Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain.
PLoS Comput Biol. 2020 Apr 16;16(4):e1007818. doi: 10.1371/journal.pcbi.1007818. eCollection 2020 Apr.
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
G 蛋白偶联受体(GPCR)的激活过程已在实验和计算上得到了广泛研究。特别是,分子动力学(MD)模拟已被证明在探索 GPCR 构象空间方面非常有用。当从其结晶的非活性状态进行无偏 MD 模拟时,典型的 A 类 GPCR 行为是在非活性和中间(s)构象之间波动,即使与结合的激动剂也是如此。除非结合 G 蛋白,否则很少能稳定完全活性构象(s)。尽管已经解析了几种与共结晶激动剂和 Gs 蛋白结合的腺苷 A2a 受体(A2aR)的晶体结构,但它的激动剂介导的激活过程仍不完全清楚。为了彻底检查 A2aR 激活的构象景观,我们进行了无偏微秒长度的 MD 模拟,重复了四次,从非活性构象开始,无论是在apo 状态还是与结合的激动剂结合:内源性腺苷或合成的 NECA,嵌入在两种均相磷脂膜中:1,2-二油酰基-sn-甘油-3-磷酸甘油(DOPG)或 1,2-二油酰基-sn-甘油-3-磷酸胆碱(DOPC)。在结合了腺苷或 NECA 的 DOPC 中,我们观察到向与已知的结合了腺苷的晶体状态一致的中间受体构象的转变。在 DOPG 的 apo 状态下,获得了两种不同的中间构象。一种与在 DOPC 中结合的腺苷观察到的相似,而另一种则更接近活性状态,但尚未完全活性。仅在结合了腺苷或 NECA 的 DOPG 中,我们可重复识别具有完全活性特征的受体构象,这些构象能够与 Gs 蛋白结合。这些不同的受体构象可归因于激动剂的作用/缺失以及磷脂介导的对受体细胞内侧面的变构效应。