Citation: Xu Jie, Wei Yuchen, Wu Zhiwei, Yi Zhongsheng. Spectral and Computational Simulations of HSA and BDE154 Based on Acidity Induction[J]. Acta Chimica Sinica, ;2018, 76(5): 408-414. doi: 10.6023/A18020060 shu

Spectral and Computational Simulations of HSA and BDE154 Based on Acidity Induction

Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004

Corresponding author: Yi Zhongsheng, yzs@glut.edu.cn
Received Date: 6 February 2018
Available Online: 11 May 2018
Fund Project: the National Natural Science Foundation of China 21565012the National Natural Science Foundation of China 21467006the Guangxi Natural Science Foundation of China 2017GXNSFAA198354Project supported by the National Natural Science Foundation of China (Nos. 21467006 and 21565012) and the Guangxi Natural Science Foundation of China (2017GXNSFAA198354)

Figures(4)

In this paper, human serum albumin (HSA) binding to small molecule 2, 2', 4, 4', 5, 6'-hexabromodiphenyl ether (BDE154) is studied by means of inducing protonation or deprotonation at four different pH levels (pH=3.0, 6.0, 7.4, 9.0). Firstly, it has been indicated that the charge distribution on HSA is very uniform even after protonation of HSA at different pH levels. From this, it can be inferred that the uniform charge distribution makes the electrostatic forces between the amino acid residues of the ⅡA region of HSA aspartic acid (Asp), glutamate (Glu) and histidine (His) to gradually reach a relative equilibrium and thus stabilize the HSA conformation. The results from synchronous fluorescence spectroscopy show that BDE154 has been bind to the ⅡA region of HSA, and is more closely to tryptophan (Try), and that causes the fluorescence quenching of HSA. After that, the semi-flexible docking of HSA with BDE 154 reveals that BDE154 has a cationic-π-conjugated effect and strong hydrophobic interaction with the surrounding amino acids, such as tyrosine 150 (Tyr150), lysine 195 (Lys195), lysine 199 (Lys199), etc. Next, the dynamic and thermodynamic properties of HSA under different protonation conditions have been studied by using molecular dynamic simulation. The results of simulation also show that too much positive charge deteriorates the system stability of HSA or HSA-BDE154 complex. Then, the binding free energy of HSA-BDE154 complex under different protonation states has been predicted by MM-PBSA method, and the contribution of amino acid residues to free energy of binding has also been analyzed. In addition, lysine 199 (Lys199), leucine 238 (Leu238), arginine 257 (Arg257), alanine 261 (Ala261), and isoleucine 264 (Ile264) in the HSA, being located in the hydrophobic cavity in subdomain ⅡA, are the most important residues when binding with BDE154. Therefore, the hydrophobic interaction has been identified as the major driving force for the binding between HSA-BDE154 systems, which is consistent with the results of molecular docking and the analysis of binding free energy. Finally, the results of secondary structure analysis of molecular dynamics simulation show that the binding could promote the de-helix process of HSA by increasing the acidity in HSA-BDE154 complex system.
