Dear protein modelers,
while preparing a protein structure as input for MD simulations, I
encountered the following points, which I would like to ask your advice:
- How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ?
Are all of them simply taken in their ionized forms ? Would it be good
to try to rationalize the ionization states of these residues by
manually inspecting their environment ? Which methods/rules of thumb are
available for the estimation of these ionization states ?
- In my case the protein has an experimentally determined isoelectric
point of roughly pH=4.7. Does this mean, that the protein will have a
negative net charge at pH=7 ? Then, is there a method to correlate the
isoelectric point with this net charge ? And, are MD calculations
reasonable, when the net charge of the system differs from zero ?
- In case the net charge is neutralized by counter ions: how and where
should these be positioned ? Should one counter ion be placed directly
at each titratable residue (i.e. number of counter ions = number of
ioniziable residues) or should counter ions be placed (arbitrarily ?)
around the protein structure (i.e. number counter ions = net charge of
the whole system) ?
Any comments are highly appreciated.
Cheers,
Christian
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Dr. Christian Pilger Uni-GH Paderborn
FB 13 - Organische Chemie
Warburger Str. 100
D-33098 Paderborn/Germany
Tel.: 05251-602498
Fax : 05251-603245 email: cpilger_at_oc30.uni-paderborn.de
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Received on Mon May 28 2001 - 04:49:36 PDT
