研究生: |
簡雯棋 Chien, Wen-Chi |
---|---|
論文名稱: |
利用定點突變4,5多巴-雙加氧酶探討其受質選擇性及動力學之影響 Effect of site-specific mutations on substrate selectivity and kinetics of 4,5-DOPA-dioxygenase |
指導教授: |
葉怡均
Yeh, Yi-Chun |
口試委員: |
徐駿森
Hsu, Chun-Hua 陳頌方 Chen, Sung-Fang 葉怡均 Yeh, Yi-Chun |
口試日期: | 2022/07/25 |
學位類別: |
碩士 Master |
系所名稱: |
化學系 Department of Chemistry |
論文出版年: | 2022 |
畢業學年度: | 110 |
語文別: | 中文 |
論文頁數: | 99 |
中文關鍵詞: | 左旋多巴 、多巴胺 、4,5-多巴雙加氧酶 、蛋白質工程 、定點突變 |
英文關鍵詞: | Dopamine, Levodopa, The kinetic of enzymes, Mutant protein, 4,5-dopa dioxygenase, Betalamic acid, Michaelis-Menten equation |
DOI URL: | http://doi.org/10.6345/NTNU202201309 |
論文種類: | 學術論文 |
相關次數: | 點閱:95 下載:9 |
分享至: |
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本研究主題就是在紫茉莉花中萃取的4,5-多巴雙加氧酶 (DOPA 4,5-dixoygenase, MjDOD)可催化左旋多巴 (Levodopa, L-DOPA),但對多巴胺 (Dopamine, DA)也會產生相似的催化,然後運用不同位點突變胺基酸得其突變體,分別針對左旋多巴以及多巴胺進行酵素催化反應使其產生兩種不同的甜菜黃素 (Betaxanthin),而這兩種不同的甜菜黃素在430 nm有最高吸收鋒,因此可以最終產物甜菜黃素在430 nm的吸收值與濃度作圖,再透過Michaelis–Menten equation得出最大反應速率 (Vmax) 和酵素親和力 (Km)。此外,4,5-多巴雙加氧酶中特定的氨基酸位置突變以改變對於基質的選擇性與活性,從中挑選出對於多巴胺或左旋多巴具有獨特專一性的4,5-多巴雙加氧酶突變體,分別有比起野生型對於L-DOPA更專一的F252Y突變體,還有對於DA有良好選擇性的雙點突變體N249D&F252Y。
The 4,5-dopa dioxygenase purified from Mirabilis jalapa can catalyze levodopa (L-DOPA) and dopamine (DA) to produce two different betaxanthins (Betaxanthin). We thus performed site-directed mutagenesis to generate several mutants, and studied kinetics of mutated enzymes for L-DOPA and DA, respectively. In order to improve specificity, we changed the amino acids near the active sites to alter the hydrophilicity and steric barriers of the entire molecule, which results in changes in the binding ability to dopamine or L-DOPA. The four mutants that undergo site-directed mutagenesis were used for whole-cell bioassays. The detailed enzyme kinetics test was carried out. We totally build over 100 mutate strains, and using whole-cell biosensor for high-throughput screening. Finally, we use protein purification and Michaelis–Menten equation, successfully select the dopamine-specific mutation F252Y and the L-DOPA-specific double mutation N249D&F252Y.
1. Site-Directed Mutagenesis.
2. del Prado, A.; Villar, L.; de Vega, M.; Salas, M., Involvement of residues of the ϕ29 terminal protein intermediate and priming domains in the formation of a stable and functional heterodimer with the replicative DNA polymerase. Nucleic acids research 2012, 40 (9), 3886-3897.
3. Dale, H. H., Otto Loewi, 1873-1961. The Royal Society London: 1962.
4. Loewi, O., Chemical transmission of nerve impulses. American Scientist 1945, 33 (3), 159-174.
5. Daubner, S. C.; Le, T.; Wang, S., Tyrosine hydroxylase and regulation of dopamine synthesis. Archives of biochemistry and biophysics 2011, 508 (1), 1-12.
6. Kuhar, M. J.; Couceyro, P. R.; Lambert, P. D., Catecholamines. Basic neurochemistry: Molecular, cellular and medical aspects 1999, 243-262.
