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

JIN Yi ¹ ,
WANG Yue ¹ ,
BIAN Fu-Yong ¹ ,
SHI Qiang ² ,
GE Mao-Fa ² ,
WANG Shu ³ ,
ZHANG Xing-Kang ² ,
XU Si-Chuan ^1,2,

1.
1. Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China;
2. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China;
3. CAS Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China

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 (E_b) 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 E_b 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 E_b of -80.5 kJ·mol^-1 between them.
- Ab initio,
- Dopamine 3-subtype receptor,
- 3PBL,
- Active site,
- Molecular dynamics simulation,
- Homology modeling
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