Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics
Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics
复制标题
DOI：
10.1111/j.1742-4658.2007.06027.x
复制
发表时间：
2007-10-01
期刊：
影响因子：
5.4
通讯作者：
Rigden, Daniel J.
中科院分区：
文献类型：
--
作者：
Navarro, Marcos V. de A. S.;Dias, Sandra M. Gomes;Rigden, Daniel J.
在布氏锥虫中，烯醇化酶是一个有效的药物靶点。为了更好地表征其性质并指导药物设计工作，我们确定了该酶在不同连接状态和构象下的六个新的晶体结构，并进行了互补的分子动力学模拟。结果表明，催化中心附近的环具有显著的结构多样性，其变化可以解释为在分子动力学模拟中探索的不同的构象变化模式。我们的结果表明，硫酸盐可能意外地导致催化位点环的完全关闭，而相反，阻滞剂磷酸-乙酰异羟基甲酸酯的结合可能会打开一条从催化位到蛋白质表面的隧道，为药物开发提供了可能性。我们还提出了第一个烯醇化酶与一种新的抑制剂2-氟-2-膦-乙酰羟氨酸酯的复合体。分子动力学结果进一步鼓励了设计不可逆的物种特异性抑制剂的努力：它们揭示了寄生虫酶特异性赖氨酸可能比晶体结构所显示的更接近催化部位，并揭示了寄生虫酶特异性半胱氨酸对化学修饰剂的可及性问题。其中一个新的硫酸盐结构在催化位裂隙中包含一个新的金属结合位IV。
Enolase is a validated drug target in Trypanosoma brucei. To better characterize its properties and guide drug design efforts, we have determined six new crystal structures of the enzyme, in various ligation states and conformations, and have carried out complementary molecular dynamics simulations. The results show a striking structural diversity of loops near the catalytic site, for which variation can be interpreted as distinct modes of conformational variability that are explored during the molecular dynamics simulations. Our results show that sulfate may, unexpectedly, induce full closure of catalytic site loops whereas, conversely, binding of inhibitor phosphonoacetohydroxamate may leave open a tunnel from the catalytic site to protein surface offering possibilities for drug development. We also present the first complex of enolase with a novel inhibitor 2-fluoro-2-phosphonoacetohydroxamate. The molecular dynamics results further encourage efforts to design irreversible species-specific inhibitors: they reveal that a parasite enzyme-specific lysine may approach the catalytic site more closely than crystal structures suggest and also cast light on the issue of accessibility of parasite enzyme-specific cysteines to chemically modifying reagents. One of the new sulfate structures contains a novel metal-binding site IV within the catalytic site cleft.