Re: AMBER: question capping helix ends

From: Vlad Cojocaru <>
Date: Fri, 24 Mar 2006 11:51:24 +0100

Dear Jenk,

Are you sure that your capped RNA is suppose to be stable ??? What kind
of structure was it?? X-Ray? NMR? Model?

RNA is pretty flexible and sometimes even regions that one expects to be
helical fold into different structures upon protein binding, or in
higher Mg concentrations ...

So, I would assume that you want such an RNA to be stable only if you
know for sure (from experiments) that the RNA should be stable ...
Otherwise, I believe that its even a strength of MD if such RNAs are not
stable ...

Regarding Zhuang problem, at what T do you want to run MD? Why would you
like to run at higher T? If you want to follow some unfolding events,
than I believe there is nothing wrong in helices flying apart ... Anyway
at some point (T), the secondary structure should break ... After all
every RNA has a melting point ...

So, my advice is to start your simulations with exactly the RNA that you
are interested in .. Only after you observe its behavior you can make
judgements on whether what you observe makes sense or not ....

If you look at RNA structures, you'll notice an extraordinary diversity
and sometimes adding additional elements can make a huge difference in
terms of folding .. My belief is that you should consider capping or
modifying and RNA only if you have experimental data that says that the
modified RNA is still functional ...

Best wishes

Cenk Andac wrote:

> Hi Zuang,
> I have had a similar experience with an RNA system which has a 5bp
> A-RNA stem region (mainly G:::C bp ) capped with a 5nt and a 7nt RNA
> fragments from each end. After a 300 ps MD in explicit water at 300 K
> and MM-PBSA computations for 100 snapshots between 150 ps and 300 ps,
> it turned out that my RNA system was energetically not as stable due
> to high electrostatic and van der Waals energy violations. Also the
> G:::C bps at the ends of the RNA helix tends to unwind. Later I pruned
> the 5nt cap from one end to yield an RNA hairpin and rerun MM-PBSA.
> Then I found out that the electrostatic tension over the new RNA
> hairpin system was considerably reduced resulting in a more stable
> structure.
> Hope this helps you in designing your DNA system.
> best regards,
> jenk.
> */Zhuang <>/* wrote:
> Thanks for the reply. I suppose the ends are probably ok if I run my
> simulation at 300K room temperature. But I'm hoping to run it at
> higher temperature in explicit water and I'm worried the ends will fly
> apart at high temperature.
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
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Received on Sun Mar 26 2006 - 06:10:17 PST
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