Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
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DOI：
10.1002/cbic.200300732
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发表时间：
2004-02-06
期刊：
影响因子：
3.2
通讯作者：
Nussinov, R
中科院分区：
文献类型：
--
作者：
Gunasekaran, K;Nussinov, R
酶中的环柔性在正确定位催化重要残基中起着至关重要的作用。酶的灵活性和功能之间的这种密切关系为设计新的底物和抑制剂提供了机会。它还允许设计定点诱变实验，以通过控制功能环的灵活性来探索酶活性。之前，我们描述了一种新的机制，其中一个小环触发三种酶（β-1，4-半乳糖基转移酶，脂肪酶和烯醇化酶）中功能环的运动，这些酶在序列，结构或功能上无关。在这里，我们进一步解决的问题，各种灵活的循环之间的相互作用如何调制的功能环的运动。我们研究β-1，4-半乳糖基转移酶作为一个模型系统，其中一个长环经历了一个大的构象变化（在空间移动高达20埃）底物结合后，除了一个小环（色氨酸环），显示出一个相当小的构象变化。我们在隐式和显式溶剂中进行的分子动力学模拟表明，除了这两个环，其他两个相邻的环也是高度灵活的。这些环与Long环或Trp环接触。残留物的空间位移的协方差分析表明，耦合运动只发生在这两个循环之一。序列分析表明，在它们的运动相关的环也有高度保守的残基参与环-环相互作用。此外，分析，晶体结构和模拟显式水打开的可能性，触发运动的长环在未结合的构象的色氨酸环也可以发挥相同的作用，通过其与保守的和相关的第三环的基板结合的构象。我们的主张是支持的观察，在第三个循环中的五个保守的位置中的四个是在与色氨酸环的接口。进化似乎选择残基，驱动功能长环到一个大的构象变化。这些观察结果表明，改变选定的环-环相互作用可能会调节功能环的运动。
Loop flexibility in enzymes plays a vital role in correctly positioning catalytically important residues. This strong relationship between enzyme flexibility and function provides an opportunity to engineer new substrates and inhibitors. It further allows the design of site-directed mutagenesis experiments to explore enzymatic activity through the control of flexibility of a functional loop. Earlier, we described a novel mechanism in which a small loop triggers the motions of a functional loop in three enzymes (beta-1,4-galactosyltransferase, lipase, and enolase) unrelated in sequence, structure, or function. Here, we further address the question of how the interactions between various flexible loops modulate the movements of the functional loop. We examine beta-1,4-galactosyltransferase as a model system in which a Long loop undergoes a large conformational change (moves in space up to 20 Angstrom) upon substrate binding in addition to a small loop (Trp loop) that shows a considerably smaller conformational change. Our molecular-dynamics simulations carried out in implicit and explicit solvent show that, in addition to these two loops, two other neighboring loops are also highly flexible. These loops are in contact with either the Long loop or the Trp loop. Analysis of the covariance of the spatial displacement of the residues reveals that coupled motions occur only in one of these two loops. Sequence analysis indicates that loops correlated in their motions also have highly conserved residues involved in the loop-loop interactions. Further, analysis of, crystal structures and simulations in explicit water open the possibility that the Trp loop that triggers the movement of the Long loop in the unbound conformation may also play the same role in the substrate-bound conformation through its contact with the conserved and correlated third loop. Our proposition is supported by the observation that four of the five conserved positions in the third loop are at the interface with the Trp loop. Evolution appears to Select residues that drive the functional Long loop to a large conformational change. These observations suggest that altering selected loop-loop interactions might modulate the movements of the functional loop.