Deflating the RNA Mg(2+) bubble. Stereochemistry to the rescue!
Deflating the RNA Mg(2+) bubble. Stereochemistry to the rescue!
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DOI：
10.1261/rna.076067.120
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发表时间：
2020-12-02
期刊：
影响因子：
--
通讯作者：
D'Ascenzo L
中科院分区：
文献类型：
--
作者：
Auffinger P;Ennifar E;D'Ascenzo L
通过X射线和冷冻EM技术对生物分子系统的离子结构进行适当的评估仍然具有挑战性，但对于推进我们对潜在结构/活性/溶剂关系的理解至关重要。然而，许多研究高估了沉积结构中Mg 2+的数量，这是由于不正确地考虑立体化学规则而导致的分配错误。在此，为了解决这些问题，我们重新评估了核糖体离子结构的PDBid 6 QNR和6SJ 6模型。我们建立了立体化学的原则，需要仔细考虑时，检查离子结合功能，即使当K+异常信号是可用的情况下，为6 QNR PDB条目。对于核糖体，分配错误会导致对它们的溶剂结构的误解。例如，目前的立体化学分析结果在6 QNR中分配的Mg 2+的数量显着减少，这表明K+而不是Mg 2+是核糖体第一溶剂化壳中的普遍离子。我们强调，使用适当的立体化学的指导方针，结合或不与其他鉴定技术，如那些有关的过渡金属，一些阴离子和K+异常信号的检测，是至关重要的紧缩电流镁2+气泡见证了许多核糖体和其他RNA结构。我们还强调，对于较轻的离子，如Mg 2+，Na+，.，没有异常信号可以检测到，立体化学结合高分辨率结构（<2.4 μ m）仍然是目前最好的选择。
Proper evaluation of the ionic structure of biomolecular systems through X-ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we reevaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when examining ion binding features, even when K+ anomalous signals are available as is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis results in a significant decrease of the number of assigned Mg2+ in 6QNR, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome first solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K+ anomalous signals, is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remains the best currently available option.
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影响因子：
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DOI：
10.1107/s0907444913004745
发表时间：
2013-06-01
影响因子：
2.2
作者：
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通讯作者：
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