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Questions and answers => General discussions (Q&As) => Topic started by: mfb on June 25, 2010, 10:45:41 am

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Title: relative phase of two helicies
Post by: mfb on June 25, 2010, 10:45:41 am

HI!  I have just joined and am seeking advice on applying 3DNA to analysis of molecular dynamics runs on small RNAs.  I want to measure the relative orientation of two helical segments of an RNA.  I will analyze the two helicies separately, fitting thenm to the full molecule, and then use the "Global linear helical axis coordinates to get the relative angle of the two segments.  

What is described by the three numers follwing "Helix:" in this section?

I am not sure how to get relativet twists (helical phases) of the two segments.  I am considering fitting helices in a trajectory to a standard average helix and then compare the RN9/YN1 lines of the first base pair in each fit helix.  Any better sugestions?

Mike Bruist, University of the Sciences in Philadelphia (mfb)

Title: Re: relative phase of two helicies
Post by: xiangjun on June 25, 2010, 11:46:19 pm

Welcome to join the forum!

Quote

What is described by the three numers follwing "Helix:" in this section?

They are the direction cosines of the global linear helical axis, defined in the coordinate frame of the PDB file. Again, the point is best illustrated with an example. For 355d (bdl084), the portion from 3DNA analyze output is like this:

Code: [Select]

Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix:    -0.127  -0.275  -0.953
HETATM 9998  XS    X X 999      17.536  25.713  25.665
HETATM 9999  XE    X X 999      12.911  15.677  -9.080The two HETATM records are the two ends point defining the helix; using octave (matlab), we have the following relation:

Code: [Select]

XE = [12.911  15.677  -9.080]
XS = [17.536  25.713  25.665]
dd = XE - XS             % [-4.625  -10.036  -34.745]
helix = dd / norm(dd)    % [-0.12685  -0.27526  -0.95296] which is ~ [-0.127  -0.275  -0.953]
Regarding DNA bending analysis, you may also want to play with Curves+ (http://http://www.ncbi.nlm.nih.gov/pubmed/19625494) released by Dr. Lavery. As mentioned in my blog post, Curves+ vs 3DNA (http://http://xiang-jun.blogspot.com/2009/08/curves-vs-3dna.html), Curves+ has features still lacking in 3DNA.

Quote

I am not sure how to get relativet twists (helical phases) of the two segments. I am considering fitting helices in a trajectory to a standard average helix and then compare the RN9/YN1 lines of the first base pair in each fit helix. Any better sugestions?

Could you be more specific, i.e., illustrated with an example what you want to achieve?

HTH,

Xiang-Jun

Title: Re: relative phase of two helicies
Post by: mfb on June 26, 2010, 10:36:23 pm

Thanks for explaining dd.  It is simple enough.

I haven't had a chance to look at Curves+.  I will get back with details on the phasing problem.

Mike

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University