Citation: ZHANG Ji-Wei, BIAN Fu-Yong, SHI Guo-Jun, XU Si-Chuan. Molecular Dynamics Simulation of Dopamine Diffusion within and Permeation through POPC Phospholipid Bilayer Membrane[J]. Acta Physico-Chimica Sinica, ;2014, 30(1): 183-193. doi: 10.3866/PKU.WHXB201311281 shu

Molecular Dynamics Simulation of Dopamine Diffusion within and Permeation through POPC Phospholipid Bilayer Membrane

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 Chuxiong Medical College, Chuxiong 675005, Yunnan Province, P. R. China

Received Date: 2 August 2013
Available Online: 28 November 2013
Fund Project: 国家自然科学基金(21163024)资助项目 (21163024)

Dopamine, which is an important neural transmitter in brain tissue, needs to move freely within and through cell membranes to fulfill its function. The molecular dynamics of dopamine diffusion within and permeation through, cell membranes are involved in smoothing dopamine molecular protective channels, associated with schizophrenia and Parkinson's disease. In the present work, using a 1-palmitoyl-2-oleoyl-glycero-3-phosphatedylcholine (POPC) phospholipid bilayer membrane to model the cell membrane, we obtained the freeenergy changes (ΔG) for dopamine diffusion within and permeation through the cell membrane, using molecular dynamics simulations, and probed the molecular dynamics of dopamine diffusion and permeation. The obtained values of ΔG for dopamine diffusion within the cell membrane were 10-54 kJ·mol^-1 at 310 K, which implies that dopamine diffuses easily horizontally and vertically within the cell membrane to protect smoothing of the protective channel. However, it is not easy for dopamine to permeate through the cell membrane, because ΔG for this process was 117-125 kJ·mol^-1 (310 K). Superfluous dopamine passes through the dopaminemolecular protective channel and enters themiddle region of the phospholipid bilayer membrane, and then diffuses easily along the horizontal and vertical orientations within the cell membrane, even permeating through the cell membrane, preventing schizophrenia. It is therefore important for the normal function of a biological cell membrane to protect smoothing of dopamine molecular protective channels, preventing schizophrenia. These results are in agreement with other experimental observations.
- Dopamine,
- POPC,
- Cell membrane,
- MD simulation,
- Free energy
1. [1]
  
  (1) Li, F.; Shu, S. Y.; Bao, X. M. Chin. J. Neurosci. 2003, 19, 405.
2. [2]
  (2) Carlsson, A.;Waters, N.;Waters, S.; Carlsson, M. L. Brain Research Reviews 2000, 31, 342. doi: 10.1016/S0165-0173(99)00050-8
3. [3]
  (3) Suri, R. E.; Bargas, J.; Arbib, M. A. Neuroscience 2001, 103, 65.doi: 10.1016/S0306-4522(00)00554-6
4. [4]
  (4) Salum, C.; Roque, S. A.; Pickering, A. Neurocomputing 1999,26, 845.
5. [5]
  (5) Xu, S. C.; Shi, G. J.; Chi, S. M. The Active Site Residues andthe Molecular Channels for Dopamine within D3R MembraneProtein. The 28thCCS (Chinese Chemical Society) Congress,Sichuan University, Chengdu, China, April 13-16, 2012.
6. [6]
  (6) Bian, F. Y.; Shi, G. J.; Chi, S. M.; Xu, S. C. The PerspectiveInsight into the Pathology of Parkinsonism Using the MolecularChannel Theory of Dopamine inside its Receptor MembraneProtein. Chinese Chemical Society at the Second NationalConference on Bio-physical Chemistry (NCBPC2) and theInternational Forum on Development of Chinese Bio-physicalChemistry,Wuhan University,Wuhan, China, Oct. 15-18, 2012.
7. [7]
  (7) Amy, R. M.; Raul, R. G.; Marc, G. C.; Beverly, H. K. Cell 1999,98, 427. doi: 10.1016/S0092-8674(00)81972-8
8. [8]
  (8) Coyle, J. T.; Puttafreken, P. Science 1993, 262, 689. doi: 10.1126/science.7901908
9. [9]
  (9) Coyle, J. T. Harv. Rev. Psychiatry 1996, 3, 241. doi: 10.3109/10673229609017192
10. [10]
  (10) Kim, J. S.; Konrhuber, H. H.; Sehmid-Burgk,W.; Holzmuller,B. Neurosci Lett. 1980, 20, 379. doi: 10.1016/0304-3940(80)90178-0
11. [11]
  (11) Carlsson, A.; Hansson, L. O.;Waters, N.; Carlsson, M. L. Life Science 1997, 61, 75. doi: 10.1016/S0024-3205(97)00228-2
12. [12]
  (12) Moghaddam, B.; Adams, B.W. Science 1998, 281, 1349. doi: 10.1126/science.281.5381.1349
13. [13]
  (13) Krebs-Thomson, K.; Geyer, M. A. Psychopharmacology 1998,140, 69. doi: 10.1007/s002130050740
14. [14]
  (14) Fleischhacker,W.W. Acta Psychiatr Scand Suppl. 1995, 388, 24.
15. [15]
  (15) Yang, F. Y. Biological Cell; Science Press: Beijing, 2005. [杨福愉. 生物膜. 北京: 科学出版社, 2005.]
16. [16]
  (16) Hoff, B.; Strandberg, E.; Ulrich, A. S.; Tieleman, D. P.; Posten,C. Biophys. J. 2005, 88, 1818. doi: 10.1529/biophysj.104.052399
17. [17]
  (17) Janosi, L.; rfe, A. A. J. Chem. Theory Comput. 2010, 6,3267. doi: 10.1021/ct100381g
18. [18]
  (18) Su, Z. Y.;Wang, Y. T. J. Phys. Chem. B 2011, 115, 796. doi: 10.1021/jp107599v
19. [19]
  (19) Dunkin, C. M.; Pokorny, A.; Almeida, P. F.; Lee, H. S. J. Phys. Chem. B 2011, 115, 1188. doi: 10.1021/jp107763b
20. [20]
  (20) Chen, R.; Poger, D.; Mark, A. E. J. Phys. Chem. B 2011, 115,1038. doi: 10.1021/jp110002q
21. [21]
  (21) Merlino, A.; Vitiello, G.; Grimaldi, M.; Sica, F.; Busi, E.;Basosi, R.; D'Ursi, A. M.; Fragneto, G.; Paduano, L.; D'Errico,G. J. Phys. Chem. B 2012, 116, 401. doi: 10.1021/jp204781a
22. [22]
  (22) Yamamoto, E.; Akimoto, T.; Shimizu, H.; Hirano, Y.; Yasui, M.;Yasuoka, K. J. Phys. Chem. B 2012, 116, 8989.
23. [23]
  (23) Polyansky, A. A.; Volynsky, P. E.; Nolde, D. E.; Arseniev, A. S.;Efremov, R. G. J. Phys. Chem. B 2005, 109, 15052. doi: 10.1021/jp0510185
24. [24]
  (24) Puri, A.; Jang, H.; Yavlovich, A.; Masood, M. A.; Veenstra, T.D.; Luna, C.; Aranda-Espinoza, H.; Nussinov, R.; Blumenthal,R. Langmuir 2011, 27, 15120. doi: 10.1021/la203453x
25. [25]
  (25) Manna, M.; Mukhopadhyay, C. Langmuir 2009, 25, 12235. doi: 10.1021/la902660q
26. [26]
  (26) Hartshorn, M.; Jewett, C. M.; Brozik, J. A. Langmuir 2010, 26,2609. doi: 10.1021/la904308g
27. [27]
  (27) Mondal, S.; Mukhopadhyay, C. Langmuir 2008, 24, 10298. doi: 10.1021/la8015589
28. [28]
  (28) Soemo, A. R.;Wirth, M. J. Langmuir 2010, 26, 2196. doi: 10.1021/la9038914
29. [29]
  (29) Payandeh, J.; Gamal El-Din, T. M.; Scheuer, T.; Zheng, N.;Catterall,W. A. Nature 2012, 486, 135.
30. [30]
  (30) Jönsson, P.; Jonsson, M. P.; Höök, F. Nano Lett. 2010, 10, 1900.doi: 10.1021/nl100779k
31. [31]
  (31) Carr, R.;Weinstock, I. A.; Sivaprasadarao, A.; Müller, A.;Aksimentiev, A. Nano Lett. 2008, 8, 3916. doi: 10.1021/nl802366k
32. [32]
  (32) Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren,W. F.;Hermans, J.; Pullman, B. J. Am. Chem. Soc. 2001, 123, 8638.doi: 10.1021/ja0159618
33. [33]
  (33) Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952.
34. [34]
  (34) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. doi: 10.1021/ct700301q
35. [35]
  (35) Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.E.; Berendsen, H. J. C. J. Comp. Chem. 2005, 26, 1701.
36. [36]
  (36) Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43. doi: 10.1016/0010-4655(95)00042-E
37. [37]
  (37) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian 03,Revision E.01; Gaussian Inc.:Wallingford, CT, 2004.
38. [38]
  (38) Schuettelkopf, A.W.; van Aalten, D. M. F. Acta Crystallogr.2004, D60, 1355.
39. [39]
  (39) Jin, Y.;Wang, Y.; Bian, F. Y.; Shi, Q.; Ge, M. F.;Wang, S.;Zhang, X. K.; Xu, S. C. Acta Phys. -Chim. Sin. 2011, 27, 2432.[金毅, 王悦, 卞富永, 史强, 葛茂发, 王树, 张兴康, 徐四川. 物理化学学报, 2011, 27, 2432.] doi: 10.3866/PKU.WHXB20111001
40. [40]
  (40) Chien, E. Y. T.; Liu,W.; Zhao, Q.; Katritch, V.; Han, G.W.;Hanson, M. A.; Shi, L.; Newman, A. H.; Javitch, J. A.;Cherezov, V.; Stevens, R. C. Science 2010, 330, 1091. doi: 10.1126/science.1197410
41. [41]
  (41) Wang, Y.; Bian, F.; Deng, S. R.; Shi, Q.; Ge, M. F.;Wang, S.;Zhang, X. K.; Xu, S. C. Journal of Biomolecular Structure & Dynamics 2011, 28, 881. doi: 10.1080/07391102.2011.10508615
42. [42]
  (42) Xu, S. C.; Chi, S. M.; Jin, Y.; Shi, Q.; Ge, M. F.;Wang, S.;Zhang, X. K. J. Mol. Model. 2012, 18, 377. doi: 10.1007/s00894-011-1083-7
43. [43]
  (43) Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14,33. doi: 10.1016/0263-7855(96)00018-5
44. [44]
  (44) Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M.J. Comput. Chem. 1997, 18, 1463.
45. [45]
  (45) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98,10089. doi: 10.1063/1.464397
46. [46]
  (46) Essman, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.;Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577. doi: 10.1063/1.470117
47. [47]
  (47) Berendsen, H. J. C.; Postma, J. P. M.; Gunsteren,W. F.; Dinola,A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. doi: 10.1063/1.448118
48. [48]
  (48) Hub, J. S.; de Groot, B. L.; van der Spoel, D. J. Chem. Theory Comput. 2010, 6, 3713. doi: 10.1021/ct100494z
49. [49]
  (49) Marrink, S. J.; Berendsen, H. J. C. J. Phys. Chem. 1994, 98,4155. doi: 10.1021/j100066a040
50. [50]
  (50) Marrink, S. J.; Jaehnig, F.; Berendsen, H. J. C. Biophys. J. 1996,71, 632. doi: 10.1016/S0006-3495(96)79264-0
51. [51]
  (51) Zahn, D.; Brickmann, J. Chem. Phys. Lett. 2002, 352, 441. doi: 10.1016/S0009-2614(01)01437-3
52. [52]
  (52) Bemporad, D.; Essex, J.W.; Luttmann, C. J. Phys. Chem. B2004, 108, 4875. doi: 10.1021/jp035260s
53. [53]
  (53) Shinoda,W.; Mikami, M.; Baba, T.; Hato, M. J. Phys. Chem. B2004, 108, 9346. doi: 10.1021/jp035998+
54. [54]
  (54) Nichols, J.W.; Deamer, D.W. Proc. Nat. Acad. Sci. U. S. A.1980, 77, 2038. doi: 10.1073/pnas.77.4.2038
55. [55]
  (55) Benga, G.; Pop, V. I.; Popescu, O.; Borza, V. J. Biochem. Biophys. Methods 1990, 21, 87. doi: 10.1016/0165-022X(90)90057-J
56. [56]
  (56) Jansen, M.; Blume, A. Biophys. J. 1995, 68, 997. doi: 10.1016/S0006-3495(95)80275-4
57. [57]
  (57) Andrasko, J.; Forsén, S. Biochem. Biophys. Res. Commun. 1974,60, 813. doi: 10.1016/0006-291X(74)90313-1
58. [58]
  (58) Graziani, Y.; Livne, A. J. Membr. Biol. 1972, 7, 275. doi: 10.1007/BF01867920
59. [59]
  (59) Khavrutskii, I. V.; rfe, A. A.; Lu, B.; McCammon, J. A.J. Am. Chem. Soc. 2009, 131, 1706. doi: 10.1021/ja8081704
60. [60]
