Contribution of cation-pi interactions to the stability of protein-DNA complexes.
Cation-pi interactions between an aromatic ring and a positive charge located above it have proven to be important in protein structures and biomolecule associations. Here, the role of these interactions at the interface of protein-DNA complexes is investigated, by means of ab initio quantum mechanics energy calculations and X-ray structure analyses. Ab initio energy calculations indicate that Na ions and DNA bases can form stable cation-pi complexes, whose binding strength strongly depends on the type of base, on the position of the Na ion, and whether the base is isolated or included in a double-stranded B-DNA. A survey of protein-DNA complex structures using appropriate geometrical criteria revealed cation-pi interactions in 71% of the complexes. More than half of the cation-pi pairs involve arginine residues, about one-third asparagine or glutamine residues that only carry a partial charge, and one-seventh lysine residues. The most frequently observed pair, which is also the most stable as monitored by ab initio energy calculations, is arginine- guanine. Arginine-adenine interactions are also favorable in general, although to a lesser extent, whereas those with thymine and cytosine are not. Our calculations show that the major contribution to cation-pi interactions with DNA bases is of electrostatic nature. These interactions often occur concomitantly with hydrogen bonds with adjacent bases; their strength is estimated to be from three to four times lower than that of hydrogen bonds. Finally, the role of cation-pi interactions in the stability and specificity of protein-DNA complexes is discussed.
Wintjens
R
R
UMR 8525 CNRS-Université de Lille II, Institut de Biologie de Lille, Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 447, 59021 Lille cédex, France.
Liévin
J
J
Rooman
M
M
Buisine
E
E
D001120:Arginine / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002412:Cations / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D016208:Databases, Factual; D004583:Electrons; D006860:Hydrogen Bonding; D011485:Protein Binding; D012964:Sodium / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity; D013379:Substrate Specificity; D013816:Thermodynamics
D002412:Cations; D004268:DNA-Binding Proteins; D004247:DNA; D001120:Arginine; D012964:Sodium