HELP!!! Protein Graphics!!

Gerard Kleijwegt gerard at
Fri Jan 27 19:20:51 EST 1995

In article <3g8f7c$8hv at>, smb18 at (Simon Brocklehurst (Bioc)) writes:
|> gerard at (Gerard Kleijwegt) writes:
|> >And how many experimental observations went into that molecular
|> >dynamics simulation ???  
|>    Quite a lot - ... the X-ray structure was used as input to
|> the program ;-)

As any crystallographer who uses X-PLOR knows, MD is the quickest way
to screw up any perfectly good structure if you switch off the xray
pseudo-energy term; a few ps at room temperature will do it.

|> And what was that about needing 80% identity to get a reasonable 
|> comparative model - is it my imagination, or is your estimate of the 
|> required sequence simliarity going up!


|>    For those that don't know, and aren't able to persuade a crystallographer
|> or NMR spectroscopist to solve the structure of their protein - there are 
|> NO examples of proteins more than 100 residue in length and that share 30% 
|> identity or more, that don't have essentially the same folds. If you've 
|> got more than 50% identity, you probably won't even see too many shifts in 
|> structure of the core.  You can easily build "OK" models in these cases.

- "OK" for what purpose ?  Getting it published ?
  Of course, xtallographers use "homology models" all the time, namely
  when they make search models to be used in Molecular Replacement
  exercises.  Except, rather than assuming they know enough about
  nature to be able to confidently "fill in the blanks" (substitutions,
  deletions & insertions), they usually *strip* the homologous structure
  of any atoms that can be expected to be different (side chains, loops,
  areas of insertions or deletions), and with success !
  May I take the opportunity to suggest a simple test to see if homology
  models are better than random ?  Assume the structure of protein X
  is known, and that it is > 30 % homologous to protein Y.  Now, if someone
  collects xray data of protein Y, a homology model of protein Y should
  at the very least give a clearly better solution in the Molecular
  Replacement than the structure of protein X.  If not, the homology
  model does not contain more information than the structure of the
  'undisturbed' protein X itself (and is therefore equally good as anyone's
  guess, where the xtallographer's guess would be to use a stripped
  version of protein X).

- even if the fold can be predicted, this usually carries very little
  biologically-relevant information.  The most interesting parts of a
  protein are often found in one or more of its loops.  Moreover, at the
  end of the day, you'll only be interested in the conformation of a
  handful of side chains (the active site, a metal-binding site, a ligand-
  binding site, a protein-protein or protein-DNA interface), something
  which even with 80 % homology is often hard to do.  And nature is always
  full of surprises.  For an example, see the structure of cellular
  retinoic-acid binding protein: about 30% homologous to several other
  solved structures, known fold etc.  Still, the few insertions have
  a rather drastic effect on the structure (see Structure 2(12), pp. 1241-58).
  This protein was one of the targets in the prediction competition and
  of course all predictors got the fold right, but the saillant details
  hadn't been modelled correctly by anyone as far as I know.  Who would
  expect that a helix would suddenly be extended by an extra turn, that a
  strand-turn-strand corkscrews over quite some distance, that the
  ligand does not interact with the corresponding residue with which it
  interacts in a related structure, and that the ligand actually sticks
  out of the protein rather than being "engulfed" by it ?
  Not a million years of molecular dynamics is going to model such
  subtle and intricate details (unless you have an xray or noe term
  to switch on ;-).

- if you want to convince me of the contrary, try to predict the structure
  of the ligand-binding domain of any of the family of steroid-hormone
  receptors (thyroid, vitamin D, retinoic acid - have your pick).  If you
  succeed in correctly predicting the fold, the orientation of the ligand,
  and the conformations of the residues interacting with the ligand, I'll stop
  collecting data immediately and become a modeller.

- of course, this doen't mean that every xray or nmr structure is necessarily
  correct or should be believed in all its details, but that's a different

|> -- Simon
|> _________________________________________________________________________
|> |
|> |  ,_ o     Simon M. Brocklehurst,
|> | /  //\,   Oxford Centre for Molecular Sciences
|> |   \>> |   Department of Biochemistry, University of Oxford,
|> |    \\,    Oxford, UK.
|> |           E-mail: smb at
|> |           WWW:
|> |________________________________________________________________________

--Gerard Kleywegt
  BMC, Uppsala

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