Transition states. Trapping a transition state in a computationally designed protein bottle.
Transition states. Trapping a transition state in a computationally designed protein bottle.
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DOI：
10.1126/science.aaa2424
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发表时间：
2015-02-20
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影响因子：
--
通讯作者：
Schultz PG
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文献类型：
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作者：
Pearson AD;Mills JH;Song Y;Nasertorabi F;Han GW;Baker D;Stevens RC;Schultz PG
化学反应过渡态的短暂寿命使得用衍射法测定其三维结构成为一项挑战。在这里，我们使用蛋白质核心内的堆积相互作用来稳定平面TS，使其围绕联苯的中心C-C键旋转，以便可以通过X射线结晶学直接观察到。使用计算蛋白质设计软件Rosetta设计了一个口袋，该口袋位于嗜热嗜热杆菌的苏氨酰转移RNA合成酶内，与平面联苯形成互补的van der Waals相互作用。后一部分被生物合成地引入为非典型氨基酸对联苯丙氨酸的侧链。通过反复的计算设计和结构分析，我们确定了一种蛋白质，其中对联苯丙氨酸的侧链被动力学地捕获在键旋转反应的TS的能量不利的共面构象中。
The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Herein we use packing interactions within the core of a protein to stabilize the planar TS for rotation around the central C-C bond of biphenyl so that it can be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis we identified a protein in which the side chain of p-biphenylalanine is kinetically trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.