AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Kateryna Miroshnychenko (
Date: Thu Feb 16 2006 - 04:41:52 CST

Dear Dr Sponer and Dr Ross,

  Thank you very much for your time and suggestions.

> Energy minimization is not the best
> procedure for fixing the model - better would be to use positional
> restraints on the bases and run dynamics in vacuum, e.g. at 10-100K.
I'm performing now this simulation and I'll write later about the
> What I found suspicious in Kateryna's description is the
> vertical distance of base pairs 3.11 A, since each base
> pair is protonated, and thus I would expect increased
> vertical separation.
The value 3.11 A was taken from the Langridge and Rich work, as I've
not found any other information about the helical structure of double
stranded polyrC. I'll try to vary rise and twist to build some other

> Alternative way is to take the i-tetraplex, to remove
> one of its self-intercalated duplexes, and let the rest
> relaxe as duplex via MD.
I've done such two test 100ps simulations with implisit solvent
starting from the modified 190d.pdb with and without weak positional
restraints (5kcal/mol) on the edge residues. In the case when no
positional restraints were applied, the initial structure distorted
greatly and the edge residue of the second strand was caught between
the first(edge) and the second residue of the first strand. The whole
structure seemed compressed compared to the starting duplex. So
probably the rise should be significantly smaller than that of the
duplex from the i-tetraplex. Though the length of duplex in this
simulation was too short(4 bp) and this could also influence the
results. I'm planning to repeat this simulation with longer model

Best regards,

 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

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