Prominent stacking interaction with aromatic amino acid by N-quarternization of nucleic acid base: X-ray crystallographic characteristics and biological implications.
In order to investigate the mode of interaction between the N-quarternized cytosine base and the aromatic amino acid, the crystal structure of the 3-methyl-cytidine-5'-monophosphate:tryptamine complex was analyzed by X-ray diffraction. The complex crystals were stabilized by extensive hydrogen bond formations in which eight independent water molecules per complex pair participated. A prominent stacking interaction, characterized by a parallel alignment of both rings with a separation distance of ca. 3.4 A, was observed between the cytosine base and the indole ring. Combining the present results with X-ray crystallographic data on the adenine--and guanine--aromatic amino acid interactions, we summarize the structural characteristics observed in the stacking interaction of the N-quarternized nucleic acid base with the aromatic amino acid and discuss their biological implications, especially in connection with the significance of N-protonation of nucleic acid base for selective recognition by protein.
Ishida
T
T
Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, Japan.
Ueda
H
H
Segawa
K
K
Doi
M
M
Inoue
M
M
D000225:Adenine; D000596:Amino Acids; D055598:Chemical Phenomena; D002621:Chemistry; D003460:Crystallization; D003568:Cytidine Monophosphate / Q000031:analogs & derivatives; D003596:Cytosine; D003597:Cytosine Nucleotides; D006147:Guanine; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D014363:Tryptamines; D014961:X-Ray Diffraction
D000596:Amino Acids; D003597:Cytosine Nucleotides; D014363:Tryptamines; C030820:tryptamine; C063543:3-methylcytidine 5'-monophosphate; D006147:Guanine; D003596:Cytosine; D003568:Cytidine Monophosphate; D000225:Adenine