3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: harrymg on March 06, 2013, 07:55:39 am

Title: plot to show DNA conformation
Post by: harrymg on March 06, 2013, 07:55:39 am: BS"D

Dear All,

I would like to create a plot along the lines of protein Ramachandran plot, where one could see changes in the conformation of the DNA. So one could look at the plot and see that the ds DNA was ideal B DNA, or perhaps A DNA, or something else. I want to see how a given stretch of ds DNA changes during an MD simulation, and whether it goes from one type to another. Couldn't really see a previous example of this in the manual....

Thanks

Harry
Title: Re: plot to show DNA conformation
Post by: xiangjun on March 06, 2013, 12:28:44 pm: Hi Harry,

Thanks for posting on the Forum. 3DNA per se does not generate Ramachandran-like plot for DNA or RNA, or any plot of that kind. It calculates various structural parameters that can be plotted using third-party tools. Regarding Ramachandran-like plot for RNA (based on pseudo torsion angles), you may check papers from the Pyle lab (http://pylelab.org/index.html).

3DNA v2.1 has a new option "analyze -torsion" to calculate commonly used torsion angles, including the following section:

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Pseudo (virtual) eta/theta torsion angles: Note: eta: C4'(i-1)-P(i)-C4'(i)-P(i+1) theta: P(i)-C4'(i)-P(i+1)-C4'(i+1) eta': C1'(i-1)-P(i)-C1'(i)-P(i+1) theta': P(i)-C1'(i)-P(i+1)-C1'(i+1) eta": Borg(i-1)-P(i)-Borg(i)-P(i+1) theta": P(i)-Borg(i)-P(i+1)-Borg(i+1)
To follow DNA conformational changes, you may find our 2000 JMB paper titled "A-form conformational motifs in ligand-bound DNA structures (http://www.ncbi.nlm.nih.gov/pubmed/10891271)" relevant. The work examined a variety of parameters, and found Zp to be the most discriminative between A- and B-form DNAs.

Furthermore, 3DNA v2.1 has a Ruby script x3dna_ensemble that makes analysis of MD simulation trajectories straightforward. We have a new 3DNA JoVE (http://www.jove.com/) paper in press that provides protocols for such MD analysis.

HTH,

Xiang-Jun
Title: Re: plot to show DNA conformation
Post by: harrymg on March 07, 2013, 06:53:33 am: BS"D

Dear Xiang-Jun,

Thanks for the reply. It turns out that the PDB validation server also does some analyses (NUCHECK), and gives several different kinds of plots, one of which is based on your algorithm for base morphology comparison. Another one is a scattergram of torsion angles. What I want to compare is actually not so drastic as A to B conversion, rather B to modified B upon protein binding. So I will have to see which parameters allow me to reliably discriminate the changes.

Thanks for the info...

Harry
Title: Re: plot to show DNA conformation
Post by: xiangjun on March 07, 2013, 09:21:25 am: I'd suggest that you pay attention to the Zp parameter, along with some other more commonly used ones.

Good luck with you research!

Xiang-Jun