Ionizable side chains
jiang at LAPLACE.CSB.YALE.EDU
Mon Jul 3 12:43:35 EST 1995
> 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?
I believe you are right that one could include all charges
in the latter stages of refinement.
Uncharging sidechains is only used to prevent those sidechains
from attracting to others (particularly to other molecules)
in the early stages of refinement.
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