[gmx-users] Re: Salt bridge on Protein Surface

[David van der Spoel]

On Wed, 2004-11-24 at 12:55 +0000, Maarten Wolf wrote:
> >On Wed, 2004-11-24 at 07:03 +0000, Maarten Wolf >wrote:
> >> Hello,
> >>  
> >> I am doing md simulations on a small peptide in water.
> >> These calculations result in a consistent salt bridge on the
> surface
> >> of the protein. 
> >> I find this strange, because I allways thought that salt-bridges on
> >> the surface are easily solvated, and thus broken.
> >> Is this assumption wrong? Or is this force field related? Or
> something
> >> else?  
> >The assumption is wrong in the sense the some >saltbridges are stable
> and
> >others aren't. It may have to do with many things, e.g. a >Lys has
> quite
> >a long hydrophobic that likes being packed. Can also >be force field
> >related, or to the size of your box or the amount of >counterions...
> 
> How might the box size effect the stability of the salt bridge? 
By redistributing the ions, in particular if you use PME.
> 
> I performed another simulation with a lot of counterions. The whole
> protein structure changed, but the salt bridge remained there. Can I
> then say that the protein structure and the number of counterions have
> nothing to do with it?
No, because if you excise a peptide containing the salt bridge it may
still break.


> 
> 
> >>  
> >> Thanks for any help in advance
> 
> 
> >> 
> >> 
> >> MvG Maarten
> >> 
> >> ******************************************************
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> >>
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> >-- 
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assoc. Prof., Molecular >Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >phone:  46 18 471 4205          fax: 46 18 511 755
> >spoel at xray.bmc.uu.se    spoel at gromacs.org
> >http://xray.bmc.uu.se/~spoel
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> +++
> 
> 
> 
> 
> 
> 
> MvG Maarten
> 
> ******************************************************
> ** Work Adress Julianalaan 136 ** 
> ** 2628 BL Delft **
> ** Netherlands **
> ** +31(0)15-2789382 **
> ******************************************************
> 
> 
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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