本質無穩定結構基因重組蛋白質 Thymosin β4之摺疊研究

Folding study of intrinsically disordered proteins, recombinant Thymosin β4

黃詠勤

胸腺素 ； 無穩定結構蛋白質 ； 蛋白質摺疊 ； Thymosin β4(Tβ4) ； intrinsically disordered proteins(IDPs) ； protein folding

交通大學生物科技學系學位論文

2016年

碩士

張家靖

繁體中文

1. 1. Sharan SK, Thomason LC, Kuznetsov SG, & Court DL (2009) Recombineering: a homologous recombination-based method of genetic engineering. Nature protocols 4:206-223.
   連結：
2. 2. Guo, LiHe, Stepien, Piotr P, Tso, J Yun, Brousseau, Roland, Narang, Saran, Thomas, David Y& Wu, Ray (1984) Synthesis of human insulin gene VIII. Construction of expression vectors for fused proinsulin production in Escherichia coli. Gene 29:251-254.
   連結：
3. 3. Basu A, Li X, & Leong SS (2011) Refolding of proteins from inclusion bodies: rational design and recipes. Appl Microbiol Biotechnol 92:241-251.
   連結：
4. 4. Singh SM & Panda AK (2005) Solubilization and refolding of bacterial inclusion body proteins. J Biosci Bioeng 99:303-310.
   連結：
5. 5. Dobson CM (2003) Protein folding and misfolding. Nature 884-890.
   連結：
6. 6. Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) Funnels, Pathways, and the Energy Landscape of Protein Folding- A Synthesis. Proteins: Structure, Function, and Bioinformatics:167-195.
   連結：
7. 7. Dunker, A. K., Oldfield, C. J., Meng, J., Romero, P., Yang, J. Y., Chen, J. W., Vacic, V., Obradovic, Z. & Uversky, V. N. (2008) The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 9 Suppl 2:S1.
   連結：
8. 8. Hogg PJ (2003) Disulfide bonds as switches for protein function. Trends in Biochemical Sciences 28:210-214.
   連結：
9. 10. Nölting B (2005) Protein Folding Kinetics. biophysical methods.
   連結：
10. 11. Anfinsen CB (1972) Studies on the principles that govern the folding of protein chains.
    連結：
11. 12. Dill KA & Shortle D (1991) Denatured states of proteins. Annual review of biochemistry 60:795-825.
    連結：
12. 13. Mirsky AE & Pauling L (1936) On the structure of native, denatured, and coagulated proteins. Proceedings of the National Academy of Sciences 22.7:439-447.
    連結：
13. 14. Thanassoulas, A., Nomikos, M., Theodoridou, M., Stavros, P., Mastellos, D., & Nounesis, G. (2011) Thermal and chemical denaturation of the BRCT functional module of human 53BP1. Int J Biol Macromol 49:297-304.
    連結：
14. 15. Chen BL, Walter A. Baase & John A. Schellman. (1989) Low-Temperature Unfolding of a Mutant of Phage T4 Lysozyme. 2. Kinetic Investigationst Biochemistry 28.2: 691-699.
    連結：
15. 16. Vladimir A. Sirotkin RW (2010) Volume Changes Associated with Guanidine Hydrochloride, Temperature, and Ethanol Induced Unfolding of Lysozyme. J. Phys. Chem. B.
    連結：
16. 17. Jahromi RR, Morris P, Martinez-Torres RJ, & Dalby PA (2011) Structural stability of E. coli transketolase to temperature and pH denaturation. J Biotechnol 155:209-216.
    連結：
17. 18. Heyda, J., Kožíšek, M., Bednárova, L., Thompson, G., Konvalinka, J., Vondrášek, J., & Jungwirth, P. (2011) Urea and guanidinium induced denaturation of a Trp-cage miniprotein. J Phys Chem B 115:8910-8924.
    連結：
18. 19. Nielsen MM, Andersen KK, Westh P, & Otzen DE (2007) Unfolding of beta-sheet proteins in SDS. Biophys J 92:3674-3685.
    連結：
19. 20. Anfinsen CB & Edgar Haber. (1961) Studies on the Reduction and Re-formation of Protein Disulfide Bonds J Biol Chem 236.5:1361-1363.
