CCL: Regarding sulfate ions

 Sent to CCL by: Greg Warren [greg(_)eyesopen.com]
 Dear Don,
 I must disagree with your statement below and say that sulfate ions are
 physiologically important.  A publication in Am J Physiol Cell Physiol 264:
 C1231-C1237, 1993 estimated that sulfate concentration in the cytoplasm of human
 bronchial epithelial cell was greater than 0.3 mM.  In cases of low chloride
 concentrations the level can be as high as 2 mM.   Sulfate is a physiologically
 important ion and while sulfate present in a crystal structure may and probably
 is an artifact of the experiment it may not be.  There is no way to prove that
 the sulfate modeled or observed isn't structurally or functionally relevant.
 One could attempt to solve the structure under different conditions where
 sulfate concentrations are physiological and show that no sulfate is present in
 the low sulfate concentration structure.  Unfortunately, even that experiment is
 not proof but a strong indication.  The wholesale removal of experimental data
 (sulfate, chloride, ammonium ions, etc.) is a dangerous practice.  In the case
 of protein crystal structures I would be very hesitant to remove (and remodel -
 most likely in the absence of experimental data) information without
 overwhelming evidence that the data is an artifact.
 Regards,
 Greg
 -----Original Message-----
 > From: owner-chemistry+greg==eyesopen.com.:.ccl.net [mailto:owner-chemistry+greg==eyesopen.com.:.ccl.net] On Behalf Of comp chem
 Group compchemgroup1=-=gmail.com
 Sent: Monday, May 24, 2010 3:02 AM
 To: Greg Warren
 Subject: CCL: Regarding sulfate ions
 Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com]
 Dear M. Ibrahim,
 I still remember the questions related to sulfate ions. The person sent this
 message asked very important questions, but so far, no body couldnt answer
 his/her questions. I am amazing from your answer, how you want to consider
 strange ion in the docking process, even though it is not found in the nature
 and consequentially, it has not any biological or chemical role i.e. it has not
 any effect on the active center. However, how and why you goverened his or her
 trial as a blind trick? The principle of simulation is to try to mimic the
 nature not to consider a strange ion come from crystallization.  My believing is
 if the colleague found the sulfate ions dont not belong to the interested
 protein, he/she should remove them. He/she expected all things you said in your
 answers and removing the sulfate ions will affect the geometry and thus he/she
 inquires about the validity of alternatives he/she suggested.  My recommendation
 to the colleague is if he/she found the sulfate ions be!
  long to the pocket of protein, they should be considered otherwise they must be
 removed. And replacing them by water molecules need to test because as I think
 it is a new trick and may be a good trick. Hopefully from the colleague, to tell
 CCL what is happen for geometry including the active center with and without the
 explicit water molecules.
 Don,
 CCG1
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