Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state
Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state
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DOI：
10.1073/pnas.1410144111
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发表时间：
2014-12-16
影响因子：
11.1
通讯作者：
Sagi, Irit
中科院分区：
文献类型：
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作者：
Dielmann-Gessner, Jessica;Grossman, Moran;Sagi, Irit
酶学的主要研究重点是酶的速率、底物结构和反应活性，而溶剂动力学由于其复杂的分子行为，在调节生物反应中的作用往往被忽视。我们使用基于X射线和太赫兹的集成时间分辨光谱工具来研究基质金属蛋白酶降解类胶原底物过程中的蛋白质-水动力学。在具有不同超二级结构和柔韧性的两种模型底物胶原和明胶的降解过程中，我们在毫秒时间尺度上显示了结构动力学转变的平衡。出乎意料的是，检测到的酶-底物-水耦合运动的集体变化远远超过了两种底物的稳定状态，同时显示了底物特有的行为。分子动力学模拟进一步表明，水化漏斗(即氢键(HB)动力学向活性位置延缓的梯度)依赖于底物，对于更复杂的酶-胶原系统表现出更陡峭的梯度。蛋白质-水动力学的长期变化反映了底物转化过程中形成的一系列局部能量平衡状态。因此，观察到的长期水动力学有助于净酶反应活性、影响底物结合、位置催化和产物释放。
The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz-based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.