    連結：
20. 21. Chang CC, Yeh XC, Lee HT, Lin PY, & Kan LS (2004) Refolding of lysozyme by quasistatic and direct dilution reaction paths: a first-order-like state transition. Phys Rev E Stat Nonlin Soft Matter Phys 70:011904.
    連結：
21. 22. Tsumoto K, Ejima D, Kumagai I, & Arakawa T (2003) Practical considerations in refolding proteins from inclusion bodies. Protein Expression and Purification 28:1-8.
    連結：
22. 23. Chang CC, Su YC, Cheng MS, & Kan LS (2002) Protein folding by a quasi-static-like process: a first-order state transition. Phys Rev E Stat Nonlin Soft Matter Phys 66:021903.
    連結：
23. 24. Liu Y-L, Lee H-T, Chang C-C, & Kan L-S (2003) Reversible folding of cysteine-rich metallothionein by an overcritical reaction path. Biochemical and Biophysical Research Communications 306:59-63.
    連結：
24. 25. Chang CC, Cheng MS, Su YC, & Kan LS (2003) A first-order-like state transition for recombinant protein folding. J Biomol Struct Dyn 21:247-256.
    連結：
25. 26. Uversky VN (2009) Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Protein J 28:305-325.
    連結：
26. 27. Dunker AK, Silman I, Uversky VN, & Sussman JL (2008) Function and structure of inherently disordered proteins. Curr Opin Struct Biol 18:756-764.
    連結：
27. 28. Dyson PEWaHJ (1999) Intrinsically Unstructured Proteins- Re-assessing the Protein Structure-Function Paradigm. Journal of Molecular Biology 293.2:321-331.
    連結：
28. 30. Tompa P (2012) Intrinsically disordered proteins: a 10-year recap. Trends Biochem Sci 37:509-516.
    連結：
29. 32. Dunker, A. Keith, Babu, M. Madan, Barbar, Elisar, Blackledge, Martin, Bondos, Sarah E., Dosztányi, Zsuzsanna, Dyson, H. Jane, Forman-Kay, Julie, Fuxreiter, Monika, Gsponer, Jörg, Han, Kyou-Hoon, Jones, David T., Longhi, Sonia, Metallo, Steven J., Nishikawa, Ken, Nussinov, Ruth, Obradovic, Zoran, Pappu, Rohit V., Rost, Burkhard, Selenko, Philipp, Subramaniam, Vinod, Sussman, Joel L., Tompa, Peter & Uversky, Vladimir N. (2014) What’s in a name? Why these proteins are intrinsically disordered. Intrinsically Disordered Proteins 1:e24157.
    連結：
30. 33. Uversky VN (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci 11:739-756.
    連結：
31. 34. Crockford D, Turjman N, Allan C, & Angel J (2010) Thymosin beta4: structure, function, and biological properties supporting current and future clinical applications. Ann N Y Acad Sci 1194:179-189.
    連結：
32. 35. Philp, D., St-Surin, S., Cha, H. J., Moon, H. S., Kleinman, H. K. & Elkin, M. (2007) Thymosin beta 4 induces hair growth via stem cell migration and differentiation. Ann N Y Acad Sci 1112:95-103.
    連結：
33. 36. Kozaczuk A, Selmi A, & Bednarek R (2013) Bacterial expression, purification and angiogenesis-promoting activity of human thymosin beta4. Protein Expr Purif 90:142-152.
    連結：
34. 37. Sosne G & Kleinman HK (2015) Primary Mechanisms of Thymosin beta4 Repair Activity in Dry Eye Disorders and Other Tissue Injuries. Invest Ophthalmol Vis Sci 56:5110-5117.
    連結：
35. 38. CZISCH, M., SCHLEICHER, M., HÖRGER, S., VOELTER, W., & HOLAK, T. A. (1993) Conformation of thymosin p4 in water determined by NMR spectroscopy. European Journal of Biochemistry 218:335-344.
    連結：
36. 40. Sosne G, Qiu P, Goldstein AL, & Wheater M (2010) Biological activities of thymosin beta4 defined by active sites in short peptide sequences. FASEB J 24:2144-2151.
