Subject: Summary for Examples for Main Chain Flexible Docking

From: "Prof. Luhua LAI" <[email-masked]>
Date: Thu, 20 Nov 1997 14:15:44 -0800 (PST)

Dear CCLers:

Several days ago, I posted the following question:  

We are studying main chain flexibility in protein-protein or protein-ligand
docking. We would like to find some examples where protein main chain
conformation changes significantly when binds with other molecule. Could
someone give me a few examples? 

Thanks for all who responded to the question. The following is a summary for
all the answers. 
 
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 German Sastre                       URL: http://www.ri.ac.uk/DFRL/G.Sastre
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  it could be of interest bearing in mind what happens in some organic bases
  called 'proton sponges':

  some of them have this 'basic group':      

    			R#	 R*
			 \      /
			R-N    N-R
			  |    |       well, sorry about the picture but,
			  C----C       believe it or not, the 'square' is
			  |    |       a naftalene molecule
			  |    |
			  ------

  Now the important thing: in the basic form (as depicted) the repulsion between
  the lone pairs makes the dihedral R#-N-N-R* to have a certain value (the
  dihedral changes through nearly free rotation around the N-C bonds). In the 
  acid form (after getting a H+) that repulsion becomes attraction (now there
  is only one lone pair and the proton), and the dihedral changes accordingly.

  May be you can find a similar effect in your protein-ligand interactions.
  In your case protein makes the role of sponge and ligand plays the role
  of the proton.

  good luck!
  German
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 German Sastre                       URL: http://www.ri.ac.uk/DFRL/G.Sastre
 Instituto de Tecnologia Quimica                 e-mail: [email-masked]
 Universidad Politecnica de Valencia               Phone: +34 (9)6-387-7803
 Camino de Vera s/n; 46071 Valencia (Spain)        Fax:   +34 (9)6-387-7809
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