Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7
Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7
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DOI：
10.1016/j.bcp.2008.08.026
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发表时间：
2008-12-01
影响因子：
5.8
通讯作者：
Tramontano, Anna
中科院分区：
文献类型：
--
作者：
Raimondo, Domenico;Giorgetti, Alejandro;Tramontano, Anna
Itch是泛素E3连接酶E6AP羧基端（HECT）结构域家族的一员，与泛素激活酶（E1）和泛素偶联酶（E2）协同作用，催化蛋白靶点的泛素化。这个E3s亚家族共享350个残基c端HECT结构域，具有严格保守的催化Cys，并招募其同源的泛素负载E2。HECT结构域具有内在的酶活性，通过从E2中接受泛素，形成泛素硫酯中间体，并直接催化靶蛋白的泛素化。对于HECT-E2结合和随后的泛素转移的结构关系的生化机制，已经提出了几个假设。尽管如此，对这一过程的详细描述仍然缺失。在这项工作中，我们使用了分子动力学模拟、自由能计算、蛋白质建模技术和正常模式分析来更深入地表征这种相互作用机制的静态和动态特性。我们假设一个相关的慢频运动涉及HECT域的两个不同的铰链区域。鉴定负责HECT-E2相互作用的氨基酸残基，以及泛素转移过程的动力学特性，可能对药理学和治疗目的有相关的兴趣。(c) 2008爱思唯尔公司版权所有。
Itch, a member of the E6AP carboxy terminus (HECT) domain-containing family of ubiquitin E3 ligases, acts in concert with the ubiquitin activating enzyme (E1) and the ubiquitin conjugating enzyme (E2) to catalyze ubiquitylation of protein targets. This sub-family of E3s shares a 350 residue C-terminal HECT domain having a strictly conserved catalytic Cys, and recruiting its cognate ubiquitin-loaded E2. HECT domains possess intrinsic enzymatic activity, by accepting ubiquitin from an E2, forming a ubiquitin thiolester intermediate, and directly catalyzing ubiquitylation of the target protein. Several hypotheses have been proposed for the biochemical mechanism underlying the structural relationship of the HECT-E2 association and subsequent ubiquitin transfer. Nonetheless, a detailed characterization of the process is still missing. In this work, we have used molecular dynamic simulations, free energy calculations, protein modelling techniques and normal modes analysis to get a deeper characterization of the static and dynamical properties of this interaction mechanism. We hypothesize a correlated slow-frequency motion that involves two different hinge regions of the HECT domain. The identification of the amino acid residues responsible for the HECT-E2 interaction, and for the dynamical properties of the ubiquitin transfer process, may be of relevant interest for pharmacological and therapeutical purposes. (c) 2008 Elsevier Inc. All rights reserved.