User:Amy Kerzmann/Sandbox 100710

From Proteopedia

Jump to: navigation, search

Kissing Hairpin Interactions

The structure files shown below were published by Reblova, et al. [1] in the supplementary information portion of their 2003 paper.

 
2-bp Kiss (MMLV), resolution 2.00 Å ().

PDB ID 2cha

Drag the structure with the mouse to rotate
6-bp Kiss (HIV-Lai), resolution 1.34 Å ().

PDB ID 1aq7

Drag the structure with the mouse to rotate
6-bp Kiss (HIV-Mal), resolution 1.78 Å ().

PDB ID 4est

Drag the structure with the mouse to rotate

View the kissing hairpins in cartoons: , , and .

Analyzing nucleobase stacking interactions

  • Highlight the of HIV-Lai.
  • Compare with the , two of which are guanine instead of adenine.
  • Note that the stack of adenines in HIV-Lai is (each base is flipped outside of the helical core).
  • Although the guanine and adenine bases are not stacked in HIV-Mal, those four bases are .

Analyzing electrostatic potential through charge density

  • To examine charge density,highlight of MMLV 2-bp kiss. for clarity.
  • The also provides a region of charge density (or high electrostatic potential) to attract cations.


References

  1. ↑ Reblova K, Spackova N, Sponer JE, Koca J, Sponer J. Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res. 2003 Dec 1;31(23):6942-52. PMID:14627827

Proteopedia Page Contributors and Editors (what is this?)

Amy Kerzmann

Retrieved from "http://52.214.119.220/wiki/index.php/User:Amy_Kerzmann/Sandbox_100710"
Personal tools