普恩蛋白疾病是一種腦神經疾病，又稱感染性海綿狀腦病(transmissible spongiform encephalopathies;TSE)，是由正常的普恩蛋白(PrPC)產生錯誤折疊成致病普恩蛋白(PrPSc)，進而聚集堆積成纖維造成疾病，目前 PrPC如何轉變成PrPSc的途徑，還尚未被釐清，但目前有越來越多的證據表示，可溶性的寡聚體比纖維狀組織更具有有毒性，而聚集成寡聚體的最小單位為二聚體，本文利用分子動力學模擬可溶性二聚體普恩蛋白原生型和突變D178N在不同的溫度和酸鹼值環境，探討模擬數據分析結構與毒性的關係，利用如下分析: 均方根誤差、均方根波動、迴轉半徑、二級結構分析、鹽橋和氫鍵數量等，三維子域交換被認為是PrPC轉變成聚集的PrPSc相當重要的一步，但二聚體普恩蛋白的功能和動態行為還是未知，本文比較原生型普恩蛋白結構域交換和突變型D178N無結構域交換在不同環境下結構與動態行為，結構交換只會發生在原生普恩蛋白上，而突變的D178N無結構域交換，利用不同二聚體結構進行研究，模擬結果可進一步探討普恩蛋白聚集的行為。

Prion disease is neurodegenerative diseases, also called transmissible spongiform encephalopathies (TSE). Such neurodegeneration event produces the structural misfolding from nomal PrPC to the pathogenic PrPSc. At present the PrPC how to transform into PrPSc pathway is still an open question. Furthermore, a growing body of evidence indicates that small, soluble oligomeric species generated from a variety of proteins and peptides rather than mature amyloid fibrils are inherently highly cytotoxicity. Due to the structure of dimeric prion is belongs to the simplest aggregates form that eventually elongate to the oligomeric. In this study, the wild-type and mutant D178N of soluble dimeric prion protein at different pH values and temperatures are examined using molecular dynamics simulations. In order to treat the structure-toxicity relationship, some parameters are analyzed, e.g. RMSD, RMSF, Rg, DSSP, salt bridge, hydrogen bond numbers and so on. On the other hand, three dimensional domain-swapping-dependent oligomerization is considered an important step in the conformational change of PrPC to PrPSc, but the function and dynamics of the dimeric form of PrP is unknown. Therefore we also examined and compared the domain swapping and non-swapping phenomenon of wild-type and mutant D178N of prion dimers at different circumstance. The significant result shown that domain swapping is contrived only in wild-type dimer, nevertheless, mutant D178N of prion dimer is not contrived domain swapping. Such diverse aggregates behaviors may help us to deeply understand the further aggregation process.

1. Prusiner, S.B., Prions. Proceedings of the National Academy of Sciences of the United States of America, 1998. 95(23): p. 13363-13383.
2. Castilla, J., et al., In vitro generation of infectious scrapie prions. Cell, 2005. 121(2): p. 195-206.
3. Perl, D.P., Relationship of aluminum to Alzheimer's disease. Environ Health Perspect, 1985. 63: p. 149-53.
4. Candy, J.M., et al., Aluminosilicates and senile plaque formation in Alzheimer's disease. Lancet, 1986. 1(8477): p. 354-7.
5. Mclachlan, D.R.C., W.J. Lukiw, and T.P.A. Kruck, New Evidence for an Active-Role of Aluminum in Alzheimers-Disease. Canadian Journal of Neurological Sciences, 1989. 16(4): p. 490-497.
6. Emard, J.F., J.P. Thouez, and D. Gauvreau, Neurodegenerative diseases and risk factors: a literature review. Soc Sci Med, 1995. 40(6): p. 847-58.
7. Thompson, C.M., et al., Regional brain trace-element studies in Alzheimer's disease. Neurotoxicology, 1988. 9(1): p. 1-7.
8. Martyn, C.N., et al., GEOGRAPHICAL RELATION BETWEEN ALZHEIMERS-DISEASE AND ALUMINUM IN DRINKING-WATER. Lancet, 1989. 1(8629): p. 59-62.
