From owner-chemistry@ccl.net Fri May 14 17:46:01 2010 From: "CompChem Group compchemgroup1---gmail.com" To: CCL Subject: CCL: Effect of sulphate ions on the preparation of the enzyme Message-Id: <-41858-100514141506-22399-dUCGwPz5JgwMk+ZhzLiDsQ- -server.ccl.net> X-Original-From: CompChem Group Content-Type: multipart/alternative; boundary=0016363ba1f42bb591048691da3c Date: Fri, 14 May 2010 19:14:55 +0100 MIME-Version: 1.0 Sent to CCL by: CompChem Group [compchemgroup1]=[gmail.com] --0016363ba1f42bb591048691da3c Content-Type: text/plain; charset=ISO-8859-1 Dear Basma, Removal of sulfate ions from BDP file is sometime * necessary* because they often come from the buffer used in crystalization. Anyhow, you have to ensure that the sulfate ions do not belong to the intrested protein stucure. My recommendation is to read the experimental paper of extraction of this protein, go to BDP website, you may found information. I think all points you asked are very logic and need to answers. Regards, CCG1 2010/5/14 Mahmoud A. A. Ibrahim m.ibrahim() compchem.net < owner-chemistry[a]ccl.net> > Dear Basma > I don't see why you are doing that, replacing sulfate ion with water > molecules!!! > Removing an ion close to the active site affects the binding efficiency, > because of electrostatic interactions. I remember once I was working on a > biosystem, during files preparation step using xleap (inside AMEBR), One Na+ > ion has been added mistakely by xleap at 7 Ang. far apart from the active > site, leaded to changing the binding mode. So, I believe removing sulfate > ion (-2 charge) will dis-stabilize your system without any doubt. > You may like to post why you want to do that, and there should be other > tricks to solve your problem rather than removing the sulfate ion. > Sincerely; > M. Ibrahim > > > On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com < > owner-chemistry[*]ccl.net> wrote: > >> >> Hello, >> Because I am still beginner in the field I need the advices in the >> following items: >> >> The PDB structure that I use for docking have two sulphate ions, one of >> them is very close to the active site and make interaction with it is >> residue. The other is far from it. >> 1- If I removed the sulfate ions from the pocket containing the active >> site am I need to do partial optimization of this part? Because removing >> them give more compact pocket by partial optimization. >> 2- Instead, I think to add two water molecules in the same places of two >> sulfate ions, do you think this way will compensate the removing of sulfate >> ions to avoid the conformational change during the docking? >> 3- But the sulfate ions are *charged* and replacement them by explicit >> water molecules may not be equivalent, right? >> >> I look forward to any response. >> Thanks, >> Basma >> >> >> >> > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim[*]compchem.net > Website: www.compchem.net > Fax No.: +20862342601 > --0016363ba1f42bb591048691da3c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Basma,
Removal of sulfate ions from BDP file is so= metime=A0 necessary because they often come from the buffer used in = crystalization. Anyhow, you have to ensure that the sulfate ions do not bel= ong to the intrested protein stucure. My recommendation is to read the expe= rimental paper of extraction of this protein, go to BDP website, you may fo= und information. I think all points you asked are very logic and need to an= swers.=A0
Regards,
CCG1

2010/5/14 Mahmoud A. A. = Ibrahim m.ibrahim() compchem.net <owner-chemistry[a]= ccl.net>
Dear Basma
I = don't see why you are doing that, replacing sulfate ion with water mole= cules!!!
Removing an ion close to the active site affects the binding efficienc= y, because of electrostatic =A0 interactions. I remember once I was working= on a biosystem, during files preparation step using xleap (inside AMEBR), = One Na+ ion has been added mistakely by xleap at 7 Ang. far apart from the = active site, leaded to changing the binding mode. So, I believe removing su= lfate ion (-2 charge) will=A0dis-stabilize=A0your system without any doubt.=
You may like to post why you want to do that, and there should be othe= r tricks to solve your problem rather than removing the sulfate ion.
<= div>Sincerely;
M. Ibrahim


On Wed, May 12, 2010 at 10:50 AM, Basma Ghazal basmaghazal**ymail.com <owner-chemistry[*]c= cl.net> wrote:

Hello, Because I am still=A0beginner in the field I need the advices in the following items:

The PDB st= ructure that I use for docking have two sulphate ions, one of them is very close to the active site and make interaction with it is residue. The other is far from it.
1- If I removed the sulfate ions from the pocket containing the active site am I ne= ed to do partial optimization of this part? Because removing them give more compact pocket by partial optimization.
2- Instead, I think to add two water molecules in the same places of two sulfate ions, do you think th= is way will compensate the removing of sulfate ions to avoid the conformationa= l change during the docking?
3- But the sulfate ions are charged and replacement them by explicit water molecules may not be equivalent, I look forward to any response.
Thanks,
Basma






--
=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0= The University of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia University,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
=A0 =A0 =A0= =A0 =A0 Email: m.ibrahim[*]compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0Website: www.compchem.net
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 Fax No.: +20862342601
--0016363ba1f42bb591048691da3c--