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Questions and answers => RNA structures (DSSR) => Topic started by: zhhxu on June 25, 2020, 10:43:06 am

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Title: torsion angle distribution in C2'-endo RNA
Post by: zhhxu 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
Title: Re: torsion angle distribution in C2'-endo RNA
Post by: xiangjun 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
Title: Re: torsion angle distribution in C2'-endo RNA
Post by: zhhxu 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
Title: Re: torsion angle distribution in C2'-endo RNA
Post by: xiangjun 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
Title: Re: torsion angle distribution in C2'-endo RNA
Post by: zhhxu 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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University