Structural and Thermodynamic Studies of α-Synuclein Proteins Related to Parkinson’s Disease: Impact of Aqueous Solution and Fe3+ Coordination

Metallic Systems: A Quantum Chemist’s Perspective

Volumn , Issue , 2011, Pages 29-82

  Wise, Olivia M ^a   Xu, Liang ^a   Coskuner, Orkid ^a  

^a UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85013738525     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b10835-5     Document Type: Chapter

References (76)

1. Licker, V.; Kovari, E.; Hochstrasser, D. F.; Burkhard, P. R. Proteomics in human Parkinson’s disease research. J Proteomics 2009, 73 (1), 10-29.
2. Perlmutter, J. D.; Braun, A. R.; Sachs, J. N. Curvature dynamics of alpha-synuclein familial parkinson disease mutants molecular simulations of the micelle- and bilayerbound forms. J Biol Chem 2009, 284 (11), 7177-7189.
3. Tsigelny, I. F.; Sharikov, Y.; Miller, M. A.; Masliah, E. Mechanism of alpha-synuclein oligomerization and membrane interaction: Theoretical approach to unstructured proteins studies. Nanomedicine: Nanotechnol Biol Med 2008, 4 (4), 350-357.
4. Lundvig, D.; Lindersson, E.; Jensen, P. H. Pathogenic effects of alpha-synuclein aggregation. Mol Brain Res 2005, 134 (1), 3-17.
5. Baba, M.; Nakajo, S.; Tu, P. H.; Tomita, T.; Nakaya, K.; Lee, V. M. Y.; Trojanowski, J. Q. et al. Aggregation of alpha-synuclein in Lewy bodies of sporadic Parkinson’s disease and dementia with lewy bodies. Am J Pathol 1998, 152 (4), 879-884.
6. Giasson, B. I.; Duda, J. E.; Quinn, S. M.; Zhang, B.; Trojanowski, J. Q.; Lee, V. M. Y. Neuronal alpha-synucleinopathy with severe movement disorder in mice expressing A53T human alpha-synuclein. Neuron 2002, 34 (4), 521-533.
7. Tabner, B. J.; Turnbull, S.; El-Agnaf, O. M. A.; Allsop, D. Formation of hydrogen peroxide and hydroxyl radicals from A beta and alpha-synuclein as a possible mechanism of cell death in Alzheimer’s disease and Parkinson’s disease. Free Radical Bio Med 2002, 32 (11), 1076-1083.
8. Jarvis, L. M. The amyloid question. Chem Eng News 2010, 88 (14), 12-17.
9. Dean, R. A.; DeMattos, R.; Gelfanova, V.; Hale, J.; Lachno, R.; Racke, M.; Talbot, J. et al. ELISA-based measurement of plasma total A[beta]1-40 and A[beta]1-42, and CSF total and free A[beta]1-40 and A[beta]1-42 in the presence of solanezumab, a mid-domain anti-A beta antibody. Alzheimer’s Dementia 2009, 5 (4, Supplement 1), P133-P133.
10. DeMattos, R. B.; Racke, M. M.; Gelfanova, V.; Forster, B.; Knierman, M. D.; Bryan, M. T.; Hale, J. E. et al. Identification, characterization, and comparison of aminoterminally truncated A[beta]42 peptides in Alzheimer’s disease brain tissue and in plasma from Alzheimer’s patients receiving solanezumab immunotherapy treatment. Alzheimer’s Dementia 2009, 5 (4, Supplement 1), P156-P157.
11. Ashcroft, A. E. Mass spectrometry and the amyloid problem-How far can we go in the gas phase? J. Am. Soc. Mass. Spectrom. 2010, 21, 1087-1096.
12. Parkinson’s Disease Foundation. http://www.pdf.org/
13. Bennett, M. C. The role of alpha-synuclein in neurodegenerative diseases. Pharmacol Therapeut 2005, 105 (3), 311-331.
14. Parkinson, J. An essay on the shaking palsy (Reprinted). J Neuropsych Clin N 2002, 14 (2), 223-236.
15. National Family Caregivers Association. http://www.nfcacares.org/
16. Kaur, D.; Andersen, J. Does cellular iron dysregulation play a causative role in Parkinson’s disease? Ageing Res Rev 2004, 3 (3), 327-343.
17. Bueler, H. Impaired mitochondrial dynamics and function in the pathogenesis of Parkinson’s disease. Exp Neurol 2009, 218 (2), 235-246.
18. Fukae, J.; Mizuno, Y.; Hattori, N. Mitochondrial dysfunction in Parkinson’s disease. Mitochondrion 2007, 7 (1-2), 58-62.
19. Double, K. L.; Ben-Shachar, D.; Youdim, M. B.; Zecca, L.; Riederer, P.; Gerlach, M. Influence of neuromelanin on oxidative pathways within the human substantia nigra. Neurotoxicol Teratol 2002, 24 (5), 621-628.
