Thank you for your valuable suggestions. According to your comments, I have
rebuilt the missing amino acid loop and re-run the MD simulation. I am
looking forward to the comparing results in the future.
Thank you again.
2017-09-09 19:16 GMT+08:00 Carlos Simmerling <carlos.simmerling.gmail.com>:
> 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
> > _______________________________________________
> > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 13 2017 - 05:30:03 PDT
