Citation: Zhipeng A. Wang, Xuan Zhang, Ziliang Che, Zhenxiong Jiang, Xinyu Ma. Discussion on the Application of Novel Protein Post-Translational Modification Discovered by Mass Spectrometry in Chemistry and Biology Education[J]. University Chemistry, ;2021, 36(6): 200607. doi: 10.3866/PKU.DXHX202006075 shu

Discussion on the Application of Novel Protein Post-Translational Modification Discovered by Mass Spectrometry in Chemistry and Biology Education

Zhipeng A. Wang ^1,2,3,, ,
Xuan Zhang ⁴ ,
Ziliang Che ⁵ ,
Zhenxiong Jiang ⁶ ,
Xinyu Ma ²

1.
Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.;
2.
Department of Chemistry, Texas A&M University, College Station, TX 77840, USA.;
3.
Department of Chemistry, Tsinghua University, Beijing 100084, China;
4.
School of Life Sciences, Tsinghua University, Beijing 100084, China;
5.
Department of Mathematics, Harvard University, MA 02138, USA.;
6.
Department of Biology, Texas A&M University, College Station, TX 77840, USA.

Corresponding author: Zhipeng A. Wang, wzpchem1991@gmail.com
Received Date: 29 June 2020

Rapid development of mass spectrum technology (MS) brings about its wide applications in many fields such as chemistry, material science and life sciences, and its application in biochemistry and chemical biology have been greatly expanding the knowledge of novel protein post-translation modification (PTM). This manuscript starts from the basic principles of mass spectrum and later elaborates the application of MS in discovering lysine post-translation modifications over histones as model proteins, showing a path incorporating fundamental organic chemistry and biochemistry knowledge into cutting-edge researches. By analyzing roles of mass spectrum throughout post-translation modification studies under different research logistics, this manuscript was aimed to help establishing a way of thinking that associates fundamental chemistry and biology education with practical applications for students.
- Mass spectrum technology,
- MS/MS,
- PTM,
- Biochemistry
1. [1]
  Arnaudo, A. M.; Molden, R. C.; Garcia, B. A. Crit. Rev. Biochem. Mol. Biol. 2011, 46 (4), 284.
2. [2]
  Strahl, B. D.; Allis, C. D. Nature 2000, 403 (6765), 41.
3. [3]
  Filippakopoulos, P.; Knapp, S. Nat. Rev. Drug Discov. 2014, 13 (5), 337.
4. [4]
5. [5]
6. [6]
  Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F. Science 1989, 246 (4926), 64.
7. [7]
  Tanaka, K.; Waki, H.; Ido, Y.; Akita, S.; Yoshida, Y.; Yoshida, T.; Matsuo, T. Rapid Commun. Mass Spectrom 1988, 2, 151.
8. [8]
  Steen, H.; Mann, M. Nat. Rev. Mol. Cell Biol. 2004, 5 (9), 699.
9. [9]
10. [10]
  Chen, Y.; Chen, W.; Cobb, M. H.; Zhao, Y. Proc. Natl. Acad. Sci. USA 2009, 106 (3), 761.
11. [11]
  Allfrey, V. G.; Faulkner, R.; Mirsky, A. E. Proc. Natl. Acad. Sci. USA 1964, 51 (5), 786.
12. [12]
  Gershey, E. L.; Vidali, G.; Allfrey, V. G. J. Biol. Chem. 1968, 243 (19), 5018.
13. [13]
  Huang, H.; Lin, S.; Garcia, B. A.; Zhao, Y. Chem. Rev. 2015, 115 (6), 2376.
14. [14]
  Chen, Y.; Sprung, R.; Tang, Y.; Ball, H.; Sangras, B.; Kim, S. C.; Falck, J. R.; Peng, J.; Gu, W.; Zhao, Y. Mol. Cell Proteomics 2007, 6 (5), 812.
15. [15]
  Xie, Z.; Dai, J.; Dai, L.; Tan, M.; Cheng, Z.; Wu, Y.; Boeke, J. D.; Zhao, Y. Mol. Cell Proteomics 2012, 11 (5), 100.
16. [16]
  Tan, M.; Peng, C.; Anderson, K. A.; Chhoy, P.; Xie, Z.; Dai, L.; Park, J.; Chen, Y.; Huang, H.; Zhang, Y.; et al. Cell Metab. 2014, 19 (4), 605.
17. [17]
18. [18]
  Huang, H.; Zhang, D.; Wang, Y.; Perez-Neut, M.; Han, Z.; Zheng, Y. G.; Hao, Q.; Zhao, Y. Nat. Commun. 2018, 9 (1), 3374.
19. [19]
  Wisniewski, J. R.; Zougman, A.; Mann, M. Nucleic Acids Res. 2008, 36 (2), 570.
20. [20]
  Jiang, T.; Zhou, X.; Taghizadeh, K.; Dong, M.; Dedon, P. C. Proc. Natl. Acad. Sci. US 2007, 104 (1), 60.
21. [21]
  Sabari, B. R.; Zhang, D.; Allis, C. D.; Zhao, Y. Nat. Rev. Mol. Cell Biol. 2017, 18 (2), 90.
22. [22]
  Dai, L.; Peng, C.; Montellier, E.; Lu, Z.; Chen, Y.; Ishii, H.; Debernardi, A.; Buchou, T.; Rousseaux, S.; Jin, F.; et al. Nat. Chem. Biol. 2014, 10 (5), 365.
23. [23]
  Xie, Z.; Zhang, D.; Chung, D.; Tang, Z.; Huang, H.; Dai, L.; Qi, S.; Li, J.; Colak, G.; Chen, Y.; et al. Mol. Cell 2016, 62 (2), 194.
24. [24]
  Tan, M.; Luo, H.; Lee, S.; Jin, F.; Yang, J. S.; Montellier, E.; Buchou, T.; Cheng, Z.; Rousseaux, S.; Rajagopal, N.; et al. Cell 2011, 146 (6), 1016.
25. [25]
  Zhang, D.; Tang, Z.; Huang, H.; Zhou, G.; Cui, C.; Weng, Y.; Liu, W.; Kim, S.; Lee, S.; Perez-Neut, M.; et al. Nature 2019, 574 (7779), 575.
26. [26]
  Galligan, J. J.; Rose, K. L.; Beavers, W. N.; Hill, S.; Tallman, K. A.; Tansey, W. P.; Marnett, L. J. J. Am Chem. Soc. 2014, 136 (34), 11864.
27. [27]
  Castro, J. P.; Jung, T.; Grune, T.; Siems, W. Free Radic Biol. Med. 2017, 111, 309.
28. [28]
  Sabari, B. R.; Zhang, D.; Allis, C. D.; Zhao, Y. Nat. Rev. Mol. Cell Biol. 2017, 18 (2), 90.
29. [29]
  Huang, J. X.; Lee, G.; Cavanaugh, K. E.; Chang, J. W.; Gardel, M. L.; Moellering, R. E. Nat. Methods 2019, 16 (9), 894.
30. [30]
  Moellering, R. E.; Cravatt, B. F. Science 2013, 341 (6145), 549.
31. [31]
  Wang, Z. P.; Wang, Y. H.; Chu, G. C.; Shi, J.; Li, Y. M. Curr. Org. Synth. 2015, 12 (2), 150.
32. [32]
33. [33]
34. [34]
35. [35]
36. [36]
37. [37]
  Wang, Z. A.; Millard, C. J.; Lin, C.-L.; Gurnett, J. E.; Wu, M.; Lee, K.; Fairall, L.; Schwabe, J. W. R.; Cole, P. A. elife 2020, 9, e57663.
38. [38]
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