Details in Zp(h) definition.

[mauricio esguerra]

Dear Xiang-Jun,

In your cool  and very influential NAR 2003 paper you describe the Zp(h) parameter as:

"Zp(h), equal to half the projection on the local helical axis of the vector, P(II) -> P(I), that links the phosphorus atoms on the two strands forming a given base pair step..."

It appears to me as the only difference between Zp and Zp(h) is that of the election of the reference frame, that is, the middle-frame vs. the local helical axis reference frame.
Is this assumption right?

Thanks for your time on replying to such simple questions,


Mauricio

[xiangjun]

Hi Mauricio,

Thanks for your nice words about our 3DNA NAR03 paper. We did put lots of efforts to make it up to our satisfaction; the paper went through numerous iterations, some of which I still keep a (hard) copy. The paper got published nearly one year after I left Rutgers. It is a solid piece of work, with details (e.g., analysis of non-cannoical base pairs) yet to be fully appreciated by the community of nucleic acid structures.

Now back to your question regarding Zp vs Zp(h), your assumption is right:

the only difference between Zp and Zp(h) is that of the election of the reference frame, that is, the middle-frame vs. the local helical axis reference frame.

The Xp(h)/Yp(h)/Zp(h) set was introduced to parallel Xp/Yp/Zp, just as (X-disp, Y-disp, h-Rise, Incl., Tip, h-Twist) vs. (Shift, Slide, Rise, Tilt, Roll, Twist).

You can easily derive the Zp and Zp(h) etc values for each dinucleotide step from files "stacking.pdb" and "hstacking.pdb", respectively. The difference is most obvious for an A-DNA (e.g., 1ih2) than for a B-DNA (355d).

HTH,

Xiang-Jun