Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED, Nijmegen, The Netherlands.
Phys Chem Chem Phys. 2018 Nov 14;20(44):28319-28330. doi: 10.1039/c8cp03314e.
The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.
核苷酸三磷酸（NTPs）的分子家族，以腺嘌呤 5'-三磷酸（ATP）为最著名的成员，在生物化学上具有重要意义，因为它们的磷酸二酯键形成了自然界储存和运输能量的主要方式。在这里，我们对腺嘌呤 5'-三磷酸、胞嘧啶 5'-三磷酸和鸟嘌呤 5'-三磷酸进行了气相红外光谱研究和理论研究，以阐明 NTPs 的固有结构特性，重点研究了碱基和去质子化程度的影响。涉及碰撞诱导解离的质谱研究表明，在所选择的电荷状态下，三种研究的 NTP 具有相似的碎裂通道。双电荷阴离子表现出与自然界中释放能量的水解反应相似的碎裂，而单电荷阴离子则表现出不同的主要碎裂通道，这表明电荷状态在水解反应的有利程度中起着重要作用。红外离子光谱和量子化学计算的组合表明，所有 NTP 的单电荷阴离子优先在其β-磷酸处去质子化，而双电荷阴离子则主要是αβ-去质子化。所分配的三维结构在一方面与 ATP 和 CTP 不同，而在另一方面与 GTP 不同，因为 ATP 和 CTP 之间不存在碱基和磷酸尾巴之间的相互作用，而在 GTP 中它们通过氢键相互作用。这可以通过考虑 NTP 的结构和几何形状来合理化，其中最终的三维结构取决于氢键强度、灵活性和空间位阻之间的微妙平衡。
