Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor.
Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor.
复制标题
纳米抗体结合对β2肾上腺素能受体的配体特异性活性状态的变构效应。
DOI：
10.1021/acs.jcim.1c00826
复制
发表时间：
2021-12-27
影响因子：
5.6
通讯作者：
Delemotte L
中科院分区：
文献类型：
--
作者：
Chen Y;Fleetwood O;Pérez-Conesa S;Delemotte L
纳米抗体结合使G蛋白偶联受体（GPCR）稳定在完全活性状态，并调节它们对结合配体的亲和力。然而，这种变构调节的原子水平基础仍然难以捉摸。本文通过增强采样分子动力学模拟研究了纳米抗体（Nb80）与活性样β2肾上腺素能受体（β2AR）结合引起的构象变化。构象还原分析表明，Nb 80稳定了β 2 AR的结构特征，使跨膜螺旋6向外移动140 μ m，使跨膜（TM）螺旋5和7非常接近，并有利于受体的完全活性样构象，不依赖于配体结合，这与没有细胞内结合配偶体结合的条件相反，在这种情况下，受体仅稳定在中间活性状态。这种激活由位于TM 5、6和7上的热点处的残基支持，如监督机器学习方法所示。此外，在Nb80的存在下，从各种配体结合受体的轨迹中捕获由细胞内环2和细胞外环2假定的构象中的配体特异性细微差异。动态网络分析进一步揭示了Nb80结合触发Nb80和配体结合位点之间更紧密和更强的局部通信网络，主要涉及ICL2周围的残基和TM3、TM5、TM6的胞内末端，以及ECL 2、ECL 3和TM6和TM7的胞外末端。特别是，我们确定了独特的变构信号传输机制之间的Nb80结合位点和细胞外结构域的构象调制的完全激动剂，BI167107，和G蛋白偏置的部分激动剂，沙美特罗，主要涉及TM1和TM2，和TM5，分别。总之，我们的研究结果提供了深入了解细胞内结合伴侣对GPCR激活机制的影响，这在基于结构的药物发现中应该考虑在内。
Nanobody binding stabilizes G-protein-coupled receptors (GPCR) in a fully active state and modulates their affinity for bound ligands. However, the atomic-level basis for this allosteric regulation remains elusive. Here, we investigate the conformational changes induced by the binding of a nanobody (Nb80) on the active-like β2 adrenergic receptor (β2AR) via enhanced sampling molecular dynamics simulations. Dimensionality reduction analysis shows that Nb80 stabilizes structural features of the β2AR with an ∼14 Å outward movement of transmembrane helix 6 and a close proximity of transmembrane (TM) helices 5 and 7, and favors the fully active-like conformation of the receptor, independent of ligand binding, in contrast to the conditions under which no intracellular binding partner is bound, in which case the receptor is only stabilized in an intermediate-active state. This activation is supported by the residues located at hotspots located on TMs 5, 6, and 7, as shown by supervised machine learning methods. Besides, ligand-specific subtle differences in the conformations assumed by intracellular loop 2 and extracellular loop 2 are captured from the trajectories of various ligand-bound receptors in the presence of Nb80. Dynamic network analysis further reveals that Nb80 binding triggers tighter and stronger local communication networks between the Nb80 and the ligand-binding sites, primarily involving residues around ICL2 and the intracellular end of TM3, TM5, TM6, as well as ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular, we identify unique allosteric signal transmission mechanisms between the Nb80-binding site and the extracellular domains in conformations modulated by a full agonist, BI167107, and a G-protein-biased partial agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively. Altogether, our results provide insights into the effect of intracellular binding partners on the GPCR activation mechanism, which should be taken into account in structure-based drug discovery.
登录
查看更多内容
影响因子：
5.8
作者：
Eargle, John;Luthey-Schulten, Zaida
通讯作者：
Luthey-Schulten, Zaida
影响因子：
64.5
作者：
Du, Yang;Duc, Nguyen Minh;Chung, Ka Young
通讯作者：
Chung, Ka Young
DOI：
10.1073/pnas.1110499108
发表时间：
2011-11-15
影响因子：
11.1
作者：
Dror, Ron O.;Arlow, Daniel H.;Shaw, David E.
通讯作者：
Shaw, David E.
影响因子：
6.8
作者：
Filipek, Slawomir
通讯作者：
Filipek, Slawomir
影响因子：
11.5
作者：
Cazzola, M;Donner, CF
通讯作者：
Donner, CF