BACKGROUND Ammonia lyases are enzymes of industrial and biomedical interest. Knowledge of structure-dynamics-function relationship in ammonia lyases is instrumental for exploiting the potential of these enzymes in industrial or biomedical applications. METHODS We investigated the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. At this scope, we used microsecond all-atom molecular dynamics simulations, analyzed with dimensionality reduction techniques, as well as in terms of contact networks and correlated motions. RESULTS We identify two regulatory elements in the MAL structure, i.e., the β5-α2 loop and the helix-hairpin-loop subdomain. These regulatory elements undergo conformational changes switching from 'occluded' to 'open' states. The rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the catalytic site, making the active site more accessible to the substrate when they are in an open state. CONCLUSIONS Our work pinpoints a sequential mechanism, in which the helix-hairpin-loop subdomain of MAL needs to break a subset of intramolecular interactions first to favor the displacement of the β5-α2 loop. The coupled conformational changes of these two elements contribute to modulate the accessibility of the catalytic site. GENERAL SIGNIFICANCE Similar molecular mechanisms can have broad relevance in other ammonia lyases with similar regulatory loops. Our results also imply that it is important to account for protein dynamics in the design of variants of ammonia lyases for industrial and biomedical applications.

中文翻译：

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氨裂解酶中的构象门控。

背景技术氨裂解酶是具有工业和生物医学意义的酶。了解氨裂解酶中的结构-动力学-功能关系有助于开发这些酶在工业或生物医学应用中的潜力。方法 我们研究了作为模型系统的 3-甲基天冬氨酸解氨酶 (MAL) 催化袋附近的构象变化。在这个范围内，我们使用微秒级全原子分子动力学模拟，使用降维技术以及接触网络和相关运动进行分析。结果我们确定了MAL 结构中的两个调节元件，即β5-α2 环和螺旋-发夹-环亚结构域。这些调节元件经历从“封闭”状态到“开放”状态的构象变化。重新排列与活动站点可访问性的变化相关联。β5-α2 环和螺旋-发夹-环亚结构域调节从蛋白质表面到催化位点的隧道的形成，使活性位点在处于开放状态时更容易接近底物。结论 我们的工作确定了一种顺序机制，其中 MAL 的螺旋-发夹-环亚结构域需要首先破坏分子内相互作用的一个子集，以有利于 β5-α2 环的置换。这两种元素的耦合构象变化有助于调节催化位点的可及性。一般意义 类似的分子机制在其他具有类似调节环的氨裂解酶中可能具有广泛的相关性。