Protein and Drug Interactions in the Minor Groove of DNA

0181563 - UFCH-W 20020199 RIV GB eng J - Journal Article
Morávek, Z. - Neidle, S. - Schneider, Bohdan
Protein and Drug Interactions in the Minor Groove of DNA.
Nucleic Acids Research. Roč. 30, č. 5 (2002), s. 1182-1191. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT LN00A032
Institutional research plan: CEZ:AV0Z4040901
Keywords : protein * DNA * interactions
Subject RIV: CF - Physical ; Theoretical Chemistry
Impact factor: 7.051, year: 2002

Interactions between proteins, drugs, water and B-DNA minor groove have been analyzed in crystal structures of 60 protein-DNA and 14 drug-DNA complexes. It was found that only purine N3, pyrimidine O2, guanine N2 and deoxyribose O4'' are involved in the interactions, and that contacts to N3 and O2 are most frequent and more polar than contacts to O4''. Many protein contacts are mediated by water, possibly to increase the DNA effective surface. Fewer water-mediated contacts are observed in drug complexes. The distributions of ligands around N3 are significantly more compact than around O2, and distributions of water molecules are the most compact. Distributions around O4'' are more diffuse than for the base atoms but most distributions still have just one binding site. Ligands bind to N3 and O2 atoms in analogous positions, and simultaneous binding to N3 and N2 in guanines is extremely rare. Contacts with two consecutive nucleotides are much more frequent than base-sugar.
Permanent Link: http://hdl.handle.net/11104/0078113