20. Forloni, G.; Terreni, L.; Bertani, I.; Fogliarino, S.; Invernizzi, R.; Assini, A.; Ribizzi, G. et al. Protein misfolding in Alzheimer’s and Parkinson’s disease: Genetics and molecular mechanisms. Neurobiol Aging 2002, 23 (5), 957-976.
21. Hald, A.; Lotharius, J. Oxidative stress and inflammation in Parkinson’s disease: Is there a causal link? Exp Neurol 2005, 193 (2), 279-290.
22. Fedorow, H.; Tribl, F.; Halliday, G.; Gerlach, M.; Riederer, P.; Double, K. L. Neuromelanin in human dopamine neurons: Comparison with peripheral melanins and relevance to Parkinson’s disease. Prog Neurobiol 2005, 75 (2), 109-124.
23. Tanaka, K.; Suzuki, T.; Hattori, N.; Mizuno, Y. Ubiquitin, proteasome and parkin. Biochim Biophys Acta 2004, 1695 (1-3), 235-247.
24. McNaught, K. S. P.; Olanow, C. W. Protein aggregation in the pathogenesis of familial and sporadic Parkinson’s disease. Neurobiol Aging 2006, 27 (4), 530-545.
25. Sun, F.; Kanthasamy, A.; Anantharam, V.; Kanthasamy, A. G. Environmental neurotoxic chemicals-induced ubiquitin proteasome system dysfunction in the pathogenesis and progression of Parkinson’s disease. Pharmacol Therapeut 2007, 114 (3), 327-344.
26. Winklhofer, K. F.; Haass, C. Mitochondrial dysfunction in Parkinson’s disease. Biochim Biophys Acta 2010, 1802 (1), 29-44.
27. Xiromerisiou, G.; Dardiotis, E.; Tsimourtou, V.; Kountra, P. M.; Paterakis, K. N.; Kapsalaki, E. Z.; Fountas, K. N. et al. Genetic basis of Parkinson disease. Neurosurg Focus 2010, 28 (1), E7.
28. Maguire-Zeiss, K. A.; Hoff, S. A.; Su, X.; Yehling, E.; Federoff, H. J. Synuclein, dopainine, and oxidative stress in Parkinson’s disease. Movement Disord 2006, 21, S65-S65.
29. Ulmer, T. S.; Bax, A.; Cole, N. B.; Nussbaum, R. L. Structure and dynamics of micellebound human alpha-synuclein. J Biol Chem 2005, 280 (10), 9595-9603.
30. Li, J.; Uversky, V. N.; Fink, A. L. Conformational behavior of human [alpha]-synuclein is modulated by familial Parkinson’s disease point mutations A30P and A53T. Neurotoxicology 2002, 23 (4-5), 553-567.
31. Uversky, V. N., Fink, A. L. Folding and Misfolding of α-Synuclein. http://www. chemistry.ucsc.edu/faculty/Fink/2005/ReviewFolding-misfoldingRevd.pdf
32. El-Agnaf, O. M.; Jakes, R.; Curran, M. D.; Wallace, A. Effects of the mutations Ala30 to Pro and Ala53 to Thr on the physical and morphological properties of alpha-synuclein protein implicated in Parkinson’s disease. FEBS Lett 1998, 440 (1-2), 67-70.
33. Conway, K. A.; Harper, J. D.; Lansbury, P. T. Fibrils formed in vitro from alphasynuclein and two mutant forms linked to Parkinson’s disease are typical amyloid. Biochemistry-Us 2000, 39 (10), 2552-2563.
34. Rhodes, S. L.; Ritz, B. Genetics of iron regulation and the possible role of iron in Parkinson’s disease. Neurobiol Dis 2008, 32 (2), 183-195.
35. Hirsch, E. C. Iron transport in Parkinson’s disease. Parkinsonism Relat Disord 2009, 15 (Supplement 3), S209-S211.
36. Zhang, X.; Xie, W. J.; Qu, S.; Pan, T. H.; Wang, X. T.; Le, W. D. Neuroprotection by iron chelator against proteasome inhibitor-induced nigral degeneration. Biochem Bioph Res Co 2005, 333 (2), 544-549.
37. Peng, Y.; Wang, C.; Xu, H. H.; Liu, Y.-N.; Zhou, F. Binding of [alpha]-synuclein with Fe(III) and with Fe(II) and biological implications of the resultant complexes. J Inorg Biochem 2010, 104 (4), 365-370.
38. Silva, J. L.; Cordeiro, Y.; Foguel, D. Protein folding and aggregation: Two sides of the same coin in the condensation of proteins revealed by pressure studies. Biochim Biophys Acta (BBA)-Proteins Proteomics 2006, 1764 (3), 443-451.
39. Silva, J. L.; Foguel, D. Hydration, cavities and volume in protein folding, aggregation and amyloid assembly. Phys Biol 2009, 6 (1), 015002-12.
40. Jiang, J. S.; Brunger, A. T. Protein hydration observed by x-ray-diffraction-Solvation properties of penicillopepsin and neuraminidase crystal-structures. J Mol Biol 1994, 243 (1), 100-115.
41. Armstrong, B. D.; Han, S. G. Overhauser dynamic nuclear polarization to study local water dynamics. J Am Chem Soc 2009, 131 (13), 4641-4647.