9. Neri, L.C., D. Hewitt, and S.L. Rifat, ALUMINUM IN DRINKING WATER AND RISK FOR DIAGNOSES OF PRESENILE ALZHEIMER'S TYPE DEMENTIA. Neurobiology of Aging, 1992. 13(SUPPL. 1): p. S115.
10. Flaten, T.P., Geographical Associations between Aluminum in Drinking-Water and Death Rates with Dementia (Including Alzheimers-Disease), Parkinsons-Disease and Amyotrophic Lateral Sclerosis in Norway. Environmental Geochemistry and Health, 1990. 12(1-2): p. 152-167.
11. Detchant, W., Alzheimers-Disease and the Environment. Journal of the Royal Society of Medicine, 1992. 85(2): p. 69-70.
12. Still, C.N. and P. Kelley, On the Incidence of Primary Degenerative Dementia Vs Water Fluoride Content in South-Carolina. Neurotoxicology, 1980. 1(4): p. 125-131.
13. Wang, J.D., et al., Manganese Induced Parkinsonism - an Outbreak Due to an Unrepaired Ventilation Control-System in a Ferromanganese Smelter. British Journal of Industrial Medicine, 1989. 46(12): p. 856-859.
14. Huang, C.C., et al., Chronic Manganese Intoxication. Archives of Neurology, 1989. 46(10): p. 1104-1106.
15. Stein, E.C., et al., Multiple-Sclerosis and the Workplace - Report of an Industry-Based Cluster. Neurology, 1987. 37(10): p. 1672-1677.
16. Zahn, R., et al., NMR solution structure of the human prion protein. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(1): p. 145-150.
17. Calzolai, L. and R. Zahn, Influence of pH on NMR structure and stability of the human prion protein globular domain. Journal of Biological Chemistry, 2003. 278(37): p. 35592-35596.
18. Abalos, G.C., et al., Identifying Key Components of the PrP(C)-PrP(Sc) Replicative Interface. Journal of Biological Chemistry, 2008. 283(49): p. 34021-34028.
19. Brown, D.R., J. Herms, and H.A. Kretzschmar, MOUSE CORTICAL-CELLS LACKING CELLULAR PRP SURVIVE IN CULTURE WITH A NEUROTOXIC PRP FRAGMENT. Neuroreport, 1994. 5(16): p. 2057-2060.
20. Forloni, G., et al., NEUROTOXICITY OF A PRION PROTEIN-FRAGMENT. Nature, 1993. 362(6420): p. 543-546.
21. Supattapone, S., et al., Prion protein of 106 residues creates an artificial transmission barrier for prion replication in transgenic mice. Cell, 1999. 96(6): p. 869-878.
22. Hornshaw, M.P., J.R. McDermott, and J.M. Candy, COPPER-BINDING TO THE N-TERMINAL TANDEM REPEAT REGIONS OF MAMMALIAN AND AVIAN PRION PROTEIN. Biochemical and Biophysical Research Communications, 1995. 207(2): p. 621-629.
23. Stockel, J., et al., Prion protein selectively binds copper(II) ions. Biochemistry, 1998. 37(20): p. 7185-7193.
24. Pauly, P.C. and D.A. Harris, Copper stimulates endocytosis of the prion protein. Journal of Biological Chemistry, 1998. 273(50): p. 33107-33110.
25. Millhauser, G.L., Copper and the prion protein: Methods, structures, function, and disease, in Annual Review of Physical Chemistry2007, Annual Reviews: Palo Alto. p. 299-320.
26. Singh, A., et al., Prion Protein Modulates Cellular Iron Uptake: A Novel Function with Implications for Prion Disease Pathogenesis. Plos One, 2009. 4(2).
27. Viles, J.H., M. Klewpatinond, and R.C. Nadal, Copper and the structural biology of the prion protein. Biochemical Society Transactions, 2008. 36: p. 1288-1292.
28. Stevens, D.J., et al., Early Onset Prion Disease from Octarepeat Expansion Correlates with Copper Binding Properties. Plos Pathogens, 2009. 5(4).
29. Prusiner, S.B., Shattuck lecture - Neurodegenerative diseases and prions. New England Journal of Medicine, 2001. 344(20): p. 1516-1526.
