Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics.
Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics.
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从微秒分子动力学确定的GT-B结构超家族的功能分歧糖基转移酶的保守构象等级。
DOI：
10.3390/ijms22094619
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发表时间：
2021-04-28
影响因子：
5.6
通讯作者：
Sham YY
中科院分区：
文献类型：
--
作者：
Ramirez-Mondragon CA;Nguyen ME;Milicaj J;Hassan BA;Tucci FJ;Muthyala R;Gao J;Taylor EA;Sham YY
长期以来人们已经理解，一些蛋白质在到达米氏复合物的途中经历构象转变以允许化学作用。在GT-B结构类别中的糖基转移酶的晶体结构的检查揭示了在活性位点中的配体的存在触发了它们的催化功能所必需的开放到闭合的构象转变。在这里，我们描述微秒分子动力学模拟的两个遥远的相关的糖基转移酶的一部分，GT-B结构超家族，HepI和GtfA。使用这些未结合的蛋白质的开放和封闭构象进行模拟，分别，我们试图确定的主要动力学模式和通信网络，互连的开放和封闭的结构。我们提供了第一个报告的证据，在我们的模拟参数的范围内，开放和封闭的构象之间的相互转换是一个分层的多步骤的过程，可以是一个保守的功能相同的结构超家族的酶。这些运动中的每一个都涉及分布在两个结构域中的较小分子重新取向的集合，突出了相互转化过程中所涉及的蛋白质动力学的复杂性。此外，采用动态互相关分析来探讨远端残基对HepI催化效率的潜在影响。多个远端不可电离的残基的C-末端结构域表现出的运动与带正电荷的残基在活性位点的N-末端结构域参与底物结合。这些残基的突变导致负相关运动的减少和改变的酶促效率，其主要是由较低的Km值与kcat有效不变。研究结果表明，在开放和关闭的bidomain HepI蛋白的参与与相反的构象运动的残基可以变构改变的人口和构象的“封闭”状态，必不可少的米氏复合物的形成。这些突变的稳定效应可能同样影响催化反应的基态和过渡态的能量，导致kcat不变。我们的研究提供了新的见解构象动力学的作用，糖基转移酶的功能和新的方式来调节酶的效率。
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Simulations were performed using the open and closed conformations of these unbound proteins, respectively, and we sought to identify the major dynamical modes and communication networks that interconnect the open and closed structures. We provide the first reported evidence within the scope of our simulation parameters that the interconversion between open and closed conformations is a hierarchical multistep process which can be a conserved feature of enzymes of the same structural superfamily. Each of these motions involves of a collection of smaller molecular reorientations distributed across both domains, highlighting the complexities of protein dynamic involved in the interconversion process. Additionally, dynamic cross-correlation analysis was employed to explore the potential effect of distal residues on the catalytic efficiency of HepI. Multiple distal nonionizable residues of the C-terminal domain exhibit motions anticorrelated to positively charged residues in the active site in the N-terminal domain involved in substrate binding. Mutations of these residues resulted in a reduction in negatively correlated motions and an altered enzymatic efficiency that is dominated by lower Km values with kcat effectively unchanged. The findings suggest that residues with opposing conformational motions involved in the opening and closing of the bidomain HepI protein can allosterically alter the population and conformation of the “closed” state, essential to the formation of the Michaelis complex. The stabilization effects of these mutations likely equally influence the energetics of both the ground state and the transition state of the catalytic reaction, leading to the unaltered kcat. Our study provides new insights into the role of conformational dynamics in glycosyltransferase’s function and new modality to modulate enzymatic efficiency.
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影响因子：
5.7
作者：
Albesa-Jove, David;Romero-Garcia, Javier;Guerin, Marcelo E.
通讯作者：
Guerin, Marcelo E.
影响因子：
2.9
作者：
Cote, Joy M.;Ramirez-Mondragon, Carlos A.;Taylor, Erika A.
通讯作者：
Taylor, Erika A.
影响因子：
19.6
作者：
Hu, Xiaohu;Hong, Liang;Smith, Jeremy C.
通讯作者：
Smith, Jeremy C.
影响因子：
15
作者：
Krieger, F;Möglich, A;Kiefhaber, T
通讯作者：
Kiefhaber, T
影响因子：
56.9
作者：
FRAUENFELDER, H;SLIGAR, SG;WOLYNES, PG
通讯作者：
WOLYNES, PG