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物理化学学报  2017, Vol. 33 Issue (5): 927-940    DOI: 10.3866/PKU.WHXB201702211
论文     
多巴胺在其第三受体蛋白结构中的分子通道上传输动力学
李爱静,谢炜,王明,徐四川*()
Molecular Dynamics of Dopamine to Transmit through Molecular Channels within D3R
Ai-Jing LI,Wei XIE,Ming WANG,Si-Chuan XU*()
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摘要:

本文基于多巴胺与其第三受体复合蛋白(D3R)结构,采用分子动力学技术Gromacs 4.5程序中的伞形样本方法,研究多巴胺在多巴胺第三受体蛋白结构中的运动轨迹及其过程中自由能变化,探讨多巴胺在其分子通道上传输运动机制动力学。分子模拟表明,处在发挥神经递质作用部位的多巴胺,通过D3R结构中的功能分子通道沿着y+轴朝细胞外方向传输运动的自由能变化数值为134.6 kJ·mol-1,沿着y-轴朝细胞内传输运动的自由能变化为211.5 kJ·mol-1。在D3R结构中,多巴胺沿着x+、x-、z+、z-轴朝细胞双层膜方向传输运动的自由能变化分别为65.8、245.0、551.4、172.8 kJ·mol-1,数值说明DOP更容易沿着x+轴方向从TM5(第五跨膜螺旋)与TM6(第六跨膜螺旋)缝隙之间离开D3R内部结构。处在细胞间隙空间的自由多巴胺,在等温等压条件下沿着逆y+轴方向通过多巴胺第三受体内功能分子通道,到达发挥神经递质作用的部位是一个自发过程,因为在该轨迹上多巴胺分子与受体相互作用是一个负自由能变化(-134.6 kJ·mol-1)。所以,多巴胺与多巴胺受体很容易相互结合,发挥神经递质作用。发挥了神经递质功能作用的多巴胺分子,沿着x+轴方向的保护分子通道从TM5与TM6缝隙之间离开D3R内部结构,避免过度发挥多巴胺神经递质功能作用。根据多巴胺功能和保护分子通道观点,我们提出帕金森病新病理和精神分裂症新病理。论文还探讨多巴胺分子通道理论及其新病理应用于治疗控制这两种病症及其相关药物研究开发。

关键词: 多巴胺多巴胺受体分子通道分子模拟帕金森病精神分裂症    
Abstract:

In this paper, based on the complex protein structure of third dopamine receptor (D3R) with dopamine (DOP), we have studied the trajectories with the free energy changes of D3R for DOP to move along its molecular channels and then probed the molecular dynamics mechanism of DOP transmitting along molecular channels, using molecular dynamics techniques including the potential mean force (PMF) of umbrella samplings from the GROMACS program (version 4.5). Simulation results show that for DOP located in the space region of D3R to act as a neurotransmitter transmitting toward the outside of cell, the free energy change is 134.6 kJ·mol-1 along the functional molecular channel of y+ axis within D3R, and 211.5 kJ·mol-1 along the y-axis towards the intracellular part. Within the structure of D3R, the free energy changes are 65.8, 245.0, 551.4, 172.8 kJ·mol-1 for DOP to transmit along the x+, x-, z+, z-axes, respectively, towards cell bilayer membrane, indicating that DOP leaves more easily along the x+ axis through the gap between TM5 (the fifth transmembrane helix) and TM6 (the sixth transmembrane helix) from the internal structure of D3R. When free DOP molecules are located in the intercellular spaces, once they start moving along the inverse y+ axis direction under constant pressure and temperature, they spontaneously pass through the functional molecular channel to reach the space region of D3R to act as a neurotransmitter, because the free energy change between DOP and D3R along the inverse y+ axis direction is negative (-134.6 kJ·mol-1). Therefore, DOP interacting with D3R can easily play the role of a neurotransmitter. After DOP molecules have performed the actions of a neurotransmitter, they leave the internal structure of D3R along the x+ axis of a protective molecular channel through the gap between TM5 and TM6 to avoid excessive function as transmitter. According to dopamine functional and protective molecular channels, we suggest new pathologies and the finding and development of new drugs for Parkinson's disease and schizophrenia.

Key words: Dopamine    Dopamine receptor    Molecular channel    Molecular simulation    Parkinson's disease    Schizophrenia
收稿日期: 2016-10-19 出版日期: 2017-02-21
中图分类号:  O641  
基金资助: 国家自然科学基金(21163024);国家自然科学基金(21563032)
通讯作者: 徐四川     E-mail: sichuan@ynu.edu.cn
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李爱静,谢炜,王明,徐四川. 多巴胺在其第三受体蛋白结构中的分子通道上传输动力学[J]. 物理化学学报, 2017, 33(5): 927-940.

Ai-Jing LI,Wei XIE,Ming WANG,Si-Chuan XU. Molecular Dynamics of Dopamine to Transmit through Molecular Channels within D3R. Acta Physico-Chimica Sinca, 2017, 33(5): 927-940.