7. McGeer, P.; McGeer, E. J. J. o. n., Enzymes associated with the metabolism of catecholamines, acetylcholine and GABA in human controls and patients with Parkinson's disease and Huntington's chorea. 1976, 26 (1), 65-76.
8. Haavik, J.; Toska, K., Tyrosine hydroxylase and Parkinson's disease. Molecular neurobiology 1998, 16 (3), 285-309.
9. Brautigam, C.; Wevers, R. A.; Jansen, R. J.; Smeitink, J. A.; Andel, J. F. d. R.-v.; Gabreëls, F. J.; Hoffmann, G. F., Biochemical hallmarks of tyrosine hydroxylase deficiency. Clinical chemistry 1998, 44 (9), 1897-1904.
10. Lüdecke, B.; Dworniczak, B.; Bartholomé, K., A point mutation in the tyrosine hydroxylase gene associated with Segawa's syndrome. Human genetics 1995, 95 (1), 123-125.
11. Willemsen, M. A.; Verbeek, M. M.; Kamsteeg, E.-J.; de Rijk-van Andel, J. F.; Aeby, A.; Blau, N.; Burlina, A.; Donati, M. A.; Geurtz, B.; Grattan-Smith, P. J., Tyrosine hydroxylase deficiency: a treatable disorder of brain catecholamine biosynthesis. Brain 2010, 133 (6), 1810-1822.
12. Hou, Y.; Liu, X.; Li, S.; Zhang, X.; Yu, S.; Zhao, G.-R., Metabolic engineering of Escherichia coli for de novo production of betaxanthins. Journal of Agricultural and Food Chemistry 2020, 68 (31), 8370-8380.
13. Liveri, M. L. T.; Sciascia, L.; Lombardo, R.; Tesoriere, L.; Passante, E.; Livrea, M. A., Spectrophotometric evidence for the solubilization site of betalain pigments in membrane biomimetic systems. Journal of agricultural and food chemistry 2007, 55 (8), 2836-2840.
14. Wang, M.; Lopez-Nieves, S.; Goldman, I. L.; Maeda, H. A., Limited tyrosine utilization explains lower betalain contents in yellow than in red table beet genotypes. Journal of Agricultural and Food Chemistry 2017, 65 (21), 4305-4313.
15. Kovaleva, E. G.; Lipscomb, J. D., Versatility of biological non-heme Fe (II) centers in oxygen activation reactions. Nature chemical biology 2008, 4 (3), 186-193.
16. Nakatsuka, T.; Yamada, E.; Takahashi, H.; Imamura, T.; Suzuki, M.; Ozeki, Y.; Tsujimura, I.; Saito, M.; Sakamoto, Y.; Sasaki, N., Genetic engineering of yellow betalain pigments beyond the species barrier. Scientific reports 2013, 3 (1), 1-7.
17. Sasaki, N.; Abe, Y.; Goda, Y.; Adachi, T.; Kasahara, K.; Ozeki, Y., Detection of DOPA 4, 5-dioxygenase (DOD) activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa. Plant and cell physiology 2009, 50 (5), 1012-1016.
18. Gandía-Herrero, F.; García-Carmona, F., Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity. Applied microbiology and biotechnology 2014, 98 (3), 1165-1174.
19. Wang, Y.; Shin, I.; Fu, Y.; Colabroy, K. L.; Liu, A., Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry 2019, 58 (52), 5339-5350.
20. Walker, D. J.; Martz, E.; Holmes, D. E.; Zhou, Z.; Nonnenmann, S. S.; Lovley, D. R., The archaellum of Methanospirillum hungatei is electrically conductive. MBio 2019, 10 (2).
21. Stentebjerg-Olesen, B.; Pallesen, L.; Jensen, L. B.; Christiansen, G.; Klemm, P., Authentic display of a cholera toxin epitope by chimeric type 1 fimbriae: effects of insert position and host background. Microbiology 1997, 143 (6), 2027-2038.
22. Bingle, W. H.; Nomellini, J. F.; Smit, J., Cell‐surface display of a Pseudomonas aeruginosa strain K pilin peptide within the paracrystalline S‐layer of Caulobacter crescentus. Molecular microbiology 1997, 26 (2), 277-288.
23. Xu, Z.; Lee, S. Y., Display of polyhistidine peptides on the Escherichia coli cell surface by using outer membrane protein C as an anchoring motif. Applied and Environmental Microbiology 1999, 65 (11), 5142-5147.
24. Suzuki, T.; Lett, M.-C.; Sasakawa, C., Extracellular Transport of VirG Protein in Shigella (∗). Journal of Biological Chemistry 1995, 270 (52), 30874-30880.
25. Stathopoulos, C.; Georgiou, G.; Earhart, C., Characterization of Escherichia coli expressing an Lpp’OmpA (46-159)-PhoA fusion protein localized in the outer membrane. Applied microbiology and biotechnology 1996, 45 (1), 112-119.
26. Nguyen, T. N.; Gourdon, M.-H.; Hansson, M.; Robert, A.; Samuelson, P.; Libon, C.; Andréoni, C.; Nygren, P.-Å.; Binz, H.; Uhlén, M., Hydrophobicity engineering to facilitate surface display of heterologous gene products on Staphylococcus xylosus. Journal of biotechnology 1995, 42 (3), 207-219.
27. Lee, S. Y.; Choi, J. H.; Xu, Z., Microbial cell-surface display. Trends in Biotechnology 2003, 21 (1), 45-52.
28. Feng, J.-J.; Guo, H.; Li, Y.-F.; Wang, Y.-H.; Chen, W.-Y.; Wang, A.-J., Single molecular functionalized gold nanoparticles for hydrogen-bonding recognition and colorimetric detection of dopamine with high sensitivity and selectivity. ACS applied materials & interfaces 2013, 5 (4), 1226-1231.
29. Huang, Q.; Lin, X.; Tong, L.; Tong, Q.-X., Graphene quantum dots/multiwalled carbon nanotubes composite-based electrochemical sensor for detecting dopamine release from living cells. ACS Sustainable Chemistry & Engineering 2020, 8 (3), 1644-1650.
30. Lin, J.; Huang, B.; Dai, Y.; Wei, J.; Chen, Y., Chiral ZnO nanoparticles for detection of dopamine. Materials Science and Engineering: C 2018, 93, 739-745.
31. Goud, K. Y.; Moonla, C.; Mishra, R. K.; Yu, C.; Narayan, R.; Litvan, I.; Wang, J., Wearable electrochemical microneedle sensor for continuous monitoring of levodopa: toward Parkinson management. ACS sensors 2019, 4 (8), 2196-2204.
32. Ahan, R. E.; Kırpat, B. M.; Saltepe, B.; Şeker, U. Ö. Ş., A Self-Actuated Cellular Protein Delivery Machine. ACS Synthetic Biology 2019, 8 (4), 686-696.
33. Chou, Y.-C., Functional and structural studies of a 4,5-DOPA dioxygenase involved in betalain pigment biosynthesis from Mirabilis jalapa. 2017.
34. Dong, H.; Sarkes, D. A.; Rice, J. J.; Hurley, M. M.; Fu, A. J.; Stratis-Cullum, D. N., Living Bacteria–Nanoparticle Hybrids Mediated through Surface-Displayed Peptides. Langmuir 2018, 34 (20), 5837-5848.
35. Chou, Y.-C.; Shih, C.-I.; Chiang, C.-C.; Hsu, C.-H.; Yeh, Y.-C., Reagent-free DOPA-dioxygenase colorimetric biosensor for selective detection of L-DOPA. Sensors and Actuators B: Chemical 2019, 297, 126717.
36. Kumar, A.; Maity, H.; Dua, A., Parallel versus off-pathway Michaelis–Menten mechanism for single-enzyme kinetics of a fluctuating enzyme. The Journal of Physical Chemistry B 2015, 119 (27), 8490-8500.
37. Wang, I.-H., Using protein engineering to modify 4,5-DOPA dioxygenase form Mirabilis jalapa to detect dopamine and L-DOPA. 2020.
1. Site-Directed Mutagenesis.
2. del Prado, A.; Villar, L.; de Vega, M.; Salas, M., Involvement of residues of the ϕ29 terminal protein intermediate and priming domains in the formation of a stable and functional heterodimer with the replicative DNA polymerase. Nucleic acids research 2012, 40 (9), 3886-3897.
3. Dale, H. H., Otto Loewi, 1873-1961. The Royal Society London: 1962.
4. Loewi, O., Chemical transmission of nerve impulses. American Scientist 1945, 33 (3), 159-174.
5. Daubner, S. C.; Le, T.; Wang, S., Tyrosine hydroxylase and regulation of dopamine synthesis. Archives of biochemistry and biophysics 2011, 508 (1), 1-12.
6. Kuhar, M. J.; Couceyro, P. R.; Lambert, P. D., Catecholamines. Basic neurochemistry: Molecular, cellular and medical aspects 1999, 243-262.
7. McGeer, P.; McGeer, E. J. J. o. n., Enzymes associated with the metabolism of catecholamines, acetylcholine and GABA in human controls and patients with Parkinson's disease and Huntington's chorea. 1976, 26 (1), 65-76.
8. Haavik, J.; Toska, K., Tyrosine hydroxylase and Parkinson's disease. Molecular neurobiology 1998, 16 (3), 285-309.
9. Brautigam, C.; Wevers, R. A.; Jansen, R. J.; Smeitink, J. A.; Andel, J. F. d. R.-v.; Gabreëls, F. J.; Hoffmann, G. F., Biochemical hallmarks of tyrosine hydroxylase deficiency. Clinical chemistry 1998, 44 (9), 1897-1904.
10. Lüdecke, B.; Dworniczak, B.; Bartholomé, K., A point mutation in the tyrosine hydroxylase gene associated with Segawa's syndrome. Human genetics 1995, 95 (1), 123-125.
11. Willemsen, M. A.; Verbeek, M. M.; Kamsteeg, E.-J.; de Rijk-van Andel, J. F.; Aeby, A.; Blau, N.; Burlina, A.; Donati, M. A.; Geurtz, B.; Grattan-Smith, P. J., Tyrosine hydroxylase deficiency: a treatable disorder of brain catecholamine biosynthesis. Brain 2010, 133 (6), 1810-1822.
12. Hou, Y.; Liu, X.; Li, S.; Zhang, X.; Yu, S.; Zhao, G.-R., Metabolic engineering of Escherichia coli for de novo production of betaxanthins. Journal of Agricultural and Food Chemistry 2020, 68 (31), 8370-8380.
13. Liveri, M. L. T.; Sciascia, L.; Lombardo, R.; Tesoriere, L.; Passante, E.; Livrea, M. A., Spectrophotometric evidence for the solubilization site of betalain pigments in membrane biomimetic systems. Journal of agricultural and food chemistry 2007, 55 (8), 2836-2840.
14. Wang, M.; Lopez-Nieves, S.; Goldman, I. L.; Maeda, H. A., Limited tyrosine utilization explains lower betalain contents in yellow than in red table beet genotypes. Journal of Agricultural and Food Chemistry 2017, 65 (21), 4305-4313.
15. Kovaleva, E. G.; Lipscomb, J. D., Versatility of biological non-heme Fe (II) centers in oxygen activation reactions. Nature chemical biology 2008, 4 (3), 186-193.
16. Nakatsuka, T.; Yamada, E.; Takahashi, H.; Imamura, T.; Suzuki, M.; Ozeki, Y.; Tsujimura, I.; Saito, M.; Sakamoto, Y.; Sasaki, N., Genetic engineering of yellow betalain pigments beyond the species barrier. Scientific reports 2013, 3 (1), 1-7.
17. Sasaki, N.; Abe, Y.; Goda, Y.; Adachi, T.; Kasahara, K.; Ozeki, Y., Detection of DOPA 4, 5-dioxygenase (DOD) activity using recombinant protein prepared from Escherichia coli cells harboring cDNA encoding DOD from Mirabilis jalapa. Plant and cell physiology 2009, 50 (5), 1012-1016.
18. Gandía-Herrero, F.; García-Carmona, F., Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity. Applied microbiology and biotechnology 2014, 98 (3), 1165-1174.
19. Wang, Y.; Shin, I.; Fu, Y.; Colabroy, K. L.; Liu, A., Crystal Structures of L-DOPA Dioxygenase from Streptomyces sclerotialus. Biochemistry 2019, 58 (52), 5339-5350.
20. Walker, D. J.; Martz, E.; Holmes, D. E.; Zhou, Z.; Nonnenmann, S. S.; Lovley, D. R., The archaellum of Methanospirillum hungatei is electrically conductive. MBio 2019, 10 (2).
21. Stentebjerg-Olesen, B.; Pallesen, L.; Jensen, L. B.; Christiansen, G.; Klemm, P., Authentic display of a cholera toxin epitope by chimeric type 1 fimbriae: effects of insert position and host background. Microbiology 1997, 143 (6), 2027-2038.
22. Bingle, W. H.; Nomellini, J. F.; Smit, J., Cell‐surface display of a Pseudomonas aeruginosa strain K pilin peptide within the paracrystalline S‐layer of Caulobacter crescentus. Molecular microbiology 1997, 26 (2), 277-288.
23. Xu, Z.; Lee, S. Y., Display of polyhistidine peptides on the Escherichia coli cell surface by using outer membrane protein C as an anchoring motif. Applied and Environmental Microbiology 1999, 65 (11), 5142-5147.
24. Suzuki, T.; Lett, M.-C.; Sasakawa, C., Extracellular Transport of VirG Protein in Shigella (∗). Journal of Biological Chemistry 1995, 270 (52), 30874-30880.
25. Stathopoulos, C.; Georgiou, G.; Earhart, C., Characterization of Escherichia coli expressing an Lpp’OmpA (46-159)-PhoA fusion protein localized in the outer membrane. Applied microbiology and biotechnology 1996, 45 (1), 112-119.
26. Nguyen, T. N.; Gourdon, M.-H.; Hansson, M.; Robert, A.; Samuelson, P.; Libon, C.; Andréoni, C.; Nygren, P.-Å.; Binz, H.; Uhlén, M., Hydrophobicity engineering to facilitate surface display of heterologous gene products on Staphylococcus xylosus. Journal of biotechnology 1995, 42 (3), 207-219.
27. Lee, S. Y.; Choi, J. H.; Xu, Z., Microbial cell-surface display. Trends in Biotechnology 2003, 21 (1), 45-52.
28. Feng, J.-J.; Guo, H.; Li, Y.-F.; Wang, Y.-H.; Chen, W.-Y.; Wang, A.-J., Single molecular functionalized gold nanoparticles for hydrogen-bonding recognition and colorimetric detection of dopamine with high sensitivity and selectivity. ACS applied materials & interfaces 2013, 5 (4), 1226-1231.
29. Huang, Q.; Lin, X.; Tong, L.; Tong, Q.-X., Graphene quantum dots/multiwalled carbon nanotubes composite-based electrochemical sensor for detecting dopamine release from living cells. ACS Sustainable Chemistry & Engineering 2020, 8 (3), 1644-1650.
30. Lin, J.; Huang, B.; Dai, Y.; Wei, J.; Chen, Y., Chiral ZnO nanoparticles for detection of dopamine. Materials Science and Engineering: C 2018, 93, 739-745.
31. Goud, K. Y.; Moonla, C.; Mishra, R. K.; Yu, C.; Narayan, R.; Litvan, I.; Wang, J., Wearable electrochemical microneedle sensor for continuous monitoring of levodopa: toward Parkinson management. ACS sensors 2019, 4 (8), 2196-2204.
32. Ahan, R. E.; Kırpat, B. M.; Saltepe, B.; Şeker, U. Ö. Ş., A Self-Actuated Cellular Protein Delivery Machine. ACS Synthetic Biology 2019, 8 (4), 686-696.
33. Chou, Y.-C., Functional and structural studies of a 4,5-DOPA dioxygenase involved in betalain pigment biosynthesis from Mirabilis jalapa. 2017.
34. Dong, H.; Sarkes, D. A.; Rice, J. J.; Hurley, M. M.; Fu, A. J.; Stratis-Cullum, D. N., Living Bacteria–Nanoparticle Hybrids Mediated through Surface-Displayed Peptides. Langmuir 2018, 34 (20), 5837-5848.
35. Chou, Y.-C.; Shih, C.-I.; Chiang, C.-C.; Hsu, C.-H.; Yeh, Y.-C., Reagent-free DOPA-dioxygenase colorimetric biosensor for selective detection of L-DOPA. Sensors and Actuators B: Chemical 2019, 297, 126717.
36. Kumar, A.; Maity, H.; Dua, A., Parallel versus off-pathway Michaelis–Menten mechanism for single-enzyme kinetics of a fluctuating enzyme. The Journal of Physical Chemistry B 2015, 119 (27), 8490-8500.
37. Wang, I.-H., Using protein engineering to modify 4,5-DOPA dioxygenase form Mirabilis jalapa to detect dopamine and L-DOPA. 2020.