AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Tue Feb 14 2006 - 04:54:05 CST

PolyC should form i-tetraplex, and this is stable in PME MD.

 Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA:
 stable trajectories on a nanosecond scale
 Spackova N et al.
 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 120 6147-6151 24 1998

 A TETRAMERIC DNA-STRUCTURE WITH PROTONATED CYTOSINE.CYTOSINE BASE-PAIRS
 GEHRING K et al.
  NATURE 363: 561-565 1993

  There is i-RNA too,
  The RNA i-motif
  Snoussi K et al
   JOURNAL OF MOLECULAR BIOLOGY 309 139-153 2001

  Models that are not based on atomic resolution x-ray are often
 incorrect, including many fiber difraction models.

 If NA simulation collapses or distorts shortly after start then
 most likely you attempt to simulate wrong structue, i.e., the
 experimental stucture is not correct.
 It is common with models based on non-atomic resolution experiments,
 happens sometimes with RNA NMR and occaccionally can be the case of atomic
 resolution x-ray, at least regarding details.

 Best wishes, Jiri

> Dear Amber users,
>
> I'm trying to perform the simulation of double stranded
> polyribocytidylic acid but I haven't succeded yet.
> I start with the structure built according to the Langridge and Rich
> data(Nature,1963): helical rise=3.11 A, helical twist=30 degrees, parralel
> strands, each strand consisting of alternating cytosine, protonated
> cytosine residues, so that each pair of the double helix contains one
> protonated cytosine. But even during the minimization my structure
> distorts greatly: bases in pairs become nonplanar and the whole
> structure looks rather like two single-stranded helices twisted one on
> the another, than a double stranded helix. The more steps of the
> minimization I perform, the more distorted structure I obtain.
>
> The parial charges of protonated cytosine I've calculated using resp
> methodology. I've tryed also partial charges of Dr Sponer and Dr
> Spackova but the results were the same. I've used multistage
> minimization with gradually removed positional restraints on the atoms
> of nucleobases, but still got the distorted structure.
> The test 100 ps md runs with implicit solvent starting with partially
> optimized structure(where the bases in base pairs were still coplanar)
> resulted also in distorted structure. When the run was carried without
> restraints the edge residues were mostly distorted, when the weak
> positional restraints were applied to the edge residues - the central
> basepairs were mostly distorted with bases flipping out the helix.
>
> Any suggestions on the problem would be helpful.
> With many thanks in advance,
> Katya
>
> ********************************************
> Kateryna Miroshnychenko
> post-graduate student
> Department of Biological Physics,
> Institute of Radiophysics and Electronics,
> National Academy of Sciences of Ukraine,
> 12, Proskura st., Kharkiv, 61085, Ukraine
> E-mail:kateryna_mirosh_at_ire.kharkov.ua
> ********************************************
>
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