Malleability of folding intermediates in the homeodomain superfamily
Malleability of folding intermediates in the homeodomain superfamily
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DOI：
10.1073/pnas.1101752108
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发表时间：
2011-04-05
影响因子：
11.1
通讯作者：
Fersht, Alan R.
中科院分区：
文献类型：
--
作者：
Banachewicz, Wiktor;Religa, Tomasz L.;Fersht, Alan R.
同源结构域超家族的成员是三螺旋束蛋白，其第二和第三螺旋形成螺旋-转角-螺旋基序（HTH）。他们的折叠机制幻灯片从超快，三态框架机制的enrailed同源结构域（EnHD），其中HTH基序是独立稳定的，一个明显的两个国家的成核缩合模型的家庭成员与不稳定的HTH基序。EnHD的折叠中间体具有接近天然的HTH结构，但它不与helix 1对接。是否两个或三个状态的折叠的决定因素被假设为HTH子结构的稳定性。在这里，我们描述了一个详细的F值分析的Pit 1同源结构域，它具有类似的超快动力学的EnHD的折叠。螺旋1的形成与HTH的形成强烈耦合，这最初是令人惊讶的，因为它们在EnHD折叠中间体中是解偶联的。然而，我们发现了Pit 1和EnHD之间的关键区别：与Pit 1中的HTH基序对应的分离肽在没有H1的情况下不折叠。Pit 1展开的独立分子动力学模拟发现H1错误折叠到HTH基序上的中间体。Pit 1折叠途径是EnHD和较慢折叠的同源结构域之间的连接，并在该超家族中提供了从两态折叠到三态折叠的机制过渡的链接。折叠中间体的延展性可以导致不稳定的亚结构通过各种非天然相互作用而稳定，从而增加了折叠机制的连续性。
Members of the homeodomain superfamily are three-helix bundle proteins whose second and third helices form a helix-turn-helix motif (HTH). Their folding mechanism slides from the ultrafast, three-state framework mechanism for the engrailed homeodomain (EnHD), in which the HTH motif is independently stable, to an apparent two-state nucleation-condensation model for family members with an unstable HTH motif. The folding intermediate of EnHD has nearly native HTH structure, but it is not docked with helix1. The determinant of whether two-or three-state folding was hypothesized to be the stability of the HTH substructure. Here, we describe a detailed F-value analysis of the folding of the Pit1 homeodomain, which has similar ultrafast kinetics to that of EnHD. Formation of helix1 was strongly coupled with formation of HTH, which was initially surprising because they are uncoupled in the EnHD folding intermediate. However, we found a key difference between Pit1 and EnHD: The isolated peptide corresponding to the HTH motif in Pit1 was not folded in the absence of H1. Independent molecular dynamics simulations of Pit1 unfolding found an intermediate with H1 misfolded onto the HTH motif. The Pit1 folding pathway is the connection between that of EnHD and the slower folding homeodomains and provides a link in the transition of mechanisms from two-to three-state folding in this superfamily. The malleability of folding intermediates can lead to unstable substructures being stabilized by a variety of nonnative interactions, adding to the continuum of folding mechanisms.