30. Mead, S., et al., Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics. Science, 2003. 300(5619): p. 640-643.
31. Belay, E.D., Transmissible spongiform encephalopathies in humans, in Annual Review of Microbiology, L.N. Ornston, Editor 1999, Annual Reviews Inc. {a}, P.O. Box 10139, 4139 El Camino Way, Palo Alto, California 94306, USA. p. 283-314.
32. Collins, S.J., V.A. Lawson, and C.L. Masters, Transmissible spongiform encephalopathies. Lancet, 2004. 363(9402): p. 51-61.
33. Cornelius, J.R., et al., Visual Symptoms in the Heidenhain Variant of Creutzfeldt-Jakob Disease. Journal of Neuroimaging, 2009. 19(3): p. 283-287.
34. Parchi, P., et al., Phenotypic variability of sporadic human prion disease and its molecular basis: past, present, and future. Acta Neuropathologica, 2011. 121(1): p. 91-112.
35. Bratosiewicz-Wasik, J., et al., Regulatory sequences of the PRNP gene influence susceptibility to sporadic Creutzfeldt-Jakob disease. Neuroscience Letters, 2007. 411(3): p. 163-167.
36. Mead, S., et al., Sporadic - but not variant - Creutzfeldt-Jakob disease is associated with polymorphisms upstream of PRNP Exon 1. American Journal of Human Genetics, 2001. 69(6): p. 1225-1235.
37. Palmer, M.S., et al., HOMOZYGOUS PRION PROTEIN GENOTYPE PREDISPOSES TO SPORADIC CREUTZFELDT-JAKOB DISEASE. Nature, 1991. 352(6333): p. 340-342.
38. Windl, O., et al., Genetic basis of Creutzfeldt-Jakob disease in the United Kingdom: A systematic analysis of predisposing mutations and allelic variation in the PRNP gene. Human Genetics, 1996. 98(3): p. 259-264.
39. Brandner, S., et al., Central and peripheral pathology of kuru: pathological analysis of a recent case and comparison with other forms of human prion disease. Philosophical Transactions of the Royal Society B-Biological Sciences, 2008. 363(1510): p. 3755-3763.
40. Collinge, J., et al., Kuru in the 21st century - an acquired human prion disease with very long incubation periods. Lancet, 2006. 367(9528): p. 2068-2074.
41. Mead, S., et al., A Novel Protective Prion Protein Variant that Colocalizes with Kuru Exposure. New England Journal of Medicine, 2009. 361(21): p. 2056-2065.
42. Montagna, P., et al., Familial and sporadic fatal insomnia. Lancet Neurology, 2003. 2(3): p. 167-176.
43. Parchi, P., et al., A subtype of sporadic prion disease mimicking fatal familial insomnia. Neurology, 1999. 52(9): p. 1757-1763.
44. Gambetti, P., et al., Molecular biology and pathology of prion strains in sporadic human prion diseases. Acta Neuropathologica, 2011. 121(1): p. 79-90.
45. Gambetti, P., et al., Sporadic and familial CJD: classification and characterisation. British Medical Bulletin, 2003. 66: p. 213-+.
46. Kretzschmar, H.A., et al., MOLECULAR-CLONING OF A HUMAN PRION PROTEIN CDNA. DNA-a Journal of Molecular & Cellular Biology, 1986. 5(4): p. 315-324.
47. Nozaki, I., et al., Prospective 10-year surveillance of human prion diseases in Japan. Brain, 2010. 133: p. 3043-3057.
48. Lugaresi, E., et al., FATAL FAMILIAL INSOMNIA AND DYSAUTONOMIA WITH SELECTIVE DEGENERATION OF THALAMIC NUCLEI. New England Journal of Medicine, 1986. 315(16): p. 997-1003.
49. Capellari, S., et al., Genetic Creutzfeldt-Jakob disease and fatal familial insomnia: insights into phenotypic variability and disease pathogenesis. Acta Neuropathologica, 2011. 121(1): p. 21-37.
50. Belay, E.D., Transmissible spongiform encephalopathies in humans. Annual Review of Microbiology, 1999. 53: p. 283-314.
51. Jansen, C., et al., Prion protein amyloidosis with divergent phenotype associated with two novel nonsense mutations in PRNP. Acta Neuropathologica, 2010. 119(2): p. 189-197.
