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Author Topic: Chi torsion definition  (Read 6348 times)

Offline kailsen

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Chi torsion definition
« on: November 26, 2015, 01:58:49 pm »
HI ,
I have a doubt on chi angle definition.

My latest version 3DNA has the following definition
          chi in [165, -45(315)] for anti conformation
                 chi in [45, 95] for syn conformation

and DSSR has
  chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
    Range [170, -50(310)] is assigned to anti, and [50, 90] to syn

The following is an excerpt from ur blog on torsion angle sometime ago.
---------------------------------------------
Normally (as in A- and B-form DNA/RNA duplex), χ falls into the ranges of +90° to +180°; –90° to –180° (or 180° to 270°), corresponding to the anti conformation (Figure below, top). Occasionally, χ has values in the range of –90° to +90°, referring to the syn conformation.
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Why is there a difference in the range to define syn and anti?
Why the definition had to be changed compared to the old text definition of ..."+/-90 to +/-180"?
« Last Edit: November 26, 2015, 02:18:41 pm by kailsen »

Offline xiangjun

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Re: Chi torsion definition
« Reply #1 on: November 26, 2015, 02:57:48 pm »
Hi,

I am glad that you noticed the subtle difference in syn vs anti definition implmented in 3DNA vs DSSR for characterzing the relative sugar-base conformation. There are really no 'solid' reasons why I made the change in DSSR from the original 3DNA convention other than the fact that I observed slightly different ways in the literature.

As you can see the DSSR ranges are more restrict, leaving cases for non-syn or anti conformation. In the literature, I also noticed the so-called high-anti conformation etc. Do you have any 'definitive' references in this topic? I'd certainly like to keep it consistent.

Best regards,

Xiang-Jun
« Last Edit: November 26, 2015, 02:59:20 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Offline kailsen

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Re: Chi torsion definition
« Reply #2 on: November 26, 2015, 03:08:17 pm »
Hi  Xiang-Jun,
Thanks for the quick reply.
I am using 3dna and dssr for Left-handed L-RNA which has L-sugar.  I think logically this should not affect syn/ anti anyway. Correct me if I'm wrong.
Also, I know that most commonly standard D-RNA is used as reference.
Can you comment on the parameters that I have to be careful about considering that fact that the RNA is left-handed L-RNA.

Offline xiangjun

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Re: Chi torsion definition
« Reply #3 on: November 26, 2015, 03:26:40 pm »
Hi,

Apart from the syn and anti classification, you always have the chi torsion angle which is not affected by the different definitions. So in practice, the issue may (or should) not be that significant.

What do you mean by D-RNA or left-handed L-RNA? Any references?

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
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Offline kailsen

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Re: Chi torsion definition
« Reply #4 on: November 26, 2015, 04:55:08 pm »
I was referring to the RNA described below.
1R3O.pdb
Crystal structure of the first RNA duplex in L-conformation at 1.9A resolution
DOI: 10.2210/pdb1r3o/pdb

Offline xiangjun

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Re: Chi torsion definition
« Reply #5 on: November 26, 2015, 05:39:16 pm »
Thanks for the ref. I vaguely remember reading this paper before, but did not pay much attention to it. I will read the article on 1cro again, and presumably learn something new. I will post back later, hopefully in a few days.

Regarding syn vs anti ranges of the chi torsion angle, I thought it may help to perform a survey on high resolution RNA structures to see if any pattern emerges. This is an example where user questions prompt me to something I'd otherwise not dig deep.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.