Thursday, April 5, 2012

Catching up on RNA News.

The last post in this blog happened in January and it shied away from the meaty content of RNA.
This is my attempt to catch up, and hopefully to produce at least a brief reminder of RNA related news, mainly for personal use, sorry if this comes out too cryptic for the general public.

Very nicely sold article from the abstract description. It still is to be seen how this new parametrization of fixed charges to dielectric constants works as compared to the traditional TIP3 and SPC, time will tell.
Fennell CJ, Li L, Dill KA.
J Phys Chem B. 2012 Mar 7. [Epub ahead of print]
PMID: 22397577 [PubMed - as supplied by publisher]

Four low-resolution structure determination techniques are evaluated in combination with the MC-SYM MC-FOLD pipeline. The techniques are hydroxyl radical footprinting (OH), methidiumpropyl-EDTA (MPE), multiplexed hydroxyl radical cleavage (MOHCA), and small-angle X-ray scattering (SAXS). There are two sets of interactions proposed to compare the predicted vs. the experimental structures named low and high. The high includes tertiary interactions. As I understand it the experimental data is fit to the MC-SYM MC-FOLD pipeline results to find the best fit between them.
Parisien M, Major F.
J Struct Biol. 2012 Feb 23. [Epub ahead of print]
PMID: 22387042 [PubMed - as supplied by publisher]

These guys sound like physicists using jargon. In this case they are using the Rosetta software to bridge protein structure prediction and RNA loop models, nothing new, but they seem like a powerful group.
Sripakdeevong P, Kladwang W, Das R.
Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20573-8. Epub 2011 Dec 5.
PMID: 22143768 [PubMed - indexed for MEDLINE]

For me it was interesting to see someone combining OPLS and AMBER (old, not the newish Orozco params for nucleic acids), using a molecular dynamics program I didn't know about called MOIL (from a group in U. Texas@Austin headed by a Ron Elber).
It was also surprising to see a non-referenced value for the persistence length of dsRNA as being about 500 base-pairs, that is, > 1500 Angstroms, not even close to the old Hagerman experimental values (around 700 Angstrom), being used as justification for keeping their ARNA's frozen in the simulation, makes you wonder what will happen if they're not kept "frozen". Later I noticed that this was an error and they meant 500 Angstrom, which still is not right, but at least that's the DNA persistence length.
It is interesting also how they sort of compare their results for the radial distribution functions against counterion condensation theory.
The Ionic Atmosphere around A-RNA: Poisson-Boltzmann and Molecular Dynamics Simulations
Serdal Kirmizialtin, Alexander R.J. Silalahi, Ron Elber†, Marcia O. Fenley
Biophysical Journal
Volume 102, Issue 4, 22 February 2012, Pages 829–838

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations
Serdal Kirmizialtin, Suzette A. Pabit, Steve P. Meisburger, Lois Pollack, Ron Elber
Biophysical Journal
Volume 102, Issue 4, 22 February 2012, Pages 819–828

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