52. Alzualde, A., et al., A Novel PRNP Y218N Mutation in Gerstmann-Straussler-Scheinker Disease With Neurofibrillary Degeneration. Journal of Neuropathology and Experimental Neurology, 2010. 69(8): p. 789-800.
53. Liberski, P.P. and P. Brown, Kuru: Its ramifications after fifty years. Experimental Gerontology, 2009. 44(1-2): p. 63-69.
54. Alonso, D.O.V., et al., Mapping the early steps in the pH-induced conformational conversion of the prion protein. Proceedings of the National Academy of Sciences of the United States of America, 2001. 98(6): p. 2985-2989.
55. Alonso, D.O.V., C. An, and V. Daggett, Simulations of biomolecules: characterization of the early steps in the pH-induced conformational conversion of the hamster, bovine and human forms of the prion protein. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences, 2002. 360(1795): p. 1165-1178.
56. Colombo, G., et al., Methionine Sulfoxides on Prion Protein Helix-3 Switch on the alpha-Fold Destabilization Required for Conversion. Plos One, 2009. 4(1).
57. DeMarco, M.L. and V. Daggett, Molecular mechanism for low pH triggered misfolding of the human prion protein. Biochemistry, 2007. 46(11): p. 3045-3054.
58. Hornemann, S. and R. Glockshuber, A scrapie-like unfolding intermediate of the prion protein domain PrP(121-231) induced by acidic pH. Proceedings of the National Academy of Sciences of the United States of America, 1998. 95(11): p. 6010-6014.
59. Kelly, J.W., The environmental dependency of protein folding best explains prion and amyloid diseases. Proceedings of the National Academy of Sciences of the United States of America, 1998. 95(3): p. 930-932.
60. Santini, S., et al., Impact of the tail and mutations G131V and M129V on prion protein flexibility. Proteins-Structure Function and Genetics, 2003. 51(2): p. 258-265.
61. Prusiner, S.B., Prions. Scientific American, 1984. 251(4): p. 50-59.
62. Colby, D.W. and S.B. Prusiner, Prions. Cold Spring Harbor Perspectives in Biology, 2011. 3(1).
63. Derreumaux, P., Evidence that the 127-164 region of prion proteins has two equi-energetic conformations with beta or alpha features. Biophysical Journal, 2001. 81(3): p. 1657-1665.
64. Santini, S. and P. Derreumaux, Helix H1 of the prion protein is rather stable against environmental perturbations: molecular dynamics of mutation and deletion variants of PrP(90-231). Cellular and Molecular Life Sciences, 2004. 61(7-8): p. 951-960.
65. Malolepsza, E., et al., Theoretical model of prion propagation: A misfolded protein induces misfolding. Proceedings of the National Academy of Sciences of the United States of America, 2005. 102(22): p. 7835-7840.
66. Gsponer, J., P. Ferrara, and A. Caflisch, Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations. Journal of Molecular Graphics & Modelling, 2001. 20(2): p. 169-182.
67. Riek, R., et al., Prion protein NMR structure and familial human spongiform encephalopathies. Proceedings of the National Academy of Sciences of the United States of America, 1998. 95(20): p. 11667-11672.
68. Hsiao, K., et al., Mutant Prion Proteins in Gerstmann-Straussler-Scheinker Disease with Neurofibrillary Tangles. Nature Genetics, 1992. 1(1): p. 68-71.
69. Kitamoto, T., et al., Novel Missense Variants of Prion Protein in Creutzfeldt-Jakob Disease or Gerstmann-Straussler Syndrome. Biochemical and Biophysical Research Communications, 1993. 191(2): p. 709-714.
70. Liberski, P.P., et al., Autophagy Contributes to Widespread Neuronal Degeneration in Hamsters Infected with the Echigo-1 Strain of Creutzfeldt-Jakob Disease and Mice Infected with the Fujisaki Strain of Gerstmann-Straaussler-Scheinker (GSS) Syndrome. Ultrastructural Pathology, 2011. 35(1): p. 31-36.
71. Peoc'h, K., et al., Identification of three novel mutations (E196K, V203I, E211Q) in the prion protein gene (PRNP) in inherited prion diseases with Creutzfeldt-Jakob disease phenotype. Hum Mutat, 2000. 15(5): p. 482.
