Ciprofloxacin: Difference between revisions

A twinned structure of <scene name='Sandbox_100/Dna_gyrase_normal/1'>DNA Gyrase from Staphylococcus aureus in complex with DNA and Ciprofloxacin</scene> is shown. DNA Gyrase is characterized by its "ironing device" appearance with a <scene name='Sandbox_100/General_gyrase_form_with_dna/1'>base cleft forming the active site for interaction with DNA</scene> (in this scene, DNA Gyrase is light blue, and the dip-like cleft runs the length of the base of the protein. The DNA ligand is black and Ciprofloxacin, as in all scenes under this heading, maintains its atomic color labels). Ciprofloxacin intercalates on DNA at <scene name='Sandbox_100/Outzoom_gyrase_photo_cipro/1'>sites within this cleft</scene> (in this scence, DNA is light brown and is in ball-and-stick formation). Ciprofloxacin inhibits the progression of the action of DNA Gyrase on DNA by attacking and stabilizing successive coils of DNA for <scene name='Sandbox_100/Cipro_in_gyrase/1'>intercalation between corresponding successive grooves of DNA</scene>. The effects of this intercalation on the specific base pairs of participating nucleotides is shown <scene name='Sandbox_100/Another_angle_with_cartoon_dna/1'>here, with base pairs folding out against the interrupting Ciprofloxacin</scene>.This intercalation and consequent stabilization prevents proper unwinding of DNA by DNA Gyrase. An example of specifically interrupted sites on the DNA strand is shown <scene name='Sandbox_100/Spec_grn_dna_interruption_cipr/2'>here, with specifically interrupted DNA in green</scene>. The precise mechanism by which Ciprofloxacin interaction with DNA Gyrase ultimately leads to cell death has not been fully elaborated. However, examination of the location of intercalation of Ciprofloxacin with respect to the amino acid residues of DNA Gyrase near this location leads to the observation that the characteristically polar atoms within the structure of Ciprofloxacin (i.e. fluorine, oxygen, nitrogen) seem to interact with the <scene name='Sandbox_100/Polar_on_polar_gyrase_on_cipro/1'> characteristically polar amino acid residues of DNA Gyrase</scene> (in this scene, all polar amino acid residues are blue). A broader analysis of this location indicates that this location, the active site of the protein in general, is composed, primarily, of <scene name='Sandbox_100/Helix_composition_of_act_site/1'>alpha helices</scene> (in this scene, alpha helices are purple, beta sheets and turns are brown for comparison; DNA is portrayed in dot formation, and Ciprofloxacin is not shown).