Re: [ccp4bb] electrostatic potential and charged residues

[James Stroud]

You could do homology modeling of several homologs using 
http://protein.cribi.unipd.it/Homer/ . Then calculate the electrostatics of the 
homologs.

Better though would be actual structures. How much identity do the homologues 
have? If they are so close that homology modeling works, then you may be able 
to crystallize a few with the information available from the structure you 
already have.

Imagine how powerfully a range of experimental structures would be to support 
your argument that the electrostatics are a conserved feature of the protein.

James


On Sep 14, 2012, at 12:37 PM, Qiang Chen wrote:

> Hi all,
> 
> I'm working on a protein structure which showed a special electrostatic
> potential on its surface: positive on one end and negative on the other
> end. I wonder to what extent I can say this pattern is determined by the
> charged residues? If the residues are conserved, could I make a conclusion
> that its homologues also have such pattern?
> 
> Thanks!
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

Re: [ccp4bb] electrostatic potential and charged residues

[Joel Sussman]

14-Sep-2012   21:50 Rehovot
Dear Qiang
A good example of just such a case is acetylcholinesterase,
where homologous proteins have very similar electrostatic motifs,
with an very large electric dipole, ~1,700.
see three representative papers on this,

1. Ripoll, D. R., Faerman, C. H., Axelsen, P. H., Silman, I. & Sussman, J. L. 
(1993). An electrostatic mechanism for substrate guidance down the aromatic 
gorge of acetylcholinesterase. The Proceedings of the National Academy of 
Sciences U.S.A. 90, 5128-5132.

2. Felder, C. E., Botti, S. A., Lifson, S., Silman, I. & Sussman, J. L. (1997). 
External and internal electrostatic potentials of cholinesterase models. 
Journal of Molecular Graphics and Modelling 15, 318-327.

3. Botti, S. A., Felder, C., Sussman, J. L. & Silman, I. (1998). Electrostatic 
homology modelling of a set of ChE-like neural adhesion proteins identifies a 
shared 'annular' motif with ChEs. Structural implications for a 
cell-recognition role of ChEs. Journal of Physiology (Paris) 92, 414-416.

best regards,
Joel
-
Prof. Joel L. Sussman 
joel.suss...@weizmann.ac.il
Pickman Prof. of Structural Biology   +972 (8) 934 4531 - tel
Head, The Israel Structural Proteomics Center (ISPC)  +972 (8) 934 6312 - fax
Department of Structural Biology  
www.weizmann.ac.il/~joel
Weizmann Institute of Science 
www.weizmann.ac.il/ISPC
Rehovot 76100 ISRAEL  
www.proteopedia.org
-

On 14 Sep 2012, at 21:37, Qiang Chen wrote:

Hi all,

I'm working on a protein structure which showed a special electrostatic
potential on its surface: positive on one end and negative on the other
end. I wonder to what extent I can say this pattern is determined by the
charged residues? If the residues are conserved, could I make a conclusion
that its homologues also have such pattern?

Thanks!


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[ccp4bb] electrostatic potential and charged residues

[Qiang Chen]

Hi all,

I'm working on a protein structure which showed a special electrostatic
potential on its surface: positive on one end and negative on the other
end. I wonder to what extent I can say this pattern is determined by the
charged residues? If the residues are conserved, could I make a conclusion
that its homologues also have such pattern?

Thanks!


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.