HELP!!! Protein Graphics!!

Gerard Kleijwegt gerard at rigel.bmc.uu.se
Wed Jan 25 17:43:57 EST 1995


In article <3g5b3v$r68 at lyra.csx.cam.ac.uk>, owde100 at bioc.cam.ac.uk (Orhan Ertughrul) writes:
|> Remember though that it is only a model! Sometimes it's possible
|> to miss things even in crystal structures because the crystal 
|> latice may cause a protein to adopt a position that hides features.
|> Recently molecular dynamic work on a protein (I forget which one) 
|> revealed a channel to the active site that wasn't obvious from
|> the crystal structure for the previous reason. 

And how many experimental observations went into that molecular
dynamics simulation ???  If the answer is zero, I would bet that
the result of any such MD simulation is an artefact caused by the
particular combination of physical model + force field + algorithm
(+ random-number generator ? ;-) that is used.  At best it provides
a picture of something that may be physically possible, but without
any guarantee that it reflects biological reality.

|> If we can miss things in a crystal structure because we don't take
|> into account the experimental aspects of the procedure used to
|> create the structure, how much more careful is it necessary to

I think most crystallographers and NMR spectroscopists are aware
of the "triangle inequality":

  crystal != physiological environment != solution

|> be when attempting to interpret what is, after all, little more
|> than educated guess work? Models can provide an important insight
|> into the structure of a protein, more so if the homolgy of homologues
|> used to create them is high, however, they should never be accepted
|> as an accurate representation of a protein's structure. For this we are
|> sadly still reliant on the skill of crystallographers and NMR specialists.
|> *8)

Why is that sad ? It keeps a lot of people off the street !

|> 
|> Orhan.
|> 
|> -----------------------------------------------------------------------
|> Orhan W.D. Ertughrul       |    /\         "It's hard enough to watch
|> University of Cambridge    |   /  \ /\      the news, let alone explain
|> Department of Biochemistry |  /    /  \     it to a child to cast its
|> Tennis Court Road          | /    /    \    eyes on nature over fields
|> Cambridge CB2 1QW          |/    /      \   of rape and corn, and tell
|>                            |  /\/        \  it without flinching not to
|> owde100 at cus.cam.ac.uk      | /  \         \ fear where its been born"
|> -----------------------------------------------------------------------
|> WWW : http://nirvana.bioc.cam.ac.uk/~owde100/
|> -----------------------------------------------------------------------



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