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Ionizable side chains

Peter Swaren peter at ecstasy.cemes.fr
Mon Jul 3 10:50:45 EST 1995

--Dear Everybody,

During crystallographic refinement in X-PLOR one turns off the charges on
Glu, Asp, Lys, and Arg side chains. Now I have some (maybe stupid) questions
concerning this. I used to believe that the electrostatic interaction
energies would be too high compared to other energies and that one therefore
should turn off the charges. But since I have not seen anybody turning off the
charges on His side chains although the default is to use doubly protonated 
His, the reason might be different. And what should be done with Nter and Cter
residues? Is it simply so that the force field used in X-PLOR happens to 
produce better result when the side chains of Glu, Asp, Lys, and Arg are 
uncharged while the charges on termini and His are kept? Or is it because
that Glu, Asp, Lys, and Arg side chains are more flexible than the His side
chain (and termini) and therefore could, especially when crystallographic 
waters not yet have been included in the model, make erroneous interactions 
with backbone atoms? Could one then in the latter stages of refinement
include all charges?


Groupe de cristallographie biologique du LPTF 

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31055 TOULOUSE CEDEX 		E-mail: peter at ecstasy.cemes.fr 

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