Subject: titratable amino acids and counter ions

From: Christian Pilger <[email-masked]>
Date: Mon, 28 May 2001 13:49:36 +0200

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: [email-masked]

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