Calculating the Response of NMR Shielding Tensor 蟽(31P) and 2J(31P,13C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg2+

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• 作者：Ladislav Benda ; Bohdan Schneider ; Vladimi虂r Sychrovsky虂
• 刊名：Journal of Physical Chemistry A
• 出版年：2011
• 出版时间：March 24, 2011
• 年：2011
• 卷：115
• 期：11
• 页码：2385-2395
• 全文大小：1010K
• 年卷期：v.115,no.11(March 24, 2011)
• ISSN：1520-5215

文摘

Dependence of NMR ³¹P shielding tensor and ²J(P,C) coupling constants on solvation of nucleic acid phosphate by Mg²⁺ and water was studied using methods of bioinformatic structural analyses of crystallographic data and DFT B3LYP calculations of NMR parameters. The effect of solvent dynamics on NMR parameters was calculated using molecular dynamic. The NMR calculations for representative solvation patterns determined in crystals of B-DNA and A-RNA molecules pointed out the crucial importance of local Mg²⁺ coordination geometry, including hydration by explicit water molecules and necessity of dynamical averaging over the solvent reorientation. The dynamically averaged ³¹P chemical shift decreased by 2鈭?.5 ppm upon Mg²⁺ coordination, the chemical shielding anisotropy increased by 0鈭?0 ppm, and the ²J(P,C5鈥? coupling magnitude decreased by 0.2鈭?.8 Hz upon Mg²⁺ coordination. The calculated decrease of the ³¹P chemical shift is in excellent agreement with the 1.5鈭?0 ppm decrease of the phosphorothioate ³¹P chemical shift upon Cd²⁺ coordination probed experimentally in hammerhead ribozyme (Suzumura; et al. J. Am. Chem. Soc. 2002, 124, 8230鈭?236; Osborne; et al., Biochemistry 2009, 48, 10654鈭?0664). None of the dynamically averaged NMR parameters unequivocally distinguishes the site-specific Mg²⁺ coordination to one of the two nonesterified phosphate oxygen atoms of the phosphate determined by bioinformatic analyses. By comparing the limit cases of static and dynamically averaged solvation, we propose that mobility of the solvent has a dramatic impact on NMR parameters of nucleic acid phosphate and must be taken into account for their accurate modeling.