Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
Phys Chem Chem Phys. 2010 Nov 14;12(42):14057-66. doi: 10.1039/c004336b. Epub 2010 Sep 20.
The binding pockets within proteins often contain water molecules. The ligand-binding core of ionotropic glutamate receptors represents an example where the binding pocket has many crystallographically reported waters, but the precise role remains unclear. It is also unclear to what extent the dynamic properties of these waters are conserved across the different receptor subtypes. In order to shed some light on these aspects we have performed multiple molecular dynamics simulations of the ligand binding core of four glutamate bound iGluR structures (GluA2, GluK1, GluK2, and GluN2A) and one apo structure (GluA2). We find that the water positions are reproduced from the simulations, but they also reveal that all but one water molecule in the binding site can be rearranged or replaced with water molecules from the bulk that enter the binding site through transient water channels. This one exception is not reported in the apo crystal structure but within 15 ns of simulation, a water molecule enters the site from the bulk suggesting that it is a favoured position regardless of the state of the protein. Further calculations demonstrate that whilst it is not needed in order to be able to predict the correct binding pose, it does contribute a large favourable interaction energy. We also find that one conserved water has a much stronger interaction with the protein in GluA2, GluK1 and GluK2 compared to the GluN2A receptor. The position of this water molecule is such that it can influence the dynamics of the proposed switch in the GluA2 and GluK1/2 receptors.
蛋白质中的结合口袋通常含有水分子。离子型谷氨酸受体的配体结合核心就是一个例子，其中结合口袋中有许多晶体学报道的水分子，但确切的作用仍不清楚。这些水分子的动态特性在不同的受体亚型中是否具有保守性也不清楚。为了阐明这些方面，我们对四种结合谷氨酸的 iGluR 结构（GluA2、GluK1、GluK2 和 GluN2A）和一种apo 结构（GluA2）的配体结合核心进行了多次分子动力学模拟。我们发现，从模拟中可以重现水分子的位置，但也发现结合位点中除了一个水分子之外，所有水分子都可以重新排列或被来自溶剂的水分子取代，这些水分子通过瞬时水通道进入结合位点。这个例外在 apo 晶体结构中并没有报道，但在 15ns 的模拟中，一个水分子从溶剂中进入结合位点，这表明无论蛋白质的状态如何，这个位置都是有利的。进一步的计算表明，尽管它不是预测正确结合构象所必需的，但它确实贡献了大量有利的相互作用能。我们还发现，在 GluA2、GluK1 和 GluK2 中，一个保守的水分子与蛋白质的相互作用比 GluN2A 受体强得多。这个水分子的位置可以影响 GluA2 和 GluK1/2 受体中提出的开关的动力学。