- protonated,
- molecular docking,
- synchronous fluorescence,
- dynamic simulation
1. [1]
  Allard, J. F.; Dushek, O.; Coombs, D.; Van Der Merwe; P. A. Biophys. J. 2012, 102, 1265. doi: 10.1016/j.bpj.2012.02.006
2. [2]
  Rich, R. L.; Hoth, L. R.; Geoghegan, K. F.; Brown, T. A.; LeMotte, P. K.; Simons, S. P.; Hensley, P.; Myszka, D. G. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 8562. doi: 10.1073/pnas.142288199
3. [3]
  Ballardini, R.; Balzani, V.; Credi, A.; Gandolfi, M. T.; Kotzyba-Hibert, F.; Lehn, J. M.; Prodi, L. J. Am. Chem. Soc. 1994, 116, 5741. doi: 10.1021/ja00092a026
4. [4]
  Agasti, S. S.; Liong, M.; Tassa, C.; Chung, H. J.; Shaw, S. Y.; Lee, H.; Weissleder, R. Angew. Chem. Int. Ed. 2012, 51, 450. doi: 10.1002/anie.201105670
5. [5]
  Gellman, S. H. Chem. Rev. 1997, 97, 1231. doi: 10.1021/cr970328j
6. [6]
  Berde, C. B.; Hudson, B. S.; Simoni, R. D.; Sklar, L. A. J. Biol. Chem. 1979, 254, 391.
7. [7]
  Schneider, H. J.; Yatsimirsky, A. K. Chem. Soc. Rev. 2008, 37, 263. doi: 10.1039/B612543N
8. [8]
  Pal, B.; Bajpai, P. K.; Baul, T. B. Spectrochim. Acta A 2000, 56, 2453. doi: 10.1016/S1386-1425(00)00320-6
9. [9]
  Lyon, C. E.; Suh, E. S.; Dobson, C. M.; Hore, P. J. J. Am. Chem. Soc. 2002, 124, 13018. doi: 10.1021/ja020141w
10. [10]
  Cheng, L. T.; Wang, Z.; Setny, P.; Dzubiella, J.; Li, B.; McCammon, J. A. J. Chem. Phys. 2009, 131, 144102. doi: 10.1063/1.3242274
11. [11]
  Ma, M.; Paredes, A., Bong, D. J. Am. Chem. Soc. 2008, 130, 14456. doi: 10.1021/ja806954u
12. [12]
  Bader, A. N.; van Dongen, M. M.; van Lipzig, M. M.; Kool, J.; Meerman, J. H.; Ariese, F.; Gooijer, C. Chem. Res. Toxicol. 2005, 18, 1405. doi: 10.1021/tx050056c
13. [13]
  Colquhoun, H. M.; Zhu, Z.; Williams, D. J. Org. Lett. 2003, 5, 4353. doi: 10.1021/ol035626j
14. [14]
  Branco, T. J. F.; Ferreira, L. V.; do Rego, A. B.; Oliveira, A. S.; Da Silva, J. P. Photochem. Photobiol. Sci. 2006, 5, 1068. doi: 10.1039/B608833C
15. [15]
  Baudry, R.; Kalchenko, O.; Dumazet-Bonnamour, I.; Vocanson, F.; Lamartine, R. J. Chromatogr. Sci. 2003, 41, 157. doi: 10.1093/chromsci/41.3.157
16. [16]
  Xiao, Z.-Y.; Lin, R.-L.; Tao, Z.; Liu, Q.-Y.; Liu, J.-X.; Xiao, X. Org. Chem. Front. 2017, 4, 2422. doi: 10.1039/C7QO00708F
17. [17]
  Baudoin, O.; Gonnet, F.; Teulade-Fichou, M. P.; Vigneron, J. P.; Tabet, J. C., Lehn, J. M. Chem. Eur. J. 1999, 5, 2762. doi: 10.1002/(ISSN)1521-3765
18. [18]
  Kukić, P.; Nielsen; J. E. Future Med. Chem. 2010, 2, 647. doi: 10.4155/fmc.10.6
19. [19]
  Jakoby IV, M. G.; Miller, K. R.; Toner, J. J.; Bauman, A.; Cheng, L.; Li, E.; Cistola, D. P. Biochemistry 1993, 32, 872. doi: 10.1021/bi00054a019
20. [20]
  Quan, X.; Dong, J.; Zhou, J. Acta Chim. Sinica 2014, 72, 1075. doi: 10.7503/cjcu20140006
21. [21]
  Li, L.; Lü, M.; Lu, K.; Liu, G.; Peng, L. Chin. J. Org. Chem. 2018, 38, 246.
22. [22]
  Linderstrøm-Lang, K. C. R. Trav. Lab. Carlsberg 1924, 15, 1.
23. [23]
  Shishkov, I. F.; Khristenko, L. V.; Rudakov, F. M.; Vilkov, L. V.; Karlov, S. S.; Zaitseva, G. S.; Samdal, S. J. Mol. Struct. 2002, 641, 199. doi: 10.1016/S0022-2860(02)00339-3
