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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: lvelve0901 on October 17, 2019, 04:36:41 pm

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Title: About sugar-pi stacking
Post by: lvelve0901 on October 17, 2019, 04:36:41 pm

Hi Xiangjun,

Is sugar-pi stacking currently implemented in the most updated version of SNAP? I am trying analyze the TBP-DNA interaction by using SNAP (PDB: 1QNE)

In the paper: Wilson, K. A., et al. (2014). "DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar." Nucleic Acids Res 42(10): 6726-6741. (https://academic.oup.com/nar/article/42/10/6726/2435280).

The author detect four sugar-pi interaction in the supplementary table.

Amino Acid         Nucleotide
Res Chain ResID Res Chain ResID
F   A   74    A   C   209   sugar-π
F   A   165    T   D   225   sugar-π
F   A   148    A   C   204   sugar-π

When I tried to use x3dna-snap to analyze the structure by typing:
x3dna-snap -i=1qne.pdb --t-shape --more

The output seems only report nt-AA pi-pi stacking.
****************************************************************************
List of 2 base/amino-acid stacks
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1qne  A-phe  C.DA204      A.PHE148        3.45             18
   2  1qne  T-phe  D.DT220      A.PHE57         3.57             23

Could you please let me know whether this is what we expected? Do you know if there are other softwares that can be used to analyze the stacking interaction in general between protein and DNA?

Thank you so much.

Best,
Honglue

Title: Re: About sugar-pi stacking
Post by: xiangjun on October 17, 2019, 04:55:36 pm

Hi Honglue,

The current version of SNAP does not detect sugar-pi stacking interaction in DNA-protein complexes. Only 'classic' stacking interactions between base and planar side chains (e.g., ARG, HIS, TRP etc) are reported. This is one of the areas that would be enhanced in futures releases of SNAP.

Regarding DNA-protein interactions in general, you may want to have a look of DNAproDB (https://dnaprodb.usc.edu/index.html) from the Remo Rohs laboratory. A new paper has just been published in NAR, "DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes (https://doi.org/10.1093/nar/gkz889)".

For sugar-pi stacking in particular, why not ask the authors on how they detected the reported interactions? Hopefully, they may provide directly what you need.

Best regards,

Xiang-Jun

Title: Re: About sugar-pi stacking
Post by: xiangjun on November 08, 2019, 04:27:51 pm

Hi Honglue,

Have you found a solution to your sugar-pi stacking task? If so, you are encouraged to share your findings with the 3DNA Forum community. If you have not found a practical solution yet and you are still interested in this topic, I may consider to add this feature to SNAP.

Best regards,

Xiang-Jun

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