72. van der Kamp, M.W. and V. Daggett, Molecular Dynamics as an Approach to Study Prion Protein Misfolding and the Effect of Pathogenic Mutations. Prion Proteins, 2011. 305: p. 169-197.
73. van der Kamp, M.W. and V. Daggett, Pathogenic Mutations in the Hydrophobic Core of the Human Prion Protein Can Promote Structural Instability and Misfolding. Journal of Molecular Biology, 2010. 404(4): p. 732-748.
74. Mishra, R.S., et al., Aggresome formation by mutant prion proteins: The unfolding role of proteasomes in familial prion disorders. Journal of Alzheimer's Disease, 2003. 5(1): p. 15-23.
75. Aguzzi, A. and A.M. Calella, Prions: Protein Aggregation and Infectious Diseases. Physiological Reviews, 2009. 89(4): p. 1105-1152.
76. Weissmann, C., The state of the prion. Nature Reviews Microbiology, 2004. 2(11): p. 861-871.
77. Tompa, P., et al., The role of dimerization in prion replication. Biophysical Journal, 2002. 82(4): p. 1711-1718.
78. Lee, S., et al., Conformational diversity in prion protein variants influences intermolecular beta-sheet formation. Embo Journal, 2010. 29(1): p. 251-262.
79. Zhu, Z.-Y., A. ali, and T.L. Blundell, A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Engineering, 1992. 5(1): p. 43-51.
80. Weiner, S.J., et al., An all atom force field for simulations of proteins and nucleic acids. Journal of Computational Chemistry, 1986. 7(2): p. 230-252.
81. Van der Spoel, D., et al., GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 2005. 26(16): p. 1701-1718.
82. Hess, B., et al., GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 2008. 4(3): p. 435-447.
83. Kutzner, C., et al., Software news and update - Speeding up parallel GROMACS on high-latency networks. Journal of Computational Chemistry, 2007. 28(12): p. 2075-2084.
84. Bennett, M.J., M.P. Schlunegger, and D. Eisenberg, 3d Domain Swapping - a Mechanism for Oligomer Assembly. Protein Science, 1995. 4(12): p. 2455-2468.
85. Liu, Y. and D. Eisenberg, 3D domain swapping: As domains continue to swap. Protein Science, 2002. 11(6): p. 1285-1299.
86. Meyer, R.K., et al., A Monomer-Dimer Equilibrium of a Cellular Prion Protein (PrPC) Not Observed with Recombinant PrP. Journal of Biological Chemistry, 2000. 275(48): p. 38081-38087.
87. Knaus, K.J., et al., Crystal structure of the human prion protein reveals a mechanism for oligomerization. Nat Struct Mol Biol, 2001. 8(9): p. 770-774.
88. Lasmezas, C., et al., Highly neurotoxic monomeric alpha-helical prion protein. Prion, 2012. 6: p. 50-50.
89. Huang, L.Q., et al., Macromolecular crowding converts the human recombinant PrPC to the soluble neurotoxic beta-oligomers. Faseb Journal, 2010. 24(9): p. 3536-3543.
90. Bennett, M.J., M.P. Schlunegger, and D. Eisenberg, 3D domain swapping: A mechanism for oligomer assembly. Protein Science, 1995. 4(12): p. 2455-2468.
91. Fontaine, S.N. and D.R. Brown, Mechanisms of Prion Protein Aggregation. Protein and Peptide Letters, 2009. 16(1): p. 14-26.
92. Watanabe, Y., et al., Identification of pH-sensitive regions in the mouse prion by the cysteine-scanning spin-labeling ESR technique. Biochemical and Biophysical Research Communications, 2006. 350(3): p. 549-556.
93. Camilloni, C., et al., Energy Landscape of the Prion Protein Helix 1 Probed by Metadynamics and NMR. Biophysical Journal, 2012. 102(1): p. 158-167.
94. Xu, Z., et al., Dual Conformation of H2H3 Domain of Prion Protein in Mammalian Cells. Journal of Biological Chemistry, 2011. 286(46): p. 40060-40068.
95. Adrover, M., et al., Prion Fibrillization Is Mediated by a Native Structural Element That Comprises Helices H2 and H3. Journal of Biological Chemistry, 2010. 285(27): p. 21004-21012.