24. [24]
  Bhattacharya, B.; Nakka, S.; Guruprasad, L.; Samanta, A. J. Phys. Chem. B 2009, 113, 2143. doi: 10.1021/jp808611b
25. [25]
  Jang, H.; Hall, C. K.; Zhou, Y. Biophys. J. 2002, 83, 819. doi: 10.1016/S0006-3495(02)75211-9
26. [26]
  de Oliveira, C. A. F.; Guimarães, C. R. W.; Barreiro, G.; de Alencastro, R. B. Proteins 2003, 52, 483. doi: 10.1002/prot.10403
27. [27]
  Bolel, P.; Datta, S.; Mahapatra, N.; Halder, M. J. Phys. Chem. B 2014, 118, 26. doi: 10.1021/jp407057f
28. [28]
  Baler, K.; Martin, O. A.; Carignano, M. A.; Ameer, G. A.; Vila, J. A.; Szleifer, I. J. Phys. Chem. B 2014, 118, 921. doi: 10.1021/jp409936v
29. [29]
  Meyer, B.; Peters, T. Angew. Chem. Int. Ed. 2003, 42, 864. doi: 10.1002/anie.200390233
30. [30]
  Karplus, M.; McCammon, J. A. Nat. Struct. Biol. 2002, 9, 646. doi: 10.1038/nsb0902-646
31. [31]
  Zhang, Y.; Wu, S.; Qin, Y.; Liu, J.; Liu, J.; Wang, Q.; Ren, F.; Zhang, H. Food Chem. 2018, 240, 1072. doi: 10.1016/j.foodchem.2017.07.100
32. [32]
  De Wit, C. A. Chemosphere 2002, 46, 583. doi: 10.1016/S0045-6535(01)00225-9
33. [33]
  Zhao, N.; Xuan, S.; Fronczek, F. R.; Smith, K. M.; Vicente, M. G. J. Org. Chem. 2017, 82, 3880. doi: 10.1021/acs.joc.6b02981
34. [34]
  Balamurugan, R.; Stalin, A.; Ignacimuthu, S. Eur. J. Med. Chem. 2012, 47, 38. doi: 10.1016/j.ejmech.2011.10.007
35. [35]
  Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A. Nucleic Acids Res. 2007, 35, 522. doi: 10.1093/nar/gkm276
36. [36]
  Li, Y.; Liu, X.; Dong, X.; Zhang, L.; Sun, Y. Langmuir 2014, 30, 8500. doi: 10.1021/la5017438
37. [37]
  Aliev, A. E.; Kulke, M.; Khaneja, H. S.; Chudasama, V.; Sheppard, T. D.; Lanigan, R. M. Proteins:Structure, Function, and Bioinformatics 2014, 82, 195-215. doi: 10.1002/prot.24350
38. [38]
  Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. doi: 10.1063/1.464397
39. [39]
  Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. J. Comput. Phys. 1977, 23, 327. doi: 10.1016/0021-9991(77)90098-5
40. [40]
  Sudhamalla, B.; Gokara, M.; Ahalawat, N.; Amooru, D. G.; Subramanyam, R. J. Phys. Chem. B 2010, 114, 9054. doi: 10.1021/jp102730p
41. [41]
  Baler, K.; Martin, O. A.; Carignano, M. A.; Ameer, G. A.; Vila, J. A.; Szleifer, I. J. Phys. Chem. B 2014, 118, 921. doi: 10.1021/jp409936v
42. [42]
  Jiang, Q.; Zhang, Z.; Liu, Y.; Yao, N.; Wang, J. Chin. J. Org. Chem. 2017, 37, 1814.
43. [43]
  Lu, Z.; Qi, L.; Li, G.-X.; Li, Q.; Sun, G.-H.; Xie, R.-Z. J. Solution Chem. 2014, 43, 2010. doi: 10.1007/s10953-014-0256-2
44. [44]
  Rehman, M. T.; Shamsi, H.; Khan, A. U. Mol. Pharm. 2014, 11, 1785. doi: 10.1021/mp500116c
45. [45]
  Rahman, T.; Rahmatullah, M. Bioorg. Med. Chem. Lett. 2010, 20, 537. doi: 10.1016/j.bmcl.2009.11.106
46. [46]
  Dong, K.; Yang, X.; Zhao, T.; Zhu, X. Mol. Simulat. 2017, 43, 599. doi: 10.1080/08927022.2017.1279283
1. [1]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
2. [2]
