Shift and Tilt values of Z-DNA : 3DNA and Curves+

[mandar]

Dear Dr. Xiang-Jun Lu,
I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp

I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.

What could be the possible reason for such difference? I have searched the forum, but I did not find any discussions related to such discrepancy. 
I have attached PDB file and both output files to the mail. Thanks in advance. I look forward to your reply.

Best Regards,
Mandar Kulkarni

[xiangjun]

Dear Mandar,

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

The questions on differences between 3DNA and Curves+ for Z-DNA structures have not been asked before. Given the sample files you provided, I understand what you mean. I will look into the questions carefully. Since these questions are out of 3DNA per se and technical in nature, it may take me some time to get back to you.

Best regards,

Xiang-Jun

[xiangjun]

Hi Mandar,

I am analyzing Z-DNA duplex (PDB ID: 1I0T.pdb) using 3DNA (v2.3-2017feb08) and Curves+ both. I have removed water and other molecule from PDB and only DNA coordinates are present. The input for Curves+ is generated using find_pair -c+ option.
3DNA command:
find_pair 1I0T.pdb stdout | analyze -c stdin
Curves+ command:
find_pair -c+ 1I0T.pdb curves_1I0T.inp
./Cur+ < curves_1I0T.inp
---------------
I have attached PDB file and both output files to the mail.

Thanks for providing the detailed commands you used and attaching the corresponding data files. I can reproduce your reported results from 3DNA (v2.3) and Curves+.

3DNA is working as expected for the Z-DNA structure (1I0T). For your reference, you could run the following commands:

Code: [Select]

find_pair 1I0T.pdb | analyze   # generate 1I0T.out
rebuild -atomic bp_step.par 1I0T-3dna.pdb
find_pair 1I0T-3dna.pdb | analyze   # generate 1I0T-3dna.out
Comparing the parameters in files 1I0T.out and 1I0T-3dna.out, you'd notice that they are virtually the same. See Table 3 of the 2003 3DNA NAR paper, "Root mean square deviation (in Å ) between rebuilt 3DNA models and experimental DNA structures", for A-, B-DNA, and a DNA-protein complex. Moreover, the simple relationships between step and helical parameters,  see equations 3 and 4 of the above mentioned 3DNA paper, still hold as for right-handed A- or B-DNA.

Note also that you do not need to remove water and other molecule from the PDB file for 3DNA to work.

I observed that the Shift and TIlt values for dinucleotide steps have similar values but exactly opposite signs. Also, X-displacement, Y-displacement, Inclination values are totally different (ignoring terminal base pairs) compared to 3DNA results.

This is a sharp observation. In my understanding (from the perspective of 3DNA), the opposite signs for Shift and Tilt values in Z-DNA are due to different conventions for base-pair reference frames between 3DNA and Curves+. The differences in helical parameters (X-displacement, Y-displacement, Tip, and Inclination) are a bit more complicated, but they are also directly related to the differences in base-pair reference frames. No right or wrong parameters here, just different results based on (maybe slightly) different underneath assumptions. It is up to the users to make their own choices.

In the future, it may be possible that 3DNA and Curves+ could reach an agreement on the analysis of Z-DNA structures or those with non-canonical base pairs. Since both 3DNA and Curves+ are open source, you're welcome to dig into the details of these differences and report back your findings. User-feedbacks are always welcome on the 3DNA Forum.

Hope this clarifies your confusions a bit.

Xiang-Jun

[mandar]

Dear Dr. Xiang-Jun Lu,
I am really thankful for such a detailed reply.  It is very reassuring to know that there are "No right or wrong parameters here" 
I will surely report back discrepancies If I observe any in the further analysis. Thanks a lot once again.

Best Regards,
Mandar Kulkarni