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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 張崇毅(Chung-I Chang) | |
| dc.contributor.author | Shih-Chieh Su | en |
| dc.contributor.author | 蘇士傑 | zh_TW |
| dc.date.accessioned | 2021-06-16T09:26:02Z | - |
| dc.date.available | 2022-07-12 | |
| dc.date.copyright | 2017-07-12 | |
| dc.date.issued | 2016 | |
| dc.date.submitted | 2017-06-06 | |
| dc.identifier.citation | Bernstein, S.H., Venkatesh, S., Li, M., Lee, J., Lu, B., Hilchey, S.P., Morse, K.M., Metcalfe, H.M., Skalska, J., Andreeff, M., et al. (2012). The mitochondrial ATP-dependent Lon protease: a novel target in lymphoma death mediated by the synthetic triterpenoid CDDO and its derivatives. Blood 119, 3321-3329.
Bieniossek, C., Schalch, T., Bumann, M., Meister, M., Meier, R., and Baumann, U. (2006). The molecular architecture of the metalloprotease FtsH. Proceedings of the National Academy of Sciences of the United States of America 103, 3066-3071. Bota, D.A., Ngo, J.K., and Davies, K.J. (2005). Downregulation of the human Lon protease impairs mitochondrial structure and function and causes cell death. Free radical biology & medicine 38, 665-677. Botos, I., Melnikov, E.E., Cherry, S., Tropea, J.E., Khalatova, A.G., Rasulova, F., Dauter, Z., Maurizi, M.R., Rotanova, T.V., Wlodawer, A., et al. (2004). The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. The Journal of biological chemistry 279, 8140-8148. Brandstetter, H., Kim, J.S., Groll, M., and Huber, R. (2001). Crystal structure of the tricorn protease reveals a protein disassembly line. Nature 414, 466-470. Brauer, M.J., Yuan, J., Bennett, B.D., Lu, W., Kimball, E., Botstein, D., and Rabinowitz, J.D. (2006). Conservation of the metabolomic response to starvation across two divergent microbes. Proceedings of the National Academy of Sciences of the United States of America 103, 19302-19307. Brooks, B.R., Brooks, C.L., 3rd, Mackerell, A.D., Jr., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., et al. (2009). CHARMM: the biomolecular simulation program. Journal of computational chemistry 30, 1545-1614. Cha, S.S., An, Y.J., Lee, C.R., Lee, H.S., Kim, Y.G., Kim, S.J., Kwon, K.K., De Donatis, G.M., Lee, J.H., Maurizi, M.R., et al. (2010). Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber. The EMBO journal 29, 3520-3530. Choi, K.H., and Licht, S. (2005). Control of peptide product sizes by the energy-dependent protease ClpAP. Biochemistry 44, 13921-13931. Chung, C.H., and Goldberg, A.L. (1981). The product of the lon (capR) gene in Escherichia coli is the ATP-dependent protease, protease La. Proceedings of the National Academy of Sciences of the United States of America 78, 4931-4935. Darden, T.A., and Pedersen, L.G. (1993). Molecular modeling: an experimental tool. Environmental health perspectives 101, 410-412. Desautels, M., and Goldberg, A.L. (1982). Demonstration of an ATP-dependent, vanadate-sensitive endoprotease in the matrix of rat liver mitochondria. The Journal of biological chemistry 257, 11673-11679. Duman, R.E., and Lowe, J. (2010). Crystal structures of Bacillus subtilis Lon protease. Journal of molecular biology 401, 653-670. Ekici, O.D., Paetzel, M., and Dalbey, R.E. (2008). Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein science : a publication of the Protein Society 17, 2023-2037. Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta crystallographica Section D, Biological crystallography 60, 2126-2132. Fukui, T., Eguchi, T., Atomi, H., and Imanaka, T. (2002). A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins. Journal of bacteriology 184, 3689-3698. Garcia-Nafria, J., Ondrovicova, G., Blagova, E., Levdikov, V.M., Bauer, J.A., Suzuki, C.K., Kutejova, E., Wilkinson, A.J., and Wilson, K.S. (2010). Structure of the catalytic domain of the human mitochondrial Lon protease: proposed relation of oligomer formation and activity. Protein science : a publication of the Protein Society 19, 987-999. Glynn, S.E., Martin, A., Nager, A.R., Baker, T.A., and Sauer, R.T. (2009). Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Cell 139, 744-756. Goldberg, A.L. (1992). The mechanism and functions of ATP-dependent proteases in bacterial and animal cells. European journal of biochemistry / FEBS 203, 9-23. Gur, E. (2013). The Lon AAA+ protease. Sub-cellular biochemistry 66, 35-51. Iyer, L.M., Leipe, D.D., Koonin, E.V., and Aravind, L. (2004). Evolutionary history and higher order classification of AAA+ ATPases. Journal of structural biology 146, 11-31. Kisselev, A.F., Akopian, T.N., Woo, K.M., and Goldberg, A.L. (1999). The sizes of peptides generated from protein by mammalian 26 and 20 S proteasomes. Implications for understanding the degradative mechanism and antigen presentation. The Journal of biological chemistry 274, 3363-3371. Kuppuraj, G., Dudev, M., and Lim, C. (2009). Factors governing metal-ligand distances and coordination geometries of metal complexes. The journal of physical chemistry B 113, 2952-2960. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948. Li, J.K., Liao, J.H., Li, H., Kuo, C.I., Huang, K.F., Yang, L.W., Wu, S.H., and Chang, C.I. (2013). The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones. Acta crystallographica Section D, Biological crystallography 69, 1789-1797. Li, M., Gustchina, A., Rasulova, F.S., Melnikov, E.E., Maurizi, M.R., Rotanova, T.V., Dauter, Z., and Wlodawer, A. (2010). Structure of the N-terminal fragment of Escherichia coli Lon protease. Acta crystallographica Section D, Biological crystallography 66, 865-873. Liao, J.H., Ihara, K., Kuo, C.I., Huang, K.F., Wakatsuki, S., Wu, S.H., and Chang, C.I. (2013). Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors. Acta crystallographica Section D, Biological crystallography 69, 1395-1402. Liao, J.H., Kuo, C.I., Huang, Y.Y., Lin, Y.C., Lin, Y.C., Yang, C.Y., Wu, W.L., Chang, W.H., Liaw, Y.C., Lin, L.H., et al. (2012). A Lon-like protease with no ATP-powered unfolding activity. PloS one 7, e40226. Lin, C.C., Su, S.C., Su, M.Y., Liang, P.H., Feng, C.C., Wu, S.H., and Chang, C.I. (2016). Structural Insights into the Allosteric Operation of the Lon AAA+ Protease. Structure 24, 667-675. Lin, C.C., Su, S. C., Su, M. Y., Liang, P. Y., Feng, C. C., Wu, S. H., Chang, C. I (under revision). Structural insights into the allosteric operation of the Lon AAA+ protease. Structure, in press. Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. Journal of structural biology 128, 82-97. MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The journal of physical chemistry B 102, 3586-3616. Maehara, G., Taya, S., and Kojima, H. (2007). Changes in hemoglobin concentration in the lateral occipital regions during shape recognition: a near-infrared spectroscopy study. Journal of biomedical optics 12, 062109. Maehara, T., Hoshino, T., and Nakamura, A. (2008). Characterization of three putative Lon proteases of Thermus thermophilus HB27 and use of their defective mutants as hosts for production of heterologous proteins. Extremophiles : life under extreme conditions 12, 285-296. McCoy, A.J., Fucini, P., Noegel, A.A., and Stewart, M. (1999). Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod. Nature structural biology 6, 836-841. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007). Phaser crystallographic software. Journal of applied crystallography 40, 658-674. Menon, A.S., and Goldberg, A.L. (1987). Binding of nucleotides to the ATP-dependent protease La from Escherichia coli. The Journal of biological chemistry 262, 14921-14928. Minami, N., Yasuda, T., Ishii, Y., Fujimori, K., and Amano, F. (2011). Regulatory role of cardiolipin in the activity of an ATP-dependent protease, Lon, from Escherichia coli. Journal of biochemistry 149, 519-527. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta crystallographica Section D, Biological crystallography 53, 240-255. Neuwald, A.F., Aravind, L., Spouge, J.L., and Koonin, E.V. (1999). AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome research 9, 27-43. Nomura, K., Kato, J., Takiguchi, N., Ohtake, H., and Kuroda, A. (2004). Effects of inorganic polyphosphate on the proteolytic and DNA-binding activities of Lon in Escherichia coli. Journal of Biological Chemistry 279, 34406-34410. Ogura, T., and Wilkinson, A.J. (2001). AAA+ superfamily ATPases: common structure--diverse function. Genes to cells : devoted to molecular & cellular mechanisms 6, 575-597. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol 276, 307-326. Park, S.C., Jia, B., Yang, J.K., Van, D.L., Shao, Y.G., Han, S.W., Jeon, Y.J., Chung, C.H., and Cheong, G.W. (2006). Oligomeric structure of the ATP-dependent protease La (Lon) of Escherichia coli. Molecules and cells 21, 129-134. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. Journal of computational chemistry 25, 1605-1612. Robert, X., and Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic acids research 42, W320-324. Rotanova, T.V., Botos, I., Melnikov, E.E., Rasulova, F., Gustchina, A., Maurizi, M.R., and Wlodawer, A. (2006). Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains. Protein science : a publication of the Protein Society 15, 1815-1828. Rotanova, T.V., Melnikov, E.E., Khalatova, A.G., Makhovskaya, O.V., Botos, I., Wlodawer, A., and Gustchina, A. (2004). Classification of ATP-dependent proteases Lon and comparison of the active sites of their proteolytic domains. European journal of biochemistry / FEBS 271, 4865-4871. Rudyak, S.G., Brenowitz, M., and Shrader, T.E. (2001). Mg2+-linked oligomerization modulates the catalytic activity of the Lon (La) protease from Mycobacterium smegmatis. Biochemistry 40, 9317-9323. Russo, S., and Baumann, U. (2004). Crystal structure of a dodecameric tetrahedral-shaped aminopeptidase. The Journal of biological chemistry 279, 51275-51281. Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. (1977). Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J Comput Phys 23, 327-341. Sauer, R.T., and Baker, T.A. (2011). AAA+ proteases: ATP-fueled machines of protein destruction. Annual review of biochemistry 80, 587-612. Sauer, R.T., Bolon, D.N., Burton, B.M., Burton, R.E., Flynn, J.M., Grant, R.A., Hersch, G.L., Joshi, S.A., Kenniston, J.A., Levchenko, I., et al. (2004). Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell 119, 9-18. Su, M.Y., Peng, W.H., Ho, M.R., Su, S.C., Chang, Y.C., Chen, G.C., and Chang, C.I. (2015). Structure of yeast Ape1 and its role in autophagic vesicle formation. Autophagy 11, 1580-1593. Suno, R., Niwa, H., Tsuchiya, D., Zhang, X., Yoshida, M., and Morikawa, K. (2006). Structure of the whole cytosolic region of ATP-dependent protease FtsH. Molecular cell 22, 575-585. Swamy, K.H., and Goldberg, A.L. (1981). E. coli contains eight soluble proteolytic activities, one being ATP dependent. Nature 292, 652-654. Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., and Ludtke, S.J. (2007). EMAN2: an extensible image processing suite for electron microscopy. Journal of structural biology 157, 38-46. Van Melderen, L., Thi, M.H., Lecchi, P., Gottesman, S., Couturier, M., and Maurizi, M.R. (1996). ATP-dependent degradation of CcdA by Lon protease. Effects of secondary structure and heterologous subunit interactions. The Journal of biological chemistry 271, 27730-27738. Vieux, E.F., Wohlever, M.L., Chen, J.Z., Sauer, R.T., and Baker, T.A. (2013). Distinct quaternary structures of the AAA+ Lon protease control substrate degradation. Proceedings of the National Academy of Sciences of the United States of America 110, E2002-2008. Wang, H.M., Cheng, K.C., Lin, C.J., Hsu, S.W., Fang, W.C., Hsu, T.F., Chiu, C.C., Chang, H.W., Hsu, C.H., and Lee, A.Y. (2010). Obtusilactone A and (-)-sesamin induce apoptosis in human lung cancer cells by inhibiting mitochondrial Lon protease and activating DNA damage checkpoints. Cancer science 101, 2612-2620. Wickner, S., Maurizi, M.R., and Gottesman, S. (1999). Posttranslational quality control: folding, refolding, and degrading proteins. Science 286, 1888-1893. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59508 | - |
| dc.description.abstract | 隆蛋白酶（Lon protease)是屬於ＡＴＰ依賴性的蛋白質分解酶，在生物演化中是高度保留可以存在於原核細胞內及真核生物胞器中，例如人類的粒線體及植物的葉綠體。在生物體中溶蛋白酶將細胞內蛋白質降解提供許多重要的功能，舉例來說在細胞內選擇性降解調控蛋白質使其細胞內在不同時期有不同濃度進而有效率調控，例如降解轉錄因子或者細胞週期的調控蛋白質。另外還有個重要功能是清除細胞內不正常蛋白質像是摺疊錯誤的蛋白質或是已受損的蛋白質。文獻指出隆蛋白酶需要鎂離子才可組裝成六聚體而具有功能需要有ＡＴＰ才可以降解具有二級結構或無結構的蛋白質受質。而也發現在沒有ＡＴＰ只有鎂離子情況下隆蛋白酶可以降解無二級結構的受質。目前沒有研究解釋這現象。
利用低溫電子顯微鏡(Cryo-EM)建構隆蛋白酶在有鎂離子情況下的蛋白質結構。發現鎂離子會讓隆蛋白酶形成六聚體但是側邊有縫隙並不像有ＡＴＰ情況下形成封閉的六聚體。而建構出的蛋白質結構可以解釋沒有二級結構的蛋白質受質可以藉由擴散的方式進入到隆蛋白酶的催化活性的位置進而將受質分解而且不需依賴ＡＴＰ。也利用結晶學發現鎂離子結合到隆蛋白酶的催化活性位置附近進而改變 substrate-binding loop促進隆蛋白酶的降解活性。以上的結果指出鎂離子對於隆蛋白酶的組裝及活性是扮演重要的角色。 | zh_TW |
| dc.description.abstract | The Lon AAA+ protease (LonA) plays critical roles in protein homeostasis and regulation of diverse biological processes. LonA is thought to form a sequestered substrate-degradation chamber by fused rings of six AAA+ and six protease domains and its activity depends on magnesium (Mg2+) and ATP. Using single-particle cryo-electron microscopy reconstructions, I show that apo-LonA without Mg2+ forms a tetrameric complex, and that binding of Mg2+ drives the formation of a hexameric chamber. Without nucleotide, both the tetrameric and hexameric LonA chambers show prominent side and top openings. The tetrameric apo-LonA is proteolytically inactive but Mg2+-activated LonA degrades efficiently unstructured protein and peptide substrates. Binding of ATP further converts the open chamber of Mg2+-activated LonA into a secluded assembly. ADP and polyatomic ions are found to inhibit proteolysis by LonA, presumably by inducing the formation of an immobile secluded chamber disallowing access of protein substrates. Moreover, to understand the role of Mg2+, I have determined a 1.85Å crystal structure of a truncated LonA bound to Mg2+ and a proteasome inhibitor, which reveals a potential Mg2+-binding site in the protease domain. Specific binding of Mg2+ is further confirmed by biophysical and biochemical assays. Structural analysis and molecular dynamics (MD) simulations suggest that binding of Mg2+ activates LonA by promoting deprotonation of the catalytic Lys required for serving as the general base, opening of the proteolytic groove, and formation of the hexameric interface of the protease ring. My findings reveal the structural roles of Mg2+, ADP, and polyatomic anions in the assembly and activity of LonA. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T09:26:02Z (GMT). No. of bitstreams: 1 ntu-105-D00b46008-1.pdf: 11552202 bytes, checksum: 38f4a1defc5cd0f587c9beade7948218 (MD5) Previous issue date: 2016 | en |
| dc.description.tableofcontents | 口試委員會審定書……………………………………………………………….. I
Acknowledgements……………………………………………………………….. II Abstract…………………………………………………………………………… III Table of Contents…………………………………………………………………. IV List of Figures…………………………………………………………………….. VI List of Tables……………………………………………………………………… IX Chapter 1 Introduction 1-1 Protein quality control………………………………………………………… 1 1-2 AAA+ proteases………………………………………………………………. 2 1-3 The Lon AAA+ protease……………………………………………………… 3 1-4 LonA………………………………………………………………………….. 4 1-5 The Lon protease as an anticancer target……………………………………... 5 1-6 Motivation of research………………………………………………………... 6 Figures……………………………………………………………………………. 9 Chapter 2 Materials and Methods 2-1 Cloning, protein expression, and purification………………………………… 19 2-2 Cryo-EM and negative stain sample preparation…………………………….. 20 2-3 Image Processing and three-dimensional reconstructions……………………. 21 2-4 Protein crystallization………………………………………………………… 22 2-5 Structure determination………………………………………………………. 22 2-6 Accession numbers…………………………………………………………… 23 2-7 Peptidase activity assays……………………………………………………… 24 2-8 Substrate degradation assays…………………………………………………. 24 2-9 Analysis by circular dichroism (CD) spectroscopy…………………………... 25 2-10 Differential scanning fluorimetry (DSF)……………………………………. 26 2-11 Molecular dynamics (MD) Calculations……………………………………. 26 Figures……………………………………………………………………………. 29 Chapter 3 Results 3-1 Magnesium- and nucleotide-dependent hexameric assembly of LonA revealed by cryo-EM structures………………………………………………….. 37 3-2 Mg-activated LonA degrades unfolded protein or peptides without ATP……. 39 3-3 Binding of polyatomic anions to the ATPase site inhibits LonA activity……. 41 3-4 Magnesium is bound in the proteolytic active site……………………………. 43 3-5 Structures of open and closed proteolytic groove…………………………….. 45 3-6 Binding of Mg2+ stabilizes the active LonA structure with Lys721 deprotonated………………………………………………………………………. 46 Figures…………………………………………………………………………….. 48 Tables……………………………………………………………………………... 69 Chapter 4 Discussions 4-1 Role of the AAA+ modules in the open and closure of the LonA chamber…. 71 4-2 Role of the protease domains in the oligomerization and activity of LonA….. 72 4-3 Biological implication of ATP-independent proteolysis by Mg2+-activated LonA……………………………………………………………… 73 References……………………………………………………………. 75 Paper list……………………………………………………………... 85 | |
| dc.language.iso | en | |
| dc.subject | 低溫電子顯微鏡 | zh_TW |
| dc.subject | 隆蛋白? | zh_TW |
| dc.subject | 低溫電子顯微鏡 | zh_TW |
| dc.subject | 隆蛋白? | zh_TW |
| dc.subject | Cryo-EM | en |
| dc.subject | Lon protease | en |
| dc.title | 鎂離子對於隆蛋白酶組裝及催化活性的結構與功能分析 | zh_TW |
| dc.title | Structural and functional analysis of the magnesium activated hexamerization and proteolytic mechanism of the Lon AAA+ protease | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 105-2 | |
| dc.description.degree | 博士 | |
| dc.contributor.oralexamcommittee | 詹迺立(Nei-Li Chan),傅琪鈺(Fu-Chi Yu),曾秀如(Shiou-Ru Tzeng),鄭惠春(Hui-Chun Cheng) | |
| dc.subject.keyword | 隆蛋白?,低溫電子顯微鏡, | zh_TW |
| dc.subject.keyword | Lon protease,Cryo-EM, | en |
| dc.relation.page | 85 | |
| dc.identifier.doi | 10.6342/NTU201700896 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2017-06-06 | |
| dc.contributor.author-college | 生命科學院 | zh_TW |
| dc.contributor.author-dept | 生化科學研究所 | zh_TW |
| 顯示於系所單位： | 生化科學研究所 | |
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