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

[Justin Lemkul]

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

-- 
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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

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