[Openmd-users] Streptavidin on biotinylated gold nano-particle

[Mohammad Mahdi Salary Shahrbabaki]

Dear Prof. Gezelter,

Thank you very much for your response.

I was wondering if I can use MARTINI force-field (
http://md.chem.rug.nl/cgmartini/index.php/force-field-parameters) for
attaching PEG-thiol ligands to the surface of gold nano-particle and then
covalently attaching biotin to these ligands. If it would be possible, I
would greatly appreciate your help in implementing MARTINI force-field in
OpenMD.

Best,
Mohammad


On Sat, Nov 22, 2014 at 9:36 AM, Dan Gezelter <gezelter at nd.edu> wrote:

> Dear Mohammad,
>
>   Creating and simulating biotin / streptavidin is possible - if you have
> built OpenMD with the openbabel library, you can use the included atom2md
> program to convert to MD format:
>
> atom2md -ipdb 1STP.pdb -omd 1STP.md -h
>
> This creates the initial input file using the PDB file for the
> streptavidin / biotin complex and protonates the structure.  N.B. some of
> the added hydrogens (e.g. for GLU residues) are probably incorrect.  This
> will need significant cleanup.  If you have a structure for the isolated
> biotin molecule, you can create a simple test case:
>
> atom2md -ipdb biotin.pdb -omd biotin.md
>
> I'm attaching a processed version of the coordinate and include files
> below.  Note that no force field or other parameters have been defined, so
> they won't really be usable until you define a force field.
>
> When you use atom2md, the atom types are created assuming the Amber force
> field for proteins and generic hybridization-typed atoms for non-proteins.
> The primary difficulty with the project you've described is that there
> aren't particularly good models for the cross interactions between the
> metallic gold nanoparticle and charged atom types like the ones in use in
> Amber (and I think biotin also needs some special handling in the Amber
> force field).  The force fields for metals (e.g. EAM and Sutton-Chen) don't
> include metallic polarization, so you'd be missing important components of
> the interaction between the various protein / ligand molecules and the
> particles.
>
> If there are parametrized force fields that you know you want to use, we
> can help you set those up.
>
> Best regards,
>
>  --Dan Gezelter
>
>
>
>
>
>
> > On Nov 20, 2014, at 9:30 PM, Mohammad Mahdi Salary Shahrbabaki <
> salaryshahrbabaki.m at husky.neu.edu> wrote:
> >
> > Dear Professor Gezelter,
> >
> > I am quite naive about molecular dynamics but I need to simulate binding
> of streptavidin molecules to a 20 nm sized biotinylated gold nano-particle
> for my work. I have built the gold nano-particle using the instructions in
> the website. Now I need to add biotin ligands into gold nano-particle and
> then determine the binding sites of streptavidin on the surface of
> biotinylated particle. I was wondering if it is possible to do all of these
> simulations using OpenMD?
> >
> > I would greatly appreciate any help and suggestions you could provide.
> >
> > Best,
> > Mohammad
> > _______________________________________________
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> > Openmd-users at openmd.org
> > http://openmd.org/mailman/listinfo.cgi/openmd-users
>
> ***********************************************
>   J. Daniel Gezelter
>   Associate Professor of Chemistry
>   Department of Chemistry and Biochemistry
>   251 Nieuwland Science Hall
>   University of Notre Dame
>   Notre Dame, IN 46556-5670
>
>   phone:  +1 (574) 631-7595
>   fax:    +1 (574) 631-6652
>   e-mail: gezelter at nd.edu
>   web:    http://www.nd.edu/~gezelter
> ************************************************
>
>
>
>
>
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