[gmx-users] Re: RE: simulation of a metal binding sites (bharat gupta)

[Ran Friedman]

Hi,

If you know the structure of the zinc binding domain and assume that the zinc ion stays in place it may be all right to use the bonded representation. 

Recent publications:

@article{Lin2010,
author = {Lin, F and Wang, R},
title = {Systematic Derivation of {AMBER} Force Field Parameters Applicable to Zinc-Containing Systems},
journal = {J Chem Theory Comput},
volume = {6},
pages = {1852-1870},
year = {2010}
}


@Article{Peters2010,
author = "Peters, M B and Yang, Y and Wang, B and F{\"u}sti-Moln{\'a}r, L and Weaver, M N and Merz, K M",
title = {Structural Survey of Zinc Containing Proteins and the Development of the Zinc {AMBER} Force Field ({ZAFF})},
journal = "J Chem Theory Comput",
year = "2010",
volume = "6",
pages = "2935-2947"
}

You have to know quite a lot on the structure to use this approach.

Good luck,
Ran.

------------------------------------------------
Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se
http://lnu.se/ccbg
------------------------------------------------

Message: 6
Date: Thu, 17 Feb 2011 23:46:02 -0800
From: bharat gupta <bharat.85.monu at gmail.com>
Subject: Re: [gmx-users] RE: simulation of a metal binding sites
To: Discussion list for GROMACS users <gmx-users at gromacs.org>,
        baaden at smplinux.de
Message-ID:
        <AANLkTi=7rJZLS6B+hQvjNH5Su=Qf3y9AY75eBM9fhSJ8 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thanks for these two references ... I am trying to simulate a zinc ion
(Zn++) binding domains .. Actually the study involves grafting the Zinc ion
domain onto some other protein to check whether it binds to ions or not and
what will be the effect of ion binding onto the topology of  the other
protein to which the zinc ion binding domain is attached .....

On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden <baaden at smplinux.de> wrote:

>
> Hi,
>
> As mentioned by others, there's really lots of literature out there. I
> thought I mention a recent study we carried out, because it actually
> helped discover some new ion binding sites based on MD. By re-examining
> crystal structures based on these results, we could even find
> experimental evidence for those ions being there. [1]
>
> But actually you didn't tell us which ions you want to simulate?
> Monovalent ions should be sort of ok, although there are differences
> among the forcefields (some original KCl used to crystallize).
> Di-valent ions, in particular Ca2+, are much more tricky. Higher
> charged ones are a nightmare. The higher the charge, the more likely
> you might want things like polarization in your simulation.
>
> There are also some specific forcefields finely parameterized for ions
> based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh
> and Piquemal.
>
> Good luck,
>  Marc
>
> [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis
>
> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000
>
> [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed)
> http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html
>
>
> bharat.85.monu at gmail.com said:
> >> Thankx for the reply ...
> >> Can you refer some papers which can be helpful for me to do MD
> >> simulation of proteins with ions ... It will be of great help.. I
> >> searched the gromacs user list but couldn't get much material..
>
>
>
> --
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
>
>
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
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South Korea
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