 
structure coordinates and the real conformation in the cell is much
greater than the RMSD between the (family of) NMR structure coordinates
and the real conformation.  But "misleading" is fine too.

I'm not sure if I understand your point about allostery, though.  Of 
course, allostery implies conformational changes.  Does it always 
imply such dramatic changes as calmodulin?  Hemoglobin with and 
without bound oxygen isn't all that different.  By my definition of
"inaccurate," the hemoglobin structure seems fine.  

And most people aren't as wise as you when dealing with crystal
structure coordinates.

(Of course, I've just opened up the can of worms about whether 
the conditions in an NMR tube are close to those in vivo.  Suffice
to say that they're a whole helluva lot closer than in many crystals.)

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John Kuszewski                     ||  |/  /|  ||      
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