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Author Topic: Supplementary Figure 2 -- three similar base pairs in tRNA and its mimic  (Read 2164 times)

Offline xiangjun

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"Three similarly positioned base pairs hold the D- and T-loops of tRNA and its viral mimic in place" title="Three similarly positioned base pairs hold the D- and T-loops of tRNA and its viral mimic in place"
Figure S2: Three similarly positioned base pairs that hold the D- and T-loops of tRNAPhe (PDB id: 1ehz, gold) and its viral mimic (PDB id: 4p5j, magenta) in place. The interacting loops in the two molecules are overlaid on the reference frame of the common elbow G–C pair, which is oriented vertically with its major-groove edge facing the viewer, roughly matching Figures 2 and 3 (A-C). Since the two elbow G–C pairs have very similar base- pair parameters, they overlap nearly perfectly. Despite large structural variations between the D-loops, the H2U16+U59 pair in tRNA (B, detailed in D) is similar to the presumably semi-protonated C8+C52 pair (forming an i-motif) in the mimic (C, detailed in E). The other two pairs near the elbow (F and G) are also strikingly alike, despite dramatically dif- ferent modes of interaction. Note that DSSR identifies the C+C pair (E) with the assumed acceptor-acceptor (N3 to N3) hydrogen bond highlighted (red).

Here is the complete script -- it looks quite involved. In essence, however, the logic is quite simple. This example takes advantage of some unique features from DSSR and 3DNA. See notes below.

Code: Bash
  1. # commands for tRNA: 1ehz
  2. pdb_frag A 13:22 A 53:61 1ehz.pdb 1ehz-kissingLoops.pdb
  4. x3dna-dssr -i=1ehz-kissingLoops.pdb -o=1ehz-DT-mEdge.pdb --frame=A.G.19:wc+edge
  5. rotate_mol -r=rotDT 1ehz-DT-mEdge.pdb 1ehz-DT.pdb
  7. pdb_frag A 16 A 18:19 A 55:56 A 59 1ehz-DT.pdb 1ehz-DT-3bps.pdb
  8. x3dna-dssr -i=1ehz-DT-3bps.pdb -o=1ehz-DT-3bps-blocks.r3d --block-file
  10. pymol -qkc 1ehz-DT-3bps.pml
  11. convert -trim +repage -border 10 -bordercolor white 1ehz-DT-3bps-pymol.png 1ehz-DT-3bps.png
  13. x3dna-dssr -i=1ehz.pdb -o=1ehz.out --prefix=1ehz
  15. ex_str -17 1ehz-pairs.pdb 1ehz-p17.pdb
  16. x3dna-dssr -i=1ehz-p17.pdb -o=1ehz-p17.pml --hbfile-pymol
  17. pymol -qkc 1ehz-p17.pml
  18. convert -trim +repage -border 10 -bordercolor white 1ehz-p17-pymol.png 1ehz-p17.png
  20. ex_str -18 1ehz-pairs.pdb 1ehz-p18.pdb
  21. x3dna-dssr -i=1ehz-p18.pdb -o=1ehz-p18.pml --hbfile-pymol
  22. pymol -qkc 1ehz-p18.pml
  23. convert -trim +repage -border 10 -bordercolor white 1ehz-p18-pymol.png 1ehz-p18.png
  25. #------------------------------------------------------------------
  27. # commands for tRNA mimic: 4p5j
  28. pdb_frag A 7:14 A 46:54 4p5j.pdb 4p5j-kissingLoops.pdb
  30. x3dna-dssr -i=4p5j-kissingLoops.pdb -o=4p5j-DT-mEdge.pdb --frame=A.G.10:wc+edge
  31. rotate_mol -r=rotDT 4p5j-DT-mEdge.pdb 4p5j-DT.pdb
  33. pdb_frag A 8:10 A 48:49 A 52 4p5j-DT.pdb 4p5j-DT-3bps.pdb
  34. x3dna-dssr -i=4p5j-DT-3bps.pdb -o=4p5j-DT-3bps-blocks.r3d --block-file
  36. pymol -qkc 4p5j-DT-3bps.pml
  37. convert -trim +repage -border 10 -bordercolor white 4p5j-DT-3bps-pymol.png 4p5j-DT-3bps.png
  39. x3dna-dssr -i=4p5j.pdb -o=4p5j.out --prefix=4p5j
  41. ex_str -7 4p5j-pairs.pdb 4p5j-p7.pdb
  42. x3dna-dssr -i=4p5j-p7.pdb -o=4p5j-p7.pml --hbfile-pymol
  43. pymol -qkc 4p5j-p7.pml
  44. convert -trim +repage -border 10 -bordercolor white 4p5j-p7-pymol.png 4p5j-p7.png
  46. ex_str -8 4p5j-pairs.pdb 4p5j-p8.pdb
  47. x3dna-dssr -i=4p5j-p8.pdb -o=4p5j-p8.pml --hbfile-pymol
  48. pymol -qkc 4p5j-p8.pml
  49. convert -trim +repage -border 10 -bordercolor white 4p5j-p8-pymol.png 4p5j-p8.png
  51. #------------------------------------------------------------------
  53. # combined image
  54. pymol -qkc compare-DT-3bps.pml
  55. convert -trim +repage -border 10 -bordercolor white compare-DT-3bps-pymol.png compare-DT-3bps.png
  • The pdb_frag utility program is distribute with 3DNA. It can be used to extract fragments (here the D- and T-loops) based on chain id and residue numbers from a given PDB file.
  • The --frame option is used to reorient a structure based on specific base or base-pair reference frame. For example, "--frame=A.G.19:wc+edge" sets the kissing-loops in tRNA (1ehz) to the minor-groove edge of the Watson-Crick base-pair formed by G19 on chain A (with C56). Similar functionality may be achieved with "analyze/frame_mol/rotate_mol" using 3DNA. I have integrated some of the useful features into DSSR, mostly for personal convenience.
  • The DSSR --hbfile-pymol option is used to generate a .pml file with all required settings for rendering in PyMOL.
  • The DSSR --block-file option creates a .r3d file with bases (or Watson-Crick base pairs) in rectangular block represention.
  • The convert  program is from ImageMagick that is used here to trim extra white boundaries.
  • The multiplet-png images (here four triplets) were combined using InkScape, and annotated, to get the final illustration.
  • For completeness, here is the tarball file containing all the data files and the script ("tasks"): supp-fig2-tRNA-vs-mimic-3bps.tar.gz

Here are the images generated from the above script:

« Last Edit: August 05, 2015, 05:46:24 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]


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.