I don't think there is a simple answer to your question. My personal
feeling is that it is always good to try to simulate the same thing that is
in the experiment, and if you have missing regions of your protein then it
isn't the same. That might affect the results, it might not, I don't think
there is any way to know in advance. If I were making the decision, I would
try to rebuild the entire system because parts of a protein away from the
binding pocket can definitely influence binding - such allosteric effects
are well documented.
One thing to keep in mind is why these residues are missing. Make sure you
read the entire validation report on the RCSB site for your pdb. Which
regions are present in the sample but not in the structure? You should
rebuild them, but being absent in the same often means they are disordered
so might be expected to be flexible in your simulation. However, flexible
is not the same as being deleted.
so to summarize, I would suggest rebuilding them, especially for long time
simulations since their absence can make the protein unstable or change its
conformation and dynamics in ways that will affect your binding pocket. You
haven't said whether you have compared your results to experiment, though,
and if you still get good agreement.
On Sat, Sep 9, 2017 at 3:25 AM, jacky zhao <jackyzhao010.gmail.com> wrote:
> Thank you for your suggestions.
>
>
> I am wondering is it essential for missing amino acid rebuilt before the
> long-time MD simulation. In fact, PDB file obtained from PDB.org usually
> lose some amino acids. These missing amino acids located at binding sites
> should be rebuilded before the perform of MD simulation. However, is it
> necessary to rebuild the missing amino acids outside the binding interface
> before long timescale MD simulation?
>
> Thank you for your help.
>
>
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com>于2017年9月8日 周五下午10:39写道：
>
> > I think people may not be understanding your question. Try to describe
> > exactly what you did and what happened, or maybe get help from someone
> that
> > can help you develop a more clear explanation.
> >
> > On Sep 8, 2017 10:29 AM, "jacky zhao" <jackyzhao010.gmail.com> wrote:
> >
> > > opps,
> > > No one can answer this question?:)
> > >
> > >
> > >
> > > jacky zhao <jackyzhao010.gmail.com>于2017年9月5日 周二下午1:00写道：
> > >
> > > > Hi everyone
> > > > Recently, I have performed protein-protein complex long-time MD
> > > > simulation with more than 1µs by Amber. I am wondering that rebuilt
> the
> > > > missing amino acid gap is essential for long-time MD simulation, even
> > > > though these missing amino acids were not located at the binding
> > > interface?
> > > >
> > > >
> > > > Thank you for taking your time.
> > > >
> > > >
> > > >
> > > > --
> > > > Lei Zhao, Ph.D.
> > > > International Joint Cancer Institute of the Second Military Medical
> > > > University
> > > > National Engineering Research Center for Antibody Medicine
> > > > New Library Building 11th floor,800 Xiang Yin Road
> > > > Shanghai 200433
> > > > P.R.China
> > > >
> > > --
> > > Lei Zhao, Ph.D.
> > > International Joint Cancer Institute of the Second Military Medical
> > > University
> > > National Engineering Research Center for Antibody Medicine
> > > New Library Building 11th floor,800 Xiang Yin Road
> > > Shanghai 200433
> > > P.R.China
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> --
> Lei Zhao, Ph.D.
> International Joint Cancer Institute of the Second Military Medical
> University
> National Engineering Research Center for Antibody Medicine
> New Library Building 11th floor,800 Xiang Yin Road
> Shanghai 200433
> P.R.China
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Received on Sat Sep 09 2017 - 04:30:02 PDT
