A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase
A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase
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DOI：
10.1016/j.str.2007.08.010
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发表时间：
2007-10-01
期刊：
影响因子：
5.7
通讯作者：
Carter, Charles W., Jr.
中科院分区：
文献类型：
--
作者：
Kapustina, Maryna;Weinreb, Violetta;Carter, Charles W., Jr.
B。嗜热脂肪菌（stearothermophilus）的双氢酰-tRNA合成酶催化通过高能蛋白质构象进行。与Mg 2 + ATP和（后）过渡态类似物与腺苷四磷酸复合物的前过渡态复合物的未配体MD轨迹在相反的方向上迅速松弛，前者回归，后者沿沿着结构反应坐标前进。因此，这两种晶体结构（Rmsd 0.7 A）位于化学过渡态形成时构象自由能最大值的相对两侧。SNAPP分析说明了相关远程构象偶联的复杂性。四个非极性核心区域的开关相互作用在整个过渡过程中局部等能。然而，不同的配置，传播他们的影响，不利的，在分子表面的长程相互作用。设计突变表明，开关相互作用提高速率，可能是通过不稳定的基态之前的过渡态和限制非生产性扩散之前和之后的化学过渡态，从而降低活化熵。这种模式可以广泛地应用于能量转换酶。
B. stearothermophilus tryptophanyl-tRNA synthetase catalysis proceeds via high-energy protein conformations. Unliganded MD trajectories of the pretransition-state complex with Mg2+ ATP and the (post) transition-state analog complex with adenosine tetraphosphate relax rapidly in opposite directions, the former regressing, the latter progressing along the structural reaction coordinate. The two crystal structures (rmsd 0.7 A) therefore lie on opposite sides of a conformational free-energy maximum as the chemical transition state forms. SNAPP analysis illustrates the complexity of the associated long-range conformational coupling. Switching interactions in four nonpolar core regions are locally isoenergetic throughout the transition. Different configurations, however, propagate their effects to unfavorable, longer-range interactions at the molecular surface. Designed mutation shows that switching interactions enhance the rate, perhaps by destabilizing the ground state immediately before the transition state and limiting nonproductive diffusion before and after the chemical transition state, thereby reducing the activation entropy. This paradigm may apply broadly to energy-transducing enzymes.