Institute of Chemistry, State University of Campinas-UNICAMP, P.O. Box 6154, Campinas, SP, 13084-862, Brazil.
J Phys Chem B. 2010 Jan 28;114(3):1529-40. doi: 10.1021/jp911554p.
The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly alpha-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics simulations of the TRalpha and TRbeta LBDs in the absence and in the presence of the natural ligand Triac. The simulations show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary structure elements, while the structure remains essentially compact, resembling a molten globule state. This differs from most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TRalpha and TRbeta subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H11, and the interaction of the region between H1 and the Omega-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.
核激素受体的配体结合域（LBD）采用非常紧凑的、主要为α螺旋的结构，能够与特异性配体高亲和力结合。我们使用圆二色性光谱和高温分子动力学模拟来研究甲状腺激素受体（TR）的 LBD 解折叠。通过在不存在和存在天然配体 Triac 的情况下对 TRalpha 和 TRbeta LBD 进行分子动力学模拟，获得了变性机制的分子描述。模拟表明，LBD 的热解折叠始于天然接触和二级结构元件的丧失，而结构仍然基本紧凑，类似于无规卷曲状态。这与迄今为止报道的大多数蛋白质变性模拟不同，表明折叠机制可能从 TR LBD 的疏水塌陷开始。我们的结果表明，配体结合对 TRalpha 和 TRbeta 亚型的 LBD 稳定性的影响程度不同，并且配体结合以亚型特异性的方式赋予对热变性和解折叠的保护。我们的模拟表明，配体稳定 LBD 的两种机制：（1）通过增强 H8 和 H11 之间的相互作用，以及 H1 和 Omega 环之间的区域与 LBD 核心之间的相互作用，以及（2）通过屏蔽疏水 H6 与水的相互作用。
