From owner-chemistry@ccl.net Mon May 24 12:28:00 2010 From: "Greg Warren greg * eyesopen.com" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41941-100524113201-8116-RG4R9l9ct8ALjU4UEF3lQg:+:server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 May 2010 08:31:51 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg(_)eyesopen.com] Dear Don, I must disagree with your statement below and say that sulfate ions are phy= siologically important. A publication in Am J Physiol Cell Physiol 264: C1= 231-C1237, 1993 estimated that sulfate concentration in the cytoplasm of hu= man bronchial epithelial cell was greater than 0.3 mM. In cases of low chl= oride concentrations the level can be as high as 2 mM. Sulfate is a physi= ologically important ion and while sulfate present in a crystal structure m= ay and probably is an artifact of the experiment it may not be. There is n= o way to prove that the sulfate modeled or observed isn't structurally or f= unctionally relevant. One could attempt to solve the structure under diffe= rent conditions where sulfate concentrations are physiological and show tha= t no sulfate is present in the low sulfate concentration structure. Unfort= unately, even that experiment is not proof but a strong indication. The wh= olesale removal of experimental data (sulfate, chloride, ammonium ions, etc= .) is a dangerous practice. In the case of protein crystal structures I wo= uld 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=3D=3Deyesopen.com.:.ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com.:.ccl.net] On Behalf Of comp chem Group compchemgrou= p1=3D-=3Dgmail.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 thi= s message asked very important questions, but so far, no body couldnt answe= r his/her questions. I am amazing from your answer, how you want to conside= r strange ion in the docking process, even though it is not found in the na= ture and consequentially, it has not any biological or chemical role i.e. i= t has not any effect on the active center. However, how and why you goveren= ed 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 crystallizatio= n. 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 t= he 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 s= ulfate ions be! long to the pocket of protein, they should be considered otherwise they mu= st be removed. And replacing them by water molecules need to test because a= s I think it is a new trick and may be a good trick. Hopefully from the col= league, to tell CCL what is happen for geometry including the active center= with and without the explicit water molecules. =20 Don, CCG1 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt