Citation: Kang Wenbin, Xia Yun, Wang Jun, Wang Wei. Sulfur Dioxide Promotes the Formation of Amyloid Fibrils through Enhanced Secondary Nucleation: A Molecular Dynamics Study[J]. Acta Chimica Sinica, ;2016, 74(8): 694-702. doi: 10.6023/A16050216 shu

Sulfur Dioxide Promotes the Formation of Amyloid Fibrils through Enhanced Secondary Nucleation: A Molecular Dynamics Study

Kang Wenbin ^a,b,c,*,, ,
Xia Yun ^a,c ,
Wang Jun ^a,c,d,*,, ,
Wang Wei ^a,c,d,*,,

a.
School of Physics, Nanjing University, Nanjing 210093, China
b.
School of Public Health and Management, Hubei University of Medicine, Shiyan 442000, China
c.
National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
d.
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China

Corresponding author: Kang Wenbin, wbkang@hbmu.edu.cn Wang Jun, wbkang@hbmu.edu.cn Wang Wei, wangwei@nju.edu.cn
Received Date: 3 May 2016

Fund Project: the National Basic Research Program of China 2013CB834100the National Natural Science Foundation of China 81421091the National Natural Science Foundation of China 11334004the National Natural Science Foundation of China 11174133

Figures(9)

Air pollution is a common phenomenon in developing countries, and pollutants are suggested to be essential reasons to produce various diseases, such as cancers, neuro-degenerative diseases and so on. In present work, the effects of sulfur dioxide on the dissociation of Aβ_17～42peptides from core region of Aβ fibril were studied with umbrella sampling method. It is found that the free energy penalty related to the dissociation processes would decrease for larger concentrations of sulfur dioxide. The detailed interactions between peptides and sulfur dioxide are analyzed based on contact statistics. It is suggested that the destabilization of the Aβ fibril is realized by the binding of sulfur dioxide with the peptide backbone as well as the side chains of charged residues, which results in the decrease of hydrophobic interaction and blockage of the electrostatic interactions between charged residues. Furthermore, the positive contribution of such a marginal destabilization on the growth of fibril is also discussed with a nonlinear master equation, which is consistent with the medical knowledge. Through these computations, we disclose the characteristics of the interactions between air pollutants and protein molecules. We expect that these results could help to assess the effect of air pollutants on human health.
- sulfur dioxide,
- amyloid fibril,
- molecular dynamic simulation,
- dissociation free energy,
- secondary nucleation
1. [1]
  Dominici, F.; Greenstone, M.; Sunstein, C. Science 2014, 344, 257. doi: 10.1126/science.1247348
2. [2]
  Wang, Y.; Hu, M. Acta Chim. Sinica 2016, 74, 356 (in Chinese). doi: 10.6023/A16010008
3. [3]
  Guo, S.; Hu, M.; Guo, Q.; Shang, D. Acta Chim. Sinica 2014, 72, 658 (in Chinese). doi: 10.6023/A14040254
4. [4]
  Guo, S.; Hu, M.; Shang, D.; Guo, Q. Acta Chim. Sinica 2014, 72, 145 (in Chinese). doi: 10.6023/A13111169
5. [5]
  Li, J.; Meng, Z. Asian J. Ecotoxicol. 2012, 7, 133 (in Chinese).
6. [6]
  Yao, G.; Sang, N. Chin. J. Appl. Environ. Biol. 2015, 21, 372 (in Chinese).
7. [7]
  Yu, F.; Li, D.; Xie, M. Ecol. Sci. 2016, 35, 195 (in Chinese).
8. [8]
  Ma, Y.; Wang, J. Chin. J. Publ. Health 2011, 27, 800 (in Chinese).
9. [9]
  Wu, Y.; Meng, Q.; Wei, D.; Bai, J. Chin. Bull. Life Sci. 2011, 23, 784 (in Chinese).
10. [10]
  Zhao, D.; Tang, W.; Wang, W. J. Int. Neurology and Neurosurgery 2014, 41, 363 (in Chinese).
11. [11]
  Zuo, G. e-Sci. Technol. & Appl. 2011, 2, 63 (in Chinese).
12. [12]
  Du, J.; Ge, C. Chin. Sci. Bull. 2015, 60, 2977 (in Chinese).
13. [13]
  Wang, G.; Wang, P. Sci. Technol. Rev. 2014, 32, 72 (in Chinese).
14. [14]
  Yang, W.; Bai, Z.; Zhou, X. J. Environ. Health 2015, 32, 753 (in Chinese).
15. [15]
  Li, J.; Meng, Z. Nitric Oxide 2009, 20, 166. doi: 10.1016/j.niox.2008.12.003
16. [16]
  Wang, X.; Jin, H.; Tang, C. Eur. J. Pharmacol. 2011, 670, 1. doi: 10.1016/j.ejphar.2011.08.031
17. [17]
  Liu, D.; Huang, Y.; Bu, D. Cell Death Dis. 2014, 5, e1251. doi: 10.1038/cddis.2014.229
18. [18]
  Huang, Y.; Shen, Z.; Chen, Q. Sci. Rep. 2016, 6, 19503. doi: 10.1038/srep19503
19. [19]
  Duff, K.; Eckman, C.; Zehr, C. Nature 1996, 383, 710. doi: 10.1038/383710a0
20. [20]
  Cook, D.; Forman, M.; Sung, J. Nat. Med. 1997, 3, 1021. doi: 10.1038/nm0997-1021
21. [21]
  Knowles, T.; Waudby, C.; Devlin, G. Science 2009, 326, 1533. doi: 10.1126/science.1178250
22. [22]
  Bloom, G. JAMA Neurology 2014, 71, 505. doi: 10.1001/jamaneurol.2013.5847
23. [23]
  Xi, W.; Li, W.; Wang, W. J. Phys. Chem. B 2012, 116, 7398. doi: 10.1021/jp300389g
24. [24]
  Xi, W.; Li, W.; Wang, W. Chin. Phys. Lett. 2012, 29, 088702. doi: 10.1088/0256-307X/29/8/088702
25. [25]
  Li, W.; Zhang, J.; Su, Y.; Wang, J.; Qin, M.; Wang, W. J. Phys. Chem. B 2007, 111, 13814. doi: 10.1021/jp076213t
26. [26]
  Lührs, T.; Ritter, C.; Adrian, M. Proc. Natl. Acad. Sci. 2005, 102, 17342. doi: 10.1073/pnas.0506723102
27. [27]
  Ribeiro, M. J. Phys. Chem. B 2006, 110, 8789. doi: 10.1021/jp060518a
28. [28]
  Moin, S.; Lim, L.; Hofer, T. Inorg. Chem. 2011, 50, 3379. doi: 10.1021/ic102240p
29. [29]
  Berendsen, H.; Postma, J.; Gunsteren, W. Intermolecular Forces, Springer Netherlands, 1981, pp. 331～342.
30. [30]
  Ketko, M.; Kamath, G.; Potoff, J. J. Phys. Chem. B 2011, 115, 4949. doi: 10.1021/jp2010524
31. [31]
  Li, Z.; Guo, X.; Wang, H. Acta Phys.-Chim. Sinica 2009, 25, 6 (in Chinese).
32. [32]
  He, Z.; Zhou, J. Acta Chim. Sinica 2011, 69, 2901 (in Chinese).
33. [33]
  Izrailev, S.; Stepaniants, S.; Isralewitz, B. Computational Molecular Dynamics: Challenges, Methods, Ideas, Springer, Berlin Heidelberg, 1999, pp. 39～65.
34. [34]
  Park, S.; Khalili-Araghi, F.; Tajkhorshid, E. J. Chem. Phys. 2003, 119, 3559. doi: 10.1063/1.1590311
35. [35]
  Justin, A.; David, R. J. Phys. Chem. B 2010, 114, 1652. doi: 10.1021/jp9110794
36. [36]
  Park, S.; Schulten, K. J. Chem. Phys. 2004, 120, 5946. doi: 10.1063/1.1651473
37. [37]
  Patey, G.; Valleau, J. Chem. Phys. Lett. 1973, 21, 297. doi: 10.1016/0009-2614(73)80139-3
38. [38]
  Torrie, G.; Valleau, J. Chem. Phys. Lett. 1974, 28, 578. doi: 10.1016/0009-2614(74)80109-0
39. [39]
  Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187. doi: 10.1016/0021-9991(77)90121-8
40. [40]
  Kumar, S.; Rosenberg, J.; Bouzida, D. J. Comput. Chem. 1992, 13, 1011. doi: 10.1002/(ISSN)1096-987X
41. [41]
  Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmuller, H. J. Comput. Chem. 2015, 36, 1990. doi: 10.1002/jcc.24030
42. [42]
  Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. doi: 10.1063/1.464397
43. [43]
  Essmann, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. J. Chem. Phys. 1995, 103, 8577. doi: 10.1063/1.470117
44. [44]
  Hess, B.; Bekker, H.; Berendsen, H. J. Comput. Chem. 1997, 18, 1463. doi: 10.1002/(ISSN)1096-987X
45. [45]
  Walton, E.; Lee, S.; Van, V. Biophys. J. 2008, 94, 2621. doi: 10.1529/biophysj.107.114454
46. [46]
  Calderón-Garcidueñas, L.; Mora-Tiscareño, A.; Franco-Lira, M. J. Alzheimers Dis. 2015, 45, 757.
47. [47]
  Calderón-Garcidueñas, L.; Vojdani, A.; Blaurock-Busch, E. J. Alzheimers Dis. 2015, 43, 1039.
48. [48]
  Li, P.; Yan, R.; Yu, S. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 2739. doi: 10.1073/pnas.1502596112
49. [49]
  Radic, S.; Nedumpully-Govindan, P.; Chen, R.; Salonen, E.; Brown, J. M.; Ke, P. C.; Ding, F. Nanoscale 2014, 6, 8340. doi: 10.1039/c4nr01544d
50. [50]
  Truong, L. Ph.D. Dissertation, Oregon State University, Oregon, 2012.
51. [51]
  Violi, A.; Venkatnathan, A. J. Chem. Phys. 2006, 125, 054302. doi: 10.1063/1.2234481
52. [52]
  Kim, H.; Shin, Y. J. Am. Chem. Soc. 2010, 132, 2254. doi: 10.1021/ja908477w
53. [53]
  Risom, L.; Møller, P.; Loft, S. Mutat. Res. 2005, 592, 119. doi: 10.1016/j.mrfmmm.2005.06.012
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]
  Xiaoning TANG , Shu XIA , Jie LEI , Xingfu YANG , Qiuyang LUO , Junnan LIU , An XUE . Fluorine-doped MnO₂ with oxygen vacancy for stabilizing Zn-ion batteries. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1671-1678. doi: 10.11862/CJIC.20240149
3. [3]
  Zhiquan Zhang , Baker Rhimi , Zheyang Liu , Min Zhou , Guowei Deng , Wei Wei , Liang Mao , Huaming Li , Zhifeng Jiang . Insights into the Development of Copper-based Photocatalysts for CO₂ Conversion. Acta Physico-Chimica Sinica, 2024, 40(12): 2406029-. doi: 10.3866/PKU.WHXB202406029
4. [4]
  Caixia Lin , Zhaojiang Shi , Yi Yu , Jianfeng Yan , Keyin Ye , Yaofeng Yuan . Ideological and Political Design for the Electrochemical Synthesis of Benzoxathiazine Dioxide Experiment. University Chemistry, 2024, 39(2): 61-66. doi: 10.3866/PKU.DXHX202309005
5. [5]
  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
6. [6]
  Linbao Zhang , Weisi Guo , Shuwen Wang , Ran Song , Ming Li . Electrochemical Oxidation of Sulfides to Sulfoxides. University Chemistry, 2024, 39(11): 204-209. doi: 10.3866/PKU.DXHX202401009
7. [7]
  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
8. [8]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
9. [9]
  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
10. [10]
  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
11. [11]
  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
12. [12]
  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
13. [13]
  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
14. [14]
  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
15. [15]
  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
16. [16]
  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
17. [17]
  Qi Wang , Yicong Gao , Feng Lu , Quli Fan . Preparation and Performance Characterization of the Second Near-Infrared Phototheranostic Probe: A New Design and Teaching Practice of Polymer Chemistry Comprehensive Experiment. University Chemistry, 2024, 39(11): 342-349. doi: 10.12461/PKU.DXHX202404141
18. [18]
  Jiaxin Su , Jiaqi Zhang , Shuming Chai , Yankun Wang , Sibo Wang , Yuanxing Fang . Optimizing Poly(heptazine imide) Photoanodes Using Binary Molten Salt Synthesis for Water Oxidation Reaction. Acta Physico-Chimica Sinica, 2024, 40(12): 2408012-. doi: 10.3866/PKU.WHXB202408012
19. [19]
  Lin Ding , Jinpeng Zhang , Junfeng Li , Daying Liu . Color Catcher: A Marvelous Encounter of Starch and Iodine. University Chemistry, 2024, 39(6): 334-341. doi: 10.3866/PKU.DXHX202311064
20. [20]
  Xiaoling LUO , Pintian ZOU , Xiaoyan WANG , Zheng LIU , Xiangfei KONG , Qun TANG , Sheng WANG . Synthesis, crystal structures, and properties of lanthanide metal-organic frameworks based on 2, 5-dibromoterephthalic acid ligand. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1143-1150. doi: 10.11862/CJIC.20230271

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(670)
HTML views(85)

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