  (60) Papahadjopoulos, D.; Nir, S.; Ohki, S. Biochim. Biophys. Acta1972, 266, 561. doi: 10.1016/0005-2736(72)90354-9
61. [61]
  (61) Guptaroy, B.; Zhang, M.; Bowton, E.; Binda, F.; Shi, L.;Weinstein, H.; Galli, A.; Javitch, J. A.; Neubig, R. R.; Gnegy,M. E. Mol. Pharmacol. 2009, 75, 514. doi: 10.1124/mol.108.048744
62. [62]
  (62) Chen, N.; Rickey, J.; Reith, M. E. A. Journal of Neurochemistry,2003, 86, 678. doi: 10.1046/j.1471-4159.2003.01889.x
63. [63]
  (63) Zhu, J.; Apparsundaram, S.; Dwoskin, L. P. The Journal of Pharmacology and Experimental Therapeutics 2009, 328, 931.doi: 10.1124/jpet.108.147025
1. [1]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
2. [2]
  Jing SU , Bingrong LI , Yiyan BAI , Wenjuan JI , Haiying YANG , Zhefeng Fan . Highly sensitive electrochemical dopamine sensor based on a highly stable In-based metal-organic framework with amino-enriched pores. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1337-1346. doi: 10.11862/CJIC.20230414
3. [3]
  Tiantian MA , Sumei LI , Chengyu ZHANG , Lu XU , Yiyan BAI , Yunlong FU , Wenjuan JI , Haiying YANG . Methyl-functionalized Cd-based metal-organic framework for highly sensitive electrochemical sensing of dopamine. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 725-735. doi: 10.11862/CJIC.20230351
4. [4]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
5. [5]
  Honglian Liang , Xiaozhe Kuang , Fuping Wang , Yu Chen . Exploration and Practice of Integrating Ideological and Political Education into Physical Chemistry: a Case on Surface Tension and Gibbs Free Energy. University Chemistry, 2024, 39(10): 433-440. doi: 10.12461/PKU.DXHX202405073
6. [6]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
7. [7]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
8. [8]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
9. [9]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
10. [10]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
11. [11]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
12. [12]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
13. [13]
  Peng GENG , Guangcan XIANG , Wen ZHANG , Haichuang LAN , Shuzhang XIAO . Hollow copper sulfide loaded protoporphyrin for photothermal-sonodynamic therapy of cancer cells. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1903-1910. doi: 10.11862/CJIC.20240155
14. [14]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
15. [15]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . Kinetic Resolution Enabled by Photoexcited Chiral Copper Complex-Mediated Alkene E→Z Isomerization: A Comprehensive Chemistry Experiment for Undergraduate Students. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
16. [16]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063
17. [17]
  Lei Shi . Nucleophilicity and Electrophilicity of Radicals. University Chemistry, 2024, 39(11): 131-135. doi: 10.3866/PKU.DXHX202402018
18. [18]
  Shuyu Liu , Xiaomin Sun , Bohan Song , Gaofeng Zeng , Bingbing Du , Chongshen Guo , Cong Wang , Lei Wang . Design and Fabrication of Phospholipid-Vesicle-based Artificial Cells towards Biomedical Applications. University Chemistry, 2024, 39(11): 182-188. doi: 10.12461/PKU.DXHX202404113
19. [19]
  Yunxin Xu , Wenbo Zhang , Jing Yan , Wangchang Geng , Yi Yan . A Fascinating Saga of “Energetic Materials”. University Chemistry, 2024, 39(9): 266-272. doi: 10.3866/PKU.DXHX202307008
20. [20]
  Siyi ZHONG , Xiaowen LIN , Jiaxin LIU , Ruyi WANG , Tao LIANG , Zhengfeng DENG , Ao ZHONG , Cuiping HAN . Targeting imaging and detection of ovarian cancer cells based on fluorescent magnetic carbon dots. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1483-1490. doi: 10.11862/CJIC.20240093

Get Citation

PDF

XML

Metrics

PDF Downloads(696)
Abstract views(1172)
HTML views(57)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142