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首页> 美国卫生研究院文献>Protein Science : A Publication of the Protein Society >Lone pair ··· π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high-resolution protein structures and model compounds
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Lone pair ··· π interactions between water oxygens and aromatic residues: Quantum chemical studies based on high-resolution protein structures and model compounds

机译：水氧和芳族残基之间的孤对···π相互作用：基于高分辨率蛋白质结构和模型化合物的量子化学研究

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摘要

The π electron cloud of aromatic centers is known to be involved in several noncovalent interactions such as C—H···π, O—H···π, and π···π interactions in biomolecules. Lone-pair (lp) ··· π interactions have gained attention recently and their role in biomolecular structures is being recognized. In this article, we have carried out systematic analysis of high-resolution protein structures and identified more than 400 examples in which water oxygen atoms are in close contact (distance < 3.5 Å) with the aromatic centers of aromatic residues. Three different methods were used to build hydrogen atoms and we used a consensus approach to find out potential candidates for lp···π interactions between water oxygen and aromatic residues. Quantum mechanical calculations at MP2/6-311++G(d,p) level on model systems based on protein structures indicate that majority of the identified examples have energetically favorable interactions. The influence of water hydrogen atoms was investigated by sampling water orientations as a function of two parameters: distance from the aromatic center and the angle between the aromatic plane and the plane formed by the three water atoms. Intermolecular potential surfaces were constructed using six model compounds representing the four aromatic amino acids and 510 different water orientations for each model compound. Ab initio molecular orbital calculations at MP2/6-311++G(d,p) level show that the interaction energy is favorable even when hydrogen atoms are farthest from the aromatic plane while water oxygen is pointing toward the aromatic center. The strength of such interaction depends upon the distance of water hydrogen atoms from the aromatic substituents. Our calculations clearly show that the lp···π interactions due to the close approach of water oxygen and aromatic center are influenced by the positions of water hydrogen atoms and the aromatic substituents.
机译：已知芳族中心的π电子云参与生物分子中的几种非共价相互作用，例如CH···π，OH···π和π··π的相互作用。孤对（lp）···π相互作用最近已引起关注，并已认识到它们在生物分子结构中的作用。在本文中，我们对高分辨率的蛋白质结构进行了系统分析，并确定了400多个水氧原子与芳香族残基的芳香中心紧密接触（距离<3.5Å）的例子。三种不同的方法被用来构建氢原子，并且我们采用一种共识方法来寻找水氧与芳族残基之间的lp···π相互作用的潜在候选物。在基于蛋白质结构的模型系统上，在MP2 / 6-311 ++ G（d，p）级别进行的量子力学计算表明，大多数鉴定出的实例在能量上都具有有利的相互作用。通过采样水取向作为两个参数的函数，研究了水氢原子的影响：两个参数分别是：距芳族中心的距离以及芳族平面与三个水原子形成的平面之间的夹角。使用代表四种芳族氨基酸的六个模型化合物和每个模型化合物的510个不同的水向构造分子间势能表面。在MP2 / 6-311 ++ G（d，p）级的从头算分子轨道计算表明，即使氢原子距离芳族平面最远而水氧指向芳族中心时，相互作用能也是有利的。这种相互作用的强度取决于水氢原子与芳族取代基的距离。我们的计算清楚地表明，由于水氧和芳族中心的接近而引起的lp··π相互作用受水氢原子和芳族取代基的位置影响。

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