多巴胺第三受体蛋白三维结构及其活性位点氨基酸残基

Three-Dimensional Structure of Dopamine 3-Subtype Receptor with the Active Site Residues for the Binding of Dopamine

基于牛视紫红质模板蛋白,同源模建多巴胺第三受体(D_3R)蛋白三维结构,在1-棕榈酰-2-油酰-卵磷脂(POPC)膜-水模型环境,开展300 ns分子动力学模拟提炼优化其结构,取得稳定的D_3R蛋白三维结构(2B08-D_3R).在该蛋白基础上,采用MP2/6-31G(d,p)方法,计算多巴胺(Dop)与氨基酸残基相互作用的结合能,确定五个残基(Asp117、Ser208、His272、Phe269和Thr276)为活性位点.五个活性位点残基分别位于D_3R蛋白跨膜螺旋区TM3、TM5和TM6,组成活性空腔结构.多巴胺分子以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键结合方式保留在D_3R蛋白中,与D_3R蛋白结合能E_b为-97.8 kJ·mol^(-1)基于3PBL D_3R突变体晶体结构,构建了另外一个含有多巴胺分子的D_3R蛋白结构(Dop-3PBL-D_3R),确定在该蛋白结构中,多巴胺的活性位点氨基酸是Asp83、His272、Phe269、Phe268和Trp265.在该蛋白结构中,多巴胺分子同样以其苯基平面与TM2-TM7包围的圆柱体空腔平行和非共价键方式结合,与该蛋白相互作用的结合能是-80.5 kJ·mol^(-1).

The dopamine 3-subtype receptor （D3R） is a promising therapeutic target for the development of new drugs. Using rhodopsin as a template protein, we report homology modeling of a complete D3R structure including dopamine （Dop） in an environment of a 1-palmitoyl-2-oleoylsn-glycero-3-phospha-tidyl- choline （POPC） explicit lipid bilayer and water. A 300 ns molecular dynamics （MD） simulation was performed to obtain a stable three-dimensional structure for D3R （2B08-D3R） based on five residues （Asp117, His272, Phe269, Ser208, and Thr276）, and these were validated as active sites for the binding of dopamine to the D3R protein by the binding energies （Eb） calculated using MP2/6-31G（d,p） between Dop and each of the residues within 0.6 nm of Dop. The five key residues are locating on TM3, TM5, and TM6within the D3R helical regions, respectively, forming an active pocket for the binding of Dop to the D3R protein. The phenyl plane of Dop is parallel to the cylinder space formed by the TM2-TM7 helical regions when it bonds non-covalently to the D3R protein. The value of Eb between the Dop and D3R protein is -97.8 kJ. mol-1, which explains why dopamine is easily assimilated into the D3R protein and departs from it as a nerve material and a signal transducer. Using the crystal protein structure of mutated D3R （code： 3PBL） we built another D3R protein structure including dopamine （designated Dop-3PBL-D31R） and identified five residues （Asp83, His272, Phe269, Phe268, and Trp265） as the active sites for the binding of Dop. The phenyl plane of Dop is also parallel to the cylinder space that is formed by the TM2-TM7 helical regions when it binds non-covalently to the Dop-3PBL-D3R protein with an Eb of -80.5 k J·mol-1 between them.