Citation: JIN Yi, WANG Yue, BIAN Fu-Yong, SHI Qiang, GE Mao-Fa, WANG Shu, ZHANG Xing-Kang, XU Si-Chuan. Three-Dimensional Structure of Dopamine 3-Subtype Receptor with the Active Site Residues for the Binding of Dopamine[J]. Acta Physico-Chimica Sinica, ;2011, 27(10): 2432-2446. doi: 10.3866/PKU.WHXB20111001 shu

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

  • Received Date: 26 May 2011
    Available Online: 15 August 2011

    Fund Project: 中国科学院百人计划, 云南省人才基金(2006PY01-29) (2006PY01-29)国家自然科学基金(21163024)资助项目 (21163024)

  • 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-tidylcholine (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 TM6 within 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-D3R) 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 kJ·mol-1 between them.
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