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Questions and answers => General discussions (Q&As) => Topic started by: miriam.llamas on March 21, 2018, 07:40:15 pm

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Title: How to calculate DNA bending angles in protein/DNA complex
Post by: miriam.llamas on March 21, 2018, 07:40:15 pm
Hi Xiang-Jun

In your 2008 3DNA Nature Protocols paper, you explain how to calculate DNA bending angle, i followed the instructions and determinate the angle but in the case of CAP/DNA complex (PDB 1ZRC), i don't have the normalized vector along the "best-fit" helical axis. How can i calculate DNA bending angle of this complex?

Thanks

Miriam
Title: Re: How to calculate DNA bending angles in protein/DNA complex
Post by: xiangjun on March 22, 2018, 12:03:51 am
Hi Miriam,

Thanks for using 3DNA and for posting your question on the Forum.

I've a quick look of PDB entry 1ZRC, and found the following:

Quote
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.54(1.65)

The structure as a whole is curved to fit a sensible linear helical axis, as noted in the $X3DNA/config/misc_3dna.par:

Quote
# Section 4: is this double helix curved?
#   criterion to decide if a helix is strongly curved.
#   if relatively straight, 'analyze' will output a set of
#   global parameters, the normalized axis vector, and the
#   two end points the helical axis passes through
<std_curved>0.6</std_curved>

To calculate a bending angle, you need to divide the DNA into two fragments, each relatively straight. See also FAQ How to calculate DNA bending angle? (http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/)

You may also want to give Curves+ a try. It is frequently used for quantifying DNA curvature in literature.

HTH,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.