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Author Topic: torsion angle distribution in C2'-endo RNA  (Read 113 times)

Offline zhhxu

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torsion angle distribution in C2'-endo RNA
« on: June 25, 2020, 10:43:06 am »
Hi everyone:

RNA can adpot two sugar-pucker comformations: C3'-endo and C2'-endo. The latter is lower popolation weight. Have someone noticed any reference about statistical analysis of the torsion angle (i.e alpha-zeta) for C2'-endo RNA. Thank you in advance.

Best regards

zhonghe

Offline xiangjun

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Re: torsion angle distribution in C2'-endo RNA
« Reply #1 on: June 25, 2020, 11:15:25 am »
Hi Zhonghe,

The following paper may be of (some) interest to you: Sokoloski, Joshua E., et al. "Prevalence of syn nucleobases in the active sites of functional RNAs." RNA 17.10 (2011): 1775-1787.

Other relevant papers? Please chime in.

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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Offline zhhxu

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Re: torsion angle distribution in C2'-endo RNA
« Reply #2 on: June 25, 2020, 11:28:56 pm »
Hi Xiang-Jun,

Thanks for your prompt reply. I also found some relevant works (JANE S. RICHARDSON) about torsion angle in C2'-endo RNA, including: "RNA backbone is rotameric" , “RNA backbone: Consensus all-angle conformers and modular string nomenclature", and  "Computational methods for RNA structure validation and improvement".  Thanks again for your suggestion.

Best regards,

Zhonghe

Offline xiangjun

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Re: torsion angle distribution in C2'-endo RNA
« Reply #3 on: June 26, 2020, 12:12:58 am »
Hi Zhonghe,

Thanks for your follow-up. Yes, the Richardson publications you listed are highly relevant. Did you know that DSSR also calculate suiteness? Using 1msy as an example:

Code: Text
  1. x3dna-dssr -i=1msy.pdb
  2. more dssr-torsions.txt
  3. # A2654 and G2655 are in C2'-endo conformation

Using DSSR, it would be straightforward to survey RNA structures (of your choice) and find all nucleotides with C2'-endo sugars. The results could be easily parsed with the --json option. Moreover, DSSR provides context information.

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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Offline zhhxu

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Re: torsion angle distribution in C2'-endo RNA
« Reply #4 on: June 29, 2020, 10:56:30 am »
Hi Xiang-Jun,

Sorry for the delay in replying. It is convenient to use DSSR to charcterize the structural feature of C2'-endo RNA. Thanks for your suggestion.

Best regards


Zhonghe

 

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.