  Yufang GAO , Nan HOU , Yaning LIANG , Ning LI , Yanting ZHANG , Zelong LI , Xiaofeng LI . Nano-thin layer MCM-22 zeolite: Synthesis and catalytic properties of trimethylbenzene isomerization reaction. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1079-1087. doi: 10.11862/CJIC.20240036
3. [3]
  Yang YANG , Pengcheng LI , Zhan SHU , Nengrong TU , Zonghua WANG . Plasmon-enhanced upconversion luminescence and application of molecular detection. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 877-884. doi: 10.11862/CJIC.20230440
4. [4]
  Yuhao SUN , Qingzhe DONG , Lei ZHAO , Xiaodan JIANG , Hailing GUO , Xianglong MENG , Yongmei GUO . Synthesis and antibacterial properties of silver-loaded sod-based zeolite. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 761-770. doi: 10.11862/CJIC.20230169
5. [5]
  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
6. [6]
  Peiran ZHAO , Yuqian LIU , Cheng HE , Chunying DUAN . A functionalized Eu³⁺ metal-organic framework for selective fluorescent detection of pyrene. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 713-724. doi: 10.11862/CJIC.20230355
7. [7]
  Jiakun BAI , Ting XU , Lu ZHANG , Jiang PENG , Yuqiang LI , Junhui JIA . A red-emitting fluorescent probe with a large Stokes shift for selective detection of hypochlorous acid. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1095-1104. doi: 10.11862/CJIC.20240002
8. [8]
  Xin MA , Ya SUN , Na SUN , Qian KANG , Jiajia ZHANG , Ruitao ZHU , Xiaoli GAO . A Tb₂ complex based on polydentate Schiff base: Crystal structure, fluorescence properties, and biological activity. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1347-1356. doi: 10.11862/CJIC.20230357
9. [9]
  Zhaoyang WANG , Chun YANG , Yaoyao Song , Na HAN , Xiaomeng LIU , Qinglun WANG . Lanthanide(Ⅲ) complexes derived from 4′-(2-pyridyl)-2, 2′∶6′, 2″-terpyridine: Crystal structures, fluorescent and magnetic properties. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1442-1451. doi: 10.11862/CJIC.20240114
10. [10]
  Jinlong YAN , Weina WU , Yuan WANG . A simple Schiff base probe for the fluorescent turn-on detection of hypochlorite and its biological imaging application. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1653-1660. doi: 10.11862/CJIC.20240154
11. [11]
  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
12. [12]
  Yonghui ZHOU , Rujun HUANG , Dongchao YAO , Aiwei ZHANG , Yuhang SUN , Zhujun CHEN , Baisong ZHU , Youxuan ZHENG . Synthesis and photoelectric properties of fluorescence materials with electron donor-acceptor structures based on quinoxaline and pyridinopyrazine, carbazole, and diphenylamine derivatives. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 701-712. doi: 10.11862/CJIC.20230373
13. [13]
  Donghui PAN , Yuping XU , Xinyu WANG , Lizhen WANG , Junjie YAN , Dongjian SHI , Min YANG , Mingqing CHEN . Preparation and in vivo tracing of ⁶⁸Ga-labeled PM_2.5 mimetic particles for positron emission tomography imaging. Chinese Journal of Inorganic Chemistry, 2024, 40(4): 669-676. doi: 10.11862/CJIC.20230468

Get Citation

PDF

XML

Metrics

PDF Downloads(17)
Abstract views(1400)
HTML views(237)

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