Intrinsic motions along an enzymatic reaction trajectory
Intrinsic motions along an enzymatic reaction trajectory
复制标题
DOI：
10.1038/nature06410
复制
发表时间：
2007-12-06
期刊：
影响因子：
64.8
通讯作者：
Kern, Dorothee
中科院分区：
文献类型：
--
作者：
Henzler-Wildman, Katherine A.;Thai, Vu;Kern, Dorothee
酶实现非凡的速率加速和特异性的机制长期以来一直是生物化学中的关键兴趣。通常认为，与底物-酶复合物的构象变化偶联的底物结合使反应性基团在最佳环境中对齐以实现有效化学。虽然许多酶的化学机制已经被阐明，但酶如何达到催化活性状态的问题直到最近才通过实验和计算变得接近。在这里，我们展示了构象亚态的晶体学证据沿着朝向无配体形式的腺苷酸激酶中的催化活性“封闭”状态的轨迹。分子动力学模拟表明，这些部分封闭的构象是在纳秒采样，而核磁共振和单分子荧光共振能量转移揭示了一个完全封闭的构象发生在微秒到毫秒的时间尺度罕见的采样。因此，无底物腺苷酸激酶的大尺度运动不是随机的，而是优先遵循产生能够熟练化学的构型的途径。这种在折叠中编码的优选方向性可能有助于许多酶中的催化作用。
The mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochemistry. It is generally recognized that substrate binding coupled to conformational changes of the substrate - enzyme complex aligns the reactive groups in an optimal environment for efficient chemistry. Although chemical mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by experiment and computation. Here we show crystallographic evidence for conformational substates along the trajectory towards the catalytically competent 'closed' state in the ligand- free form of the enzyme adenylate kinase. Molecular dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas nuclear magnetic resonance and single- molecule fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond- to- millisecond timescale. Thus, the larger- scale motions in substrate- free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chemistry. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes.