Use of quantitative (1)H NMR chemical shift changes for ligand docking into barnase.
(1)H NMR complexation-induced changes in chemical shift (CIS) of HN protons have been used to characterize the complexes of barnase with the deoxyoligonucleotides d(GC) and d(CGAC). Quantitative shift changes are used not only to locate the most probable binding site (using ring-current shifts), but also to determine the orientation of the ligand within the binding site, based on a more complete shift calculation including bond magnetic anisotropies and electric field effects. For both ligands, the guanine is in the same binding site cleft, in the same position as identified in the crystal structure of the d(CGAC) complex. By contrast, a previous X-ray crystal structure of the d(GC) complex showed the ligand in the mouth of the active site, rather than at the guanyl-specific site, implying that the location may be an artifact of the crystallisation process.
Cioffi
Marina
M
Department of Chemistry, University of Sheffield, Brook Hill, UK.
Hunter
Christopher A
CA
Packer
Martin J
MJ
Pandya
Maya J
MJ
Williamson
Mike P
MP
D001426:Bacterial Proteins; D001665:Binding Sites; D020134:Catalytic Domain; D003460:Crystallization; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics; D006147:Guanine / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry* / Q000378:metabolism
D001426:Bacterial Proteins; D008024:Ligands; D009838:Oligodeoxyribonucleotides; D006147:Guanine; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease