研究生: |
張玉蓓 Chang, Yu-Pei |
---|---|
論文名稱: |
探究人類降鈣素雙位點突變變異體其低聚性的原因 Exploring the cause of reduced amyloidogenicity of human calcitonin double variants |
指導教授: |
杜玲嫻
Tu, Ling-Hsien |
口試委員: |
杜玲嫻
Tu, Ling-Hsien 葉怡均 Yeh, Yi-Chun 洪嘉呈 Horng, Jia-Cherng |
口試日期: | 2023/06/09 |
學位類別: |
碩士 Master |
系所名稱: |
化學系 Department of Chemistry |
論文出版年: | 2023 |
畢業學年度: | 111 |
語文別: | 中文 |
論文頁數: | 80 |
研究方法: | 實驗設計法 |
DOI URL: | http://doi.org/10.6345/NTNU202300544 |
論文種類: | 學術論文 |
相關次數: | 點閱:79 下載:5 |
分享至: |
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
不可逆的聚集行為經常會大幅度地限制胜肽藥物的治療效果。舉例來說,人類降鈣素(human calcitonin, hCT)是一種由32個胺基酸所組成的胜肽激素,由甲狀腺的濾泡旁細胞(C-cells)所分泌,其在生物體中有著調節血鈣水平及維持骨骼型態的生理功能,因此能夠用於治療骨骼等相關疾病,像是骨質疏鬆症和佩吉特氏病等。但由於蛋白質聚集且形成澱粉樣蛋白纖維的傾向很高,導致其作為藥物的潛力受到限制。目前的臨床藥物則由低聚集傾向的鮭魚降鈣素(salmon calcitonin, sCT)所取代,sCT的序列中在N末端也和hCT一樣,具雙硫鍵連接而成的環形結構,但有16個胺基酸的位置與hCT不同,序列同源性很低,部分患者服藥後產生嚴重的副作用。以往的研究證實,Tyr-12和Asn-17兩個位點在誘導hCT 纖維化中起著關鍵作用,雙突變可大大地增強其抗聚集特性。在這項研究中,我們分別檢查雙突變(Y12LN17H)和單突變hCT(Y12L、N17H)形成寡聚物或α-螺旋構形的難易程度,透過比較來了解雙突變體聚性降低的原因,並幫助了解 hCT 纖維化的機制。另外,我們還參考預測軟體及其他文獻的建議繼續尋找更為優化的變異體,透過一系列實驗觀察了解新變異體的聚集特性,雖然結果不如預期,並無法超越原本的雙突變變異體使蛋白質聚性再度降低,然而有這些新變異體的實驗結果比較,協助我們更進一步推測雙突變變異體聚性很低的原因,期望我們的發現也將有助於設計治療性胜肽藥物。
Irreversible aggregation greatly limits the therapeutic activity of peptide drugs. For example, human calcitonin (hCT) is a peptide hormone composed of 32 amino acids. It is secreted by the parafollicular cells (C-cells) located in the thyroid gland. The hormone plays a crucial role in regulating blood calcium levels and maintaining bone structure in the body. Due to its physiological functions, hCT is valuable in the treatment of conditions such as osteoporosis and Paget's disease. However, its potential for working as drug is limited due to the high propensity in forming amyloid. Current clinical drugs are replaced by low-aggregating salmon calcitonin (sCT) with the same disulfide bond at the N-terminus but different from hCT at the 16 amino acid positions. Low sequence homology of sCT sometimes causes severe side effects when patients are taking it as medicine. Previous studies have shown that Tyr-12 and Asn-17 play a crucial role in inducing hCT fiber formation, and double mutations on these two sites can significantly enhance their ability in preventing aggregation. In this study, we examined the oligomerization and helical formation of hCT double mutant (Y12LN17H) and two single mutants (Y12L, N17H) to help understand the mechanism of hCT fibrillization. In addition, we utilized prediction software and prediction results suggested from computational studies to find an even better substituent. Although the results are not satisfactory, the comparison between new and old hCT double mutants helps us to speculate the low aggregation propensity of the double mutant. We hope that our findings will also help design therapeutic peptide drugs.
1. Siddiqi, M.K., et al., Amyloid oligomers, protofibrils and fibrils. Subcell Biochem, 2019. 93: p. 471-503.
2. Sipe, J.D., et al., Amyloid fibril proteins and amyloidosis: chemical identification and clinical classification International Society of Amyloidosis 2016 Nomenclature Guidelines. Amyloid, 2016. 23(4): p. 209-213.
3. Goedert, M., Neurodegeneration. Alzheimer's and Parkinson's diseases: The prion concept in relation to assembled Aβ, tau, and α-synuclein. Science, 2015. 349(6248): p. 1255555.
4. Westermark, P., A. Andersson, and G.T. Westermark, Islet amyloid polypeptide, islet amyloid, and diabetes mellitus. Physiol Rev, 2011. 91(3): p. 795-826.
5. Osmand, A.P., et al., Embryonic mutant huntingtin aggregate formation in mouse models of huntington's disease. J Huntingtons Dis, 2016. 5(4): p. 343-346.
6. Jarrett, J.T. and P.T. Lansbury, Jr., Seeding "one-dimensional crystallization" of amyloid: a pathogenic mechanism in Alzheimer's disease and scrapie? Cell, 1993. 73(6): p. 1055-8.
7. Xue, W.F., S.W. Homans, and S.E. Radford, Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly. Proc Natl Acad Sci U S A, 2008. 105(26): p. 8926-31.
8. Del Pozo-Yauner, L., et al. The Structural Determinants of the Immunoglobulin Light Chain Amyloid Aggregation. in Physical Biology of Proteins and Peptides. 2015. Cham: Springer International Publishing.
9. Cao, Q., et al., Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrils. Nat Struct Mol Biol, 2020. 27(7): p. 653-659.
10. Copp, D.H. and B. Cheney, Calcitonin—a hormone from the parathyroid which lowers the calcium-level of the blood. Nature, 1962. 193(4813): p. 381-382.
11. Foster, G.V., et al., Thyroid origin of calcitonin. Nature, 1964. 202(4939): p. 1303-1305.
12. Austin, L.A. and H. Heath, 3rd, Calcitonin: physiology and pathophysiology. N Engl J Med, 1981. 304(5): p. 269-78.
13. Pondel, M., Calcitonin and calcitonin receptors: bone and beyond. Int J Exp Pathol, 2000. 81(6): p. 405-22.
14. Reginster, J.Y., Calcitonin for prevention and treatment of osteoporosis. Am J Med, 1993. 95(5a): p. 44s-47s.
15. Del Fattore, A., A. Teti, and N. Rucci, Bone cells and the mechanisms of bone remodelling. Frontiers in bioscience, 2012. 4: p. 2302-21.
16. Ji, M.X. and Q. Yu, Primary osteoporosis in postmenopausal women. Chronic Dis Transl Med, 2015. 1(1): p. 9-13.
17. Siris, E.S., Paget's disease of bone. J Bone Miner Res, 1998. 13(7): p. 1061-5.
18. Davey, R.A. and D.M. Findlay, Calcitonin: physiology or fantasy? J Bone Miner Res, 2013. 28(5): p. 973-9.
19. Masi, L. and M.L. Brandi, Calcitonin and calcitonin receptors. Clin Cases Miner Bone Metab, 2007. 4(2): p. 117-22.
20. Nicholson, G.C., et al., Abundant calcitonin receptors in isolated rat osteoclasts. Biochemical and autoradiographic characterization. J Clin Invest, 1986. 78(2): p. 355-60.
21. Stenbeck, G., Formation and function of the ruffled border in osteoclasts. Semin Cell Dev Biol, 2002. 13(4): p. 285-92.
22. Gruber, H.E., et al., Long-term calcitonin therapy in postmenopausal osteoporosis. Metabolism, 1984. 33(4): p. 295-303.
23. Peacock, M., Calcium metabolism in health and disease. Clin J Am Soc Nephrol, 2010. 5 Suppl 1: p. S23-30.
24. Liu, Y., et al., Structural perturbation of monomers determines the amyloid aggregation propensity of calcitonin variants. J Chem Inf Model, 2023. 63(1): p. 308-320.
25. Ljunghall, S., et al., Synthetic human calcitonin in postmenopausal osteoporosis: a placebo-controlled, double-blind study. Calcif Tissue Int, 1991. 49(1): p. 17-9.
26. Cudd, A., et al., Enhanced potency of human calcitonin when fibrillation is avoided. Journal of Pharmaceutical Sciences, 1995. 84(6): p. 717-719.
27. Sapir-Koren, R. and G. Livshits, Postmenopausal osteoporosis in rheumatoid arthritis: The estrogen deficiency-immune mechanisms link. Bone, 2017. 103: p. 102-115.
28. Ensrud, K.E., Bisphosphonates for postmenopausal osteoporosis. JAMA, 2021. 325(1): p. 96-96.
29. Kanaori, K. and A.Y. Nosaka, Study of human calcitonin fibrillation by proton nuclear magnetic resonance spectroscopy. Biochemistry, 1995. 34(38): p. 12138-43.
30. Ma, Y., et al., Fluorescent silicon nanoparticles inhibit the amyloid fibrillation of insulin. J Mater Chem B, 2019. 7(9): p. 1397-1403.
31. Shamloo, A., et al., Designing a new multifunctional peptide for metal chelation and Aβ inhibition. Archives of Biochemistry and Biophysics, 2018. 653: p. 1-9.
32. Das, A., et al., An amphiphilic small molecule drives insulin aggregation inhibition and amyloid disintegration. Int J Biol Macromol, 2022. 218: p. 981-991.
33. Rahamtullah, A. Ahmad, and R. Mishra, Polyol and sugar osmolytes stabilize the molten globule state of α-lactalbumin and inhibit amyloid fibril formation. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2022. 1870(11): p. 140853.
34. Hsieh, I.C., et al., Tyrosine 12 of human calcitonin modulates its amyloid formation, membrane binding, and bioactivity. Biochimie, 2022. 197: p. 121-129.
35. Garbuzynskiy, S.O., M.Y. Lobanov, and O.V. Galzitskaya, FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics, 2010. 26(3): p. 326-32.
36. Fowler, S.B., et al., Rational design of aggregation-resistant bioactive peptides: reengineering human calcitonin. Proc Natl Acad Sci U S A, 2005. 102(29): p. 10105-10.
37. Ye, H., H. Li, and Z. Gao, Y12 nitration of human calcitonin (hCT): A promising strategy to produce non-aggregation bioactive hCT. Nitric Oxide, 2020. 104-105: p. 11-19.
38. Andreotti, G., et al., Converting the highly amyloidogenic human calcitonin into a powerful fibril inhibitor by three-dimensional structure homology with a non-amyloidogenic analogue. J Biol Chem, 2011. 286(4): p. 2707-18.
39. Amodeo, P., et al., Conformational flexibility in calcitonin: the dynamic properties of human and salmon calcitonin in solution. J Biomol NMR, 1999. 13(2): p. 161-74.
40. Chen, Y.T., et al., Inhibiting human calcitonin fibril formation with its most relevant aggregation-resistant analog. J Phys Chem B, 2019. 123(48): p. 10171-10180.
41. Naito, A., et al., Structural diversity of amyloid fibril formed in human calcitonin as revealed by site-directed 13C solid-state NMR spectroscopy. Magn Reson Chem, 2004. 42(2): p. 247-57.
42. Bertolani, A., et al., Crystal structure of the DFNKF segment of human calcitonin unveils aromatic interactions between phenylalanines. Chemistry – A European Journal, 2017. 23(9): p. 2051-2058.
43. Zhao, J., et al., Insights into the mechanism of tyrosine nitration in preventing β-amyloid aggregation in Alzheimer's disease. Front Mol Neurosci, 2021. 14: p. 619836.
44. Zhao, J., et al., Nitration of hIAPP promotes its toxic oligomer formation and exacerbates its toxicity towards INS-1 cells. Nitric Oxide, 2019. 87: p. 23-30.
45. Bartesaghi, S. and R. Radi, Fundamentals on the biochemistry of peroxynitrite and protein tyrosine nitration. Redox Biol, 2018. 14: p. 618-625.
46. Siligardi, G., et al., Correlations between biological activities and conformational properties for human, salmon, eel, porcine calcitonins and elcatonin elucidated by CD spectroscopy. Eur J Biochem, 1994. 221(3): p. 1117-25.
47. Kamihira, M., et al., Conformational transitions and fibrillation mechanism of human calcitonin as studied by high-resolution solid-state 13C NMR. Protein Sci, 2000. 9(5): p. 867-77.
48. DuBay, K.F., et al., Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. J Mol Biol, 2004. 341(5): p. 1317-26.
49. Cowan, R. and R.G. Whittaker, Hydrophobicity indices for amino acid residues as determined by high-performance liquid chromatography. Pept Res, 1990. 3(2): p. 75-80.
50. Roseman, M.A., Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J Mol Biol, 1988. 200(3): p. 513-22.
51. Koehl, P. and M. Levitt, Structure-based conformational preferences of amino acids. Proc Natl Acad Sci U S A, 1999. 96(22): p. 12524-9.
52. Broome, B.M. and M.H. Hecht, Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol, 2000. 296(4): p. 961-8.
53. Kamgar-Parsi, K., et al., Structural biology of calcitonin: from aqueous therapeutic properties to amyloid aggregation. Israel Journal of Chemistry, 2017. 57(7-8): p. 634-650.
54. Chiti, F., et al., Rationalization of the effects of mutations on peptide andprotein aggregation rates. Nature, 2003. 424(6950): p. 805-808.
55. Merrifield, R.B., Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. Journal of the American Chemical Society, 1963. 85(14): p. 2149-2154.
56. Roepstorff, P., MALDI-TOF mass spectrometry in protein chemistry. Exs, 2000. 88: p. 81-97.
57. Leszyk, J.D., Evaluation of the new MALDI matrix 4-chloro-alpha-cyanocinnamic acid. J Biomol Tech, 2010. 21(2): p. 81-91.
58. Maurer-Stroh, S., et al., Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nature Methods, 2010. 7(3): p. 237-242.
59. Montgomerie, S., et al., PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Research, 2008. 36(suppl_2): p. W202-W209.
60. Ban, T., et al., Direct observation of amyloid fibril growth monitored by thioflavin T fluorescence. J Biol Chem, 2003. 278(19): p. 16462-5.
61. Biancalana, M. and S. Koide, Molecular mechanism of thioflavin-T binding to amyloid fibrils. Biochim Biophys Acta, 2010. 1804(7): p. 1405-12.
62. LeVine, H., 3rd, Stopped-flow kinetics reveal multiple phases of thioflavin T binding to Alzheimer beta (1-40) amyloid fibrils. Arch Biochem Biophys, 1997. 342(2): p. 306-16.
63. Parrish, J.R., Jr. and E.R. Blout, Spectroscopic studies of random chain and -helical polypeptides in hexafluoroisopropanol. Biopolymers, 1971. 10(9): p. 1491-512.
64. Luo, P. and R.L. Baldwin, Mechanism of helix induction by trifluoroethanol: a framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water. Biochemistry, 1997. 36(27): p. 8413-21.
65. Micsonai, A., et al., BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy. Nucleic Acids Research, 2022. 50(W1): p. W90-W98.
66. Micsonai, A., et al., Disordered–ordered protein binary classification by circular dichroism spectroscopy. Frontiers in Molecular Biosciences, 2022. 9.
67. Micsonai, A., É. Bulyáki, and J. Kardos, BeStSel: From secondary structure analysis to protein fold prediction by circular dichroism spectroscopy, in Structural Genomics: General Applications, Y.W. Chen and C.-P.B. Yiu, Editors. 2021, Springer US: New York, NY. p. 175-189.
68. Micsonai, A., et al., BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra. Nucleic Acids Research, 2018. 46(W1): p. W315-W322.
69. Greenfield, N.J., Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc, 2006. 1(6): p. 2876-90.
70. Bitan, G., A. Lomakin, and D.B. Teplow, Amyloid beta-protein oligomerization: prenucleation interactions revealed by photo-induced cross-linking of unmodified proteins. J Biol Chem, 2001. 276(37): p. 35176-84.
71. Bitan, G., Structural study of metastable amyloidogenic protein oligomers by photo-induced cross-linking of unmodified proteins. Methods Enzymol, 2006. 413: p. 217-36.
72. Rahimi, F., P. Maiti, and G. Bitan, Photo-induced cross-linking of unmodified proteins (PICUP) applied to amyloidogenic peptides. J Vis Exp, 2009(23).
73. Lopes, D.H., et al., Application of photochemical cross-linking to the study of oligomerization of amyloidogenic proteins. Methods Mol Biol, 2012. 849: p. 11-21.
74. Liddle, G.W. and J.G. Hardman, Cyclic adenosine monophosphate as a mediator of hormone action. N Engl J Med, 1971. 285(10): p. 560-6.
75. Suda, T., N. Takahashi, and T.J. Martin, Modulation of osteoclast differentiation. Endocr Rev, 1992. 13(1): p. 66-80.
76. Kanzawa, M., et al., Involvement of osteoprotegerin/osteoclastogenesis inhibitory factor in the stimulation of osteoclast formation by parathyroid hormone in mouse bone cells. Eur J Endocrinol, 2000. 142(6): p. 661-4.
77. Guo, C., et al., Inhibitory effects of magnolol and honokiol on human calcitonin aggregation. Sci Rep, 2015. 5: p. 13556.
78. Andreotti, G., et al., Structural determinants of salmon calcitonin bioactivity: The role of the Leu-based amphipathic α-helix*. Journal of Biological Chemistry, 2006. 281(34): p. 24193-24203.
79. Kawashima, H., et al., A dimer model of human calcitonin13-32 forms an α-helical structure and robustly aggregates in 50% aqueous 2,2,2-trifluoroethanol solution. J Pept Sci, 2016. 22(7): p. 480-4.
80. FINDLAY, D.M., et al., Conformational requirements for activity of salmon calcitonin*. Endocrinology, 1985. 117(3): p. 801-805.
81. Findlay, D.M., et al., Calcitonin and 1,25-dihydroxyvitamin D3 receptors in human breast cancer cell lines1. Cancer Research, 1980. 40(12): p. 4764-4767.
82. Paul, S. and S. Paul, Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations. Phys Chem Chem Phys, 2021. 23(26): p. 14496-14510.