链接本文:

http://www.whxb.pku.edu.cn/CN/10.3866/PKU.WHXB201702211        http://www.whxb.pku.edu.cn/CN/Y2017/V33/I5/927

DOPETQDOPETQDOPETQDOPETQ
Ile43 Asp110Asp110 Tyr191His349His349
Leu71 Met113Val111Ser192Ser192Val350Val350
Ala74 Met112Ser193Ser193Thr353Thr353
Asp75 Cys114Cys114 Val194 Tyr365
Leu76 Thr115Thr115 Ser196 Thr368
Val78 Ser117Leu168Phe197Phe197 Thr369
Ala79 Ile118Cys181Phe201Tyr198 Trp370
Val82Val82Leu121Ser182Phe338 Gly372Gly372
Met83Val86 Ile183Trp342Trp342Tyr373Tyr373
Leu89 Phe188Leu343 Asn375
Phe106Val189Val189Phe345Phe345Ser376
Val107 Ile190Phe346Phe346
表1  多巴胺和ETQ分子为中心选出的0.6 nm范围内多巴胺受体的残基
图1  (a) ETQ与多巴胺第三受体突变体复合蛋白晶体结构图13;(b) ETQ和DOP分子结构图;(c)人体生物型多巴胺与多巴胺第三受体复合蛋白结构14
图2  研究材料:多巴胺第三受体与多巴胺复合蛋白结构包括双层磷脂POPC-H2O膜结构
图3  (A) DOP在D3R内部结构的六个运动方向,y+轴方向设定往细胞外运动,y-轴方向往细胞内运动,x+、x-、z+、z-轴方向从D3R内部结构往细胞双层膜运动;(o, a, b, c) DOP在y+轴方向上运动轨迹上四个运动点图像图;(B) DOP在D3R内部结构y+轴方向运动的自由能变化图
n D/nm n D/nm n D/nm n D/nm n D/nm
0 (o)01000.641491.211991.852432.46
100.041030.711521.262001.902462.53
150.101050.771541.312071.932542.61
270.141110.791631.382081.96263 (c)2.65
440.201120.84169 (b)1.412112.012712.72
490.251130.881721.492152.063252.78
760.291170.921731.542212.083342.82
850.341380.981741.582232.154082.83
900.401411.031771.632252.20
920.441431.091791.712282.24
930.511451.131801.742332.28
94 (a)0.581461.181851.812372.42
表2  DOP分子沿着y+轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
图4  (o, a, b, c) DOP在y-轴方向运动轨迹上四个运动点图像图;(A) DOP在D3R内部结构y-轴方向运动的自由能变化图
n D/nm n D/nm n D/nm n D/nm n D/nm
1 (o)0610.541191.111651.702062.23
20.05660.571261.141661.712112.28
80.09670.631271.191671.802172.33
180.14680.68132 (b)1.241701.852272.39
240.18800.721351.291711.902332.44
30 (a)0.24840.781381.331751.93239 (c)2.49
370.31870.831411.441761.982472.53
390.34950.911461.501792.052632.59
410.38970.951511.551802.102812.64
490.431041.011571.601852.144132.66
510.471111.051641.651992.19
表3  DOP分子沿着y-轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
图5  (o, a, b, c) DOP在x+轴方向上从D3R内部结构往细胞双层膜运动轨迹四个运动点主视图和俯视图;(A) DOP在D3R内部结构x+轴方向运动的自由能变化图
n D/nm n D/nm n D/nm n D/nm n D/nm
4 (o)072 (a)0.41980.651221.061331.41
80.05730.42990.781241.091491.46
220.08740.471020.831251.141651.47
350.12880.531030.88129 (c)1.164631.48
470.17940.561070.911301.264641.47
670.22960.611080.971311.294781.49
710.2997 (b)0.691131.021321.384831.49
表4  DOP分子沿着x+轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
n D/nm n D/nm n D/nm n D/nm n D/nm
1 (o)0610.471150.981791.382301.83
50.04640.531171.041921.432541.86
110.09650.591321.071961.472601.90
180.13660.641381.132011.53264 (c)1.93
370.19730.681421.182041.582651.96
410.2080 (a)0.731501.222171.623911.96
420.26870.771721.242231.673971.97
470.33910.831741.282261.723991.98
480.38920.871751.312271.744091.99
570.421070.93177 (b)1.352281.784142.02
表5  DOP分子沿着x-轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
图6  (o, a, b, c) DOP在x-轴方向上从D3R内部结构往细胞双层膜运动轨迹四个运动点主视图和俯视图;(A) DOP在D3R内部结构x-轴方向运动的自由能变化图
n D/nm n D/nm n D/nm n D/nm n D/nm
5 (o)01150.521920.962261.332571.94
120.051260.581940.982281.382582.16
380.11130 (a)0.621991.022301.412622.20
520.151540.672041.08235 (b)1.472692.23
620.201590.722081.132381.53288 (c)2.26
690.241640.772151.182471.563742.29
760.301660.822201.192491.623922.30
910.361730.862211.262551.674502.31
920.391820.912251.282561.804512.32
970.47
表6  DOP分子沿着z+轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
图7  (o, a, b, c) DOP在z-轴方向上从D3R内部结构往细胞双层膜运动轨迹四个运动点主视图和俯视图;(A) DOP在D3R内部结构z-轴方向运动的自由能变化图
n D/nm n D/nm n D/nm n D/nm n D/nm
5 (o)01080.29149 (b)1.601722.12208 (c)2.39
80.051120.341501.841832.183532.42
320.111440.401511.911892.213602.48
550.161450.431571.941972.253842.51
770.211460.501641.992002.293972.53
810.23147 (a)0.921652.032012.334092.54
910.261481.171692.072042.374202.57
表7  DOP分子沿着z-轴方向通过D3R蛋白内分子通道轨迹上的伞形样本
图8  (o, a, b, c) DOP在z-轴方向上从D3R内部结构往细胞双层膜运动轨迹四个运动点主视图和俯视图;(A) DOP在D3R内部结构z-轴方向运动的自由能变化图
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