Corbett Michael S P, Mark Alan E, Poger David
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
Biophys J. 2017 Feb 28;112(4):595-604. doi: 10.1016/j.bpj.2016.12.042.
Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion.
基于配体结合形式与未结合形式的X射线晶体结构差异,最初有人提出促红细胞生成素受体(EPOR)的激活涉及一种类似剪刀交叉作用的运动。然而,最近这种类似剪刀模型中所涉及运动的有效性受到了质疑。在此,利用原子分子动力学模拟来研究在有和没有促红细胞生成素以及一系列游离于溶液中的激动剂或拮抗剂模拟肽存在的情况下,EPOR二聚体胞外结构域的结构。模拟结果表明,在没有晶体堆积效应的情况下,不同二聚体中的EPOR链采用非常相似的构象,激动剂和拮抗剂结合的复合物之间没有明显区别。这就对现有的EPOR X射线晶体结构是否真的代表活性或非活性构象提出了疑问。该研究表明,利用此类结构推断作用机制存在困难,尤其是对于膜受体而言,除了晶体结构与膜环境结构比较中可能产生的潜在混杂效应外,仅考虑了部分结构。这项工作强调了在不考虑晶格和热运动影响的情况下,赋予晶体环境中与不同配体结合的蛋白质结构间微小差异功能意义的危险性。