[gmx-users] Re: Reg: Validation of Protein-Protein Interaction through simulation

[Justin Lemkul]

On 3/21/13 7:38 AM, Amit wrote:
> Dear Dr. Lemkul,
>                           Many thanks for the reply and suggestion. I
> believe doing docking first and then going for simulation is more
> relevant as this will lessen the nonspecific interaction. Correct me
> if I am wrong. Also I would like to ask one more question. I would

That approach is probably more reasonable.

>  like to simulate gold nanoparticle and protein together. So how can i
> prepare the .pdb and topology file for the nanoparticle as it is
> composed of charged atoms? Please let me know.
>

You need a force field that can handle both protein and gold parameters.  None 
exist by default in Gromacs, but you can introduce new force fields if needed. 
There are many posts about such topics in the list archive, but if you are new 
to Gromacs, you should probably invest significant time learning how things work 
and how the force fields are organized before you try implementing a custom 
force field.  Doing so is a rather advanced task and require thorough knowledge 
of how everything works.

-Justin

> On Thu, Mar 21, 2013 at 4:42 PM, Justin Lemkul [via GROMACS]
> <ml-node+s5086n5006519h62 at n6.nabble.com> wrote:
>>
>>
>> On 3/21/13 5:11 AM, Amit wrote:
>>
>>> Dear Gromacs Users,
>>>                                       I am new to gromacs software  and
>>> currently in learning phase. Currently, I am facing a big problem. I have
>>> two proteins namely A and B. Wet lab results have shown that both A and B
>>> interacts with each other by co-immunoprecipitation techniques. Is there a
>>> way out to know weather protein A really interacts with B through
>>> simulation? Is it possible to simulate both the proteins together in a
>>> single box without doing docking? Can simulation provide the interacting
>>> regions? I want to incorporate both the proteins together in box without
>>> docking. Please correct me if I am wrong.
>>>
>>
>> Depending on the size of the proteins, doing an unbiased simulation of
>> protein-protein binding may or may not be feasible.  There is a high
>> probability
>> of nonspecific interactions, which may or may not be relevant.  If you bias
>> the
>> simulation towards interacting in some preconceived way, then the simulation
>> doesn't show much more than the fact that it did what you told it to do.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================