Floquet Nicolas, Durand Philippe, Maigret Bernard, Badet Bernard, Badet-Denisot Marie-Ange, Perahia David
Institut de Chimie des Substances Naturelles-CNRS, 1 Avenue de la Terrasse-91198 Gif-sur-Yvette, France.
J Mol Biol. 2009 Jan 16;385(2):653-64. doi: 10.1016/j.jmb.2008.10.032. Epub 2008 Oct 19.
The large protein motions of the bacterial enzyme glucosamine-6-phosphate synthase have been addressed using full atom normal modes analysis for the empty, the glucose-6-phosphate and the glucose-6-phosphate+glutamate bound proteins. The approach that was used involving energy minimizations along the normal modes coordinates identified functional motions of the protein, some of which were characterized earlier by X-ray diffraction studies. This method made it possible for the first time to highlight significant energy differences according to whether none, only one or both of the active sites of the protein were occupied. Our data favoured a specific motion of the glutamine binding domain following the fixation of fructose-6-phosphate and suggested a rigidified structure with both sites occupied. Here, we show that most of the collective large amplitude motions of glucosamine-6-phosphate synthase that are modulated by ligand binding are crucial for the enzyme catalytic cycle, as they strongly modify the geometry of both the ammonia channel and the C-tail, demonstrating their role in ammonia transfer and ligand binding.
利用全原子正常模式分析，对空的、结合6-磷酸葡萄糖的以及结合6-磷酸葡萄糖+谷氨酸的细菌酶氨基葡萄糖-6-磷酸合酶的大蛋白运动进行了研究。所采用的方法包括沿正常模式坐标进行能量最小化，从而确定了该蛋白的功能运动，其中一些运动先前已通过X射线衍射研究得以表征。这种方法首次能够根据蛋白的活性位点是未被占据、仅一个被占据还是两个都被占据，突出显示出显著的能量差异。我们的数据支持在6-磷酸果糖固定后谷氨酰胺结合结构域的特定运动，并表明两个位点都被占据时结构会刚性化。在此，我们表明，氨基葡萄糖-6-磷酸合酶的大多数受配体结合调节的集体大幅度运动对于酶催化循环至关重要，因为它们强烈改变了氨通道和C末端的几何形状，证明了它们在氨转移和配体结合中的作用。
