Although a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with intricate native state architectures. Some have a complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. Such proteins are multiply connected multidomain proteins (MMPs) with the three-domain (NMP, LID, and CORE) phosphotransferase enzyme adenylate kinase (ADK) being an example. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures (associated with two equilibrium transitions), FRET efficiency as a function of GdmCl concentration, and the folding times quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. Kinetic simulations show that, on the collapse time scale, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network of kinetically connected states reveals that the CORE domain folds only after the NMP and LID domains, reflecting the interwoven nature of the chain topology.

中文翻译：

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具有交织链拓扑的多域蛋白质的协同性和折叠动力学

尽管大部分真核蛋白质组由具有多个结构域的蛋白质组成，但对其组装机制知之甚少，尤其是那些具有复杂天然状态结构的蛋白质组。有些具有复杂的拓扑结构，其中沿序列的结构元素以这样的方式交织在一起，使得域不能通过沿序列的任何位置切割来分离。此类蛋白质是多重连接的多结构域蛋白质 (MMP)，三结构域（NMP、LID 和 CORE）磷酸转移酶腺苷酸激酶 (ADK) 就是一个例子。我们设计了一个粗粒度模型来模拟通过改变温度或氯化胍 (GdmCl) 浓度引发的 ADK 折叠。模拟再现了实验测量的熔化温度（与两个平衡转变相关），FRET 效率作为 GdmCl 浓度的函数，以及定量的折叠时间。尽管 NMP 结构域独立排序，但酶的完整组装需要 LID 和 CORE 结构域之间的协同相互作用。动力学模拟表明，在坍缩时间尺度上，填充了多个相互连接的亚稳态，证明了折叠的异质性。动力学连接状态的网络显示，CORE 域仅在 NMP 和 LID 域之后折叠，反映了链拓扑的交织性质。在坍缩时间尺度上，填充了多个相互连接的亚稳态，证明了折叠的异质性。动力学连接状态的网络显示，CORE 域仅在 NMP 和 LID 域之后折叠，反映了链拓扑的交织性质。在坍缩时间尺度上，填充了多个相互连接的亚稳态，证明了折叠的异质性。动力学连接状态的网络显示，CORE 域仅在 NMP 和 LID 域之后折叠，反映了链拓扑的交织性质。