    連結：
37. 41. Dedova IV, Nikolaeva OP, Safer D, De La Cruz EM, & dos Remedios CG (2006) Thymosin beta4 induces a conformational change in actin monomers. Biophys J 90:985-992.
    連結：
38. 42. Hertzog M, Yarmola EG, Didry D, Bubb MR, & Carlier MF (2002) Control of actin dynamics by proteins made of beta-thymosin repeats: the actobindin family. J Biol Chem 277:14786-14792.
    連結：
39. 43. Kuznetsova IM, Povarova OI, Uversky VN, & Turoverov KK (2016) Native globular actin has a thermodynamically unstable quasi-stationary structure with elements of intrinsic disorder. FEBS J 283:438-445.
    連結：
40. 44. Schüler H, Karlsson R, Schutt CE, & Lindberg U (2006) The Connection Between Actin ATPase and Polymerization. 37:49-66.
    連結：
41. 45. Korn ED, Carlier M-F, & Pantaloni D (Actin Polymerization and ATP Hydrolysis. Science:638-644.
    連結：
42. 46. Mannherz HG & Hannappel E (2009) The beta-thymosins: intracellular and extracellular activities of a versatile actin binding protein family. Cell Motil Cytoskeleton 66:839-851.
    連結：
43. 47. Wittig I, Braun HP, & Schagger H (2006) Blue native PAGE. Nat Protoc 1:418-428.
    連結：
44. 48. Sun H & Pan Y-CE (1999) Using native gel in two-dimensional PAGE for the detection of protein interactions in protein extract. Journal of biochemical and biophysical methods:143-151.
    連結：
45. 50. Cassimeris L, Safer D, Nachmias VT, & Zigmond S (1992) Thymosin beta 4 sequesters the majority of G-actin in resting human polymorphonuclear leukocytes. The Journal of cell biology 119:1261-1270.
    連結：
46. 51. Lakowicz JR (2013) Principles of fluorescence spectroscopy (Springer Science & Business Media).
    連結：
47. 53. Eftink MR (2002) Intrinsic fluorescence of proteins. Topics in fluorescence spectroscopy, (Springer), pp 1-15.
    連結：
48. 54. Panda D & Datta A (2007) Evidence for covalent binding of epicocconone with proteins from synchronous fluorescence spectra and fluorescence lifetimes. Journal of Chemical Sciences 119:99-104.
    連結：
49. 56. Kaszuba M, McKnight D, Connah MT, McNeil-Watson FK, & Nobbmann U (2008) Measuring sub nanometre sizes using dynamic light scattering. Journal of Nanoparticle Research 10:823-829.
    連結：
50. 57. Paatero P (1997) Least squares formulation of robust non-negative factor analysis. Chemometrics and intelligent laboratory systems 37:23-35.
    連結：
51. 59. Woody RW (1995) Circular dichroism. Methods in enzymology 246:34-71.
    連結：
52. 60. Johnson WC (1990) Protein secondary structure and circular dichroism: a practical guide. Proteins: Structure, Function, and Bioinformatics 7:205-214.
    連結：
53. 61. Greenfield NJ (2006) Using circular dichroism spectra to estimate protein secondary structure. Nat Protoc 1:2876-2890.
    連結：
54. 62. Sreerama N, Venyaminov SY, & Woody RW (2000) Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis. Analytical biochemistry 287:243-251.
    連結：
55. 63. Sturtevant JM (1987) Biochemical applications of differential scanning calorimetry. Annual review of physical chemistry 38:463-488.
    連結：
56. 64. Fekecs T, Zapf I, Ferencz A, & Lőrinczy D (2011) Differential scanning calorimetry (DSC) analysis of human plasma in melanoma patients with or without regional lymph node metastases. Journal of thermal analysis and calorimetry 108:149-152.
    連結：
