Vanni Stefano, Neri Marilisa, Tavernelli Ivano, Rothlisberger Ursula
Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology, EPFL, CH-1015 Lausanne, Switzerland.
Biochemistry. 2009 Jun 9;48(22):4789-97. doi: 10.1021/bi900299f.
G protein coupled receptors (GPCRs) are a large family of integral membrane proteins involved in signal transduction pathways, making them appealing drug targets for a wide spectrum of diseases. The recently crystallized structures of two engineered adrenergic receptors have opened new avenues for the understanding of the molecular mechanisms of action of GPCRs. Taking the two crystal structures as a starting point, we carried out submicrosecond molecular dynamics simulations of wild-type beta(1) and beta(2) adrenergic receptors in a lipid bilayer under physiological conditions. These simulations give access to structural and dynamic properties of the receptors in pseudo in vivo conditions. For both systems the overall fold properties of the transmembrane region as well as the binding pocket remain close to the crystal structure of the engineered systems, thus suggesting that the ligand binding mode is not affected by the introduced modifications. Both simulations indicate the presence of one or two internal water molecules absent in both crystal structures and essential for the stabilization of the binding pocket at the interface between transmembrane helices III, IV, and V. The different interactions arising from the substitution of Tyr308 in beta(2)AR into Phe325 in beta(1)AR induce different conformations of the homologous Asn(6.55) inside the binding pockets of the two receptors, suggesting a possible origin of receptor specificity in agonist binding. The equilibrated structures of both receptors recover all of the previously suggested features of inactive GPCRs including formation of a salt bridge between the cytoplasmatic moieties of helices III and VI ("ionic lock") that is absent in the crystal structures.
G蛋白偶联受体（GPCRs）是一大类参与信号转导途径的整合膜蛋白，这使得它们成为治疗多种疾病的有吸引力的药物靶点。最近两种工程化肾上腺素能受体的晶体结构为理解GPCRs的分子作用机制开辟了新途径。以这两种晶体结构为起点，我们在生理条件下对脂质双分子层中的野生型β(1)和β(2)肾上腺素能受体进行了亚微秒级分子动力学模拟。这些模拟能够获取受体在拟体内条件下的结构和动力学性质。对于这两个系统，跨膜区域的整体折叠性质以及结合口袋与工程化系统的晶体结构保持接近，因此表明配体结合模式不受引入修饰的影响。两种模拟均表明在两种晶体结构中均不存在且对于在跨膜螺旋III、IV和V之间的界面处稳定结合口袋至关重要的一个或两个内部水分子的存在。β(2)肾上腺素能受体中Tyr308被替换为β(1)肾上腺素能受体中的Phe325所产生的不同相互作用，诱导了两个受体结合口袋内同源Asn(6.55)的不同构象，这表明了激动剂结合中受体特异性的可能起源。两种受体的平衡结构恢复了所有先前提出的非活性GPCRs的特征，包括在晶体结构中不存在的螺旋III和VI的胞质部分之间形成盐桥（“离子锁”）。
