Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
Structure. 2021 Sep 2;29(9):940-950.e4. doi: 10.1016/j.str.2021.02.006. Epub 2021 Mar 12.
Ligands bind to an occluded orthosteric ligand-binding pocket within the nuclear receptor ligand-binding domain. Molecular simulations have revealed theoretical ligand entry/exit pathways to the orthosteric pocket; however, it remains unclear whether ligand binding proceeds through induced fit or conformational selection mechanisms. Here, using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and surface plasmon resonance analysis, we provide evidence that structurally distinct agonists bind peroxisome proliferator-activated receptor γ (PPARγ) via a two-step induced fit mechanism involving an initial fast kinetic step followed by a slow conformational change. The agonist encounter complex binding pose is suggested in crystal structures where ligands bind to a surface pore suggested as a ligand entry site in molecular simulations. Our findings suggest an activation mechanism for PPARγ whereby agonist binding occurs through an initial encounter complex followed by a transition of the ligand into the final binding pose within the orthosteric pocket, inducing a transcriptionally active conformation.
配体结合到核受体配体结合域内的封闭的变构配体结合口袋。分子模拟已经揭示了进入变构口袋的理论配体进入/退出途径；然而，配体结合是通过诱导契合还是构象选择机制进行，目前仍不清楚。在这里，我们使用核磁共振波谱、等温滴定量热法和表面等离子体共振分析，提供了结构不同的激动剂通过两步诱导契合机制结合过氧化物酶体增殖物激活受体γ（PPARγ）的证据，该机制涉及初始快速动力学步骤，随后是缓慢的构象变化。在晶体结构中，配体结合到一个表面孔中，在分子模拟中，该表面孔被认为是配体进入位点，提出了激动剂结合复合物的结合构象。我们的发现为 PPARγ 的激活机制提供了线索，即激动剂结合是通过初始的结合复合物发生的，然后配体在变构口袋内转变为最终的结合构象，诱导出转录活性构象。