57. 65. Kamiyama T, Tanaka T, Satoh M, & Kimura T (2013) Destabilization of cytochrome c by modified β-cyclodextrin. Journal of thermal analysis and calorimetry 113:1491-1496.
    連結：
58. 67. Rezwan, Kurosch, Meier, Lorenz P, Rezwan, Mandana, Vörös, Janos, Textor, Marcus & Gauckler, Ludwig J (2004) Bovine serum albumin adsorption onto colloidal Al2O3 particles: A new model based on Zeta potential and UV-Vis measurements. Langmuir 20:10055-10061.
    連結：
59. 68. Frieden C, Hoeltzli SD, & Ropson IJ (1993) NMR and protein folding: Equilibrium and stopped‐flow studies. protein Science 2:2007-2014.
    連結：
60. 70. Kuwajima K, Yamaya H, Miwa S, Sugai S, & Nagamura T (1987) Rapid formation of secondary structure framework in protein folding studied by stopped‐flow circular dichroism. FEBS letters 221:115-118.
    連結：
61. 71. Fabian H & Naumann D (2004) Methods to study protein folding by stopped-flow FT-IR. Methods 34:28-40.
    連結：
62. 72. Gruebele M (1999) The fast protein folding problem. Annual review of physical chemistry 50:485-516.
    連結：
63. 74. Wallace B (2000) Synchrotron radiation circular-dichroism spectroscopy as a tool for investigating protein structures. Journal of synchrotron radiation 7:289-295.
    連結：
64. 75. Matagne A & Dobson CM (1998) The folding process of hen lysozyme: a perspective from the ‘new view’. Cellular and Molecular Life Sciences CMLS 54:363-371.
    連結：
65. 9. Schulz GE & Schirmer RH (2013) Principles of protein structure (Springer Science & Business Media).
66. 29. Jin, Shengkan, Martinek, Sebastian, Joo, Woo S, Wortman, Jennifer R, Mirkovic, Nebojsa, Sali, Andrej, Yandell, Mark D, Pavletich, Nikola P, Young, Michael W & Levine, Arnold J (2000) Identification and characterization of a p53 homologue in Drosophila melanogaster. Proceedings of the National Academy of Sciences 97:7301-7306.
67. 31. Chu, Hsueh-Liang, Chen, Tzu-Hsuan, Wu, Chang-You, Yang, Yao-Chen, Tseng, Shin-Hua, Cheng, Tsai-Mu, Ho, Li-Ping, Tsai, Li-Yun, Li, Hsing-yuan, Chang, Chia-Seng, Chang, Chia-Ching (2014) Thermal stability and folding kinetics analysis of disordered protein, securin. Journal of Thermal Analysis and Calorimetry 115:2171-2178.
68. 39. Huff T, Müller CS, Otto AM, Netzker R, & Hannappel E (2001) β-Thymosins, small acidic peptides with multiple functions. The international journal of biochemistry & cell biology 33:205-220.
69. 49. Arndt C (2012) Native polyacrylamide gels. Protein Electrophoresis: Methods and Protocols:49-53.
70. 52. Valeur B & Brochon J-C (2012) New trends in fluorescence spectroscopy: applications to chemical and life sciences (Springer Science & Business Media).
71. 55. Pecora R (2000) Dynamic light scattering measurement of nanometer particles in liquids. Journal of nanoparticle research 2:123-131.
72. 58. Kelly SM, Jess TJ, & Price NC (2005) How to study proteins by circular dichroism. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1751:119-139.
73. 66. Hunter RJ (2013) Zeta potential in colloid science: principles and applications (Academic press).
74. 69. Clarke DT, Doig AJ, Stapley BJ, & Jones GR (1999) The α-helix folds on the millisecond time scale. Proceedings of the National Academy of Sciences 96:7232-7237.
75. 73. Zwanzig R (1997) Two-state models of protein folding kinetics. Proceedings of the National Academy of Sciences of the United States of America:148-150.