42. Karplus, M. Molecular dynamics of biological macromolecules: A brief history and perspective. Biopolymers 2003, 68 (3), 350-358.
43. Karplus, M. Molecular-dynamics-Applications to proteins. Stud Phys Theo Chem 1990, 71, 427-461, 788.
44. Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems. Angew Chem Int Ed 2009, 48 (7), 1198-1229.
45. Kumar, S.; Sarkar, A.; Sundar, D. Controlling aggregation propensity in A53T mutant of alpha-synuclein causing Parkinson’s disease. Biochem Bioph Res Co 2009, 387 (2), 305-309.
46. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications. 2nd edn., Academic Press: San Diego, 2002; p xxii, 638 p.
47. van Gunsteren, W. F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P. et al. Biomolecular modeling: Goals, problems, perspectives. Angew Chem Int Ed 2006, 45 (25), 4064-4092.
48. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular-dynamics with coupling to an external bath. J Chem Phys 1984, 81 (8), 3684-3690.
49. Evans, D. J.; Holian, B. L. The Nose-Hoover thermostat. J Chem Phys 1985, 83 (8), 4069-4074.
50. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids. Clarendon Press; Oxford University Press: Oxford, England, New York, 1987; p xix, 385 p.
51. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998, 102 (18), 3586-3616.
52. Jorgensen, W. L. Quantum and statistical mechanical studies of liquids.10. Transferable intermolecular potential functions for water, alcohols, and ethers- Application to liquid water. J Am Chem Soc 1981, 103 (2), 335-340
53. Jorgensen, W. L. Quantum and statistical mechanical studies of liquids.24. Revised tips for simulations of liquid water and aqueous-solutions. J Chem Phys 1982, 77 (8), 4156-4163.
54. Toukmaji, A. Y.; Board, J. A. Ewald summation techniques in perspective: A survey. Comput Phys Commun 1996, 95 (2-3), 73-92.
55. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald-an N.Log(N) method for Ewald sums in large systems. J Chem Phys 1993, 98 (12), 10089-10092.
56. Andersen, H. C. Rattle-A velocity version of the shake algorithm for moleculardynamics calculations. J Comput Phys 1983, 52 (1), 24-34.
57. Tuckerman, M. E.; Martyna, G. J. Understanding modern molecular dynamics: Techniques and applications. J Phys Chem B 2000, 104 (2), 159-178.
58. Zhang, Z. Y.; Lu, L. Y.; Noid, W. G.; Krishna, V.; Pfaendtner, J.; Voth, G. A. A systematic methodology for defining coarse-grained sites in large biomolecules. Biophys J 2008, 95 (11), 5073-5083
59. Noid, W. G.; Chu, J. W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A., Andersen, H. C. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys 2008, 128 (24), 244114-11.
60. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory. McGraw-Hill, New York, 1989.
61. Kohn, W.; Sham, L. J. Self-consistent equations including exchange and correlation effects. Phys Rev 1965, 140 (4A), A1133.
62. Massova, I.; Kollman, P. A. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect Drug Discovery Des 2000, 18, 113-135.
63. Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J Phys Chem B 2001, 105 (28), 6507-6514
64. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. J Comput Chem 2002, 23 (1), 128-137.
65. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc 1998, 120 (37), 9401-9409
66. Massova, I.; Kollman, P. A. Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc 1999, 121 (36), 8133-8143.
67. Andricioaei, I.; Karplus, M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001, 115 (14), 6289-6292.
68. Ulmer, T. S.; Bax, A. Comparison of structure and dynamics of micelle-bound human alpha-synuclein and Parkinson disease variants. J Biol Chem 2005, 280 (52), 43179-43187.
69. Eliezer, D.; Kutluay, E.; Bussell, R.; Browne, G. Conformational properties of alphasynuclein in its free and lipid-associated states. J Mol Biol 2001, 307 (4), 1061-1073
70. Sung, Y.-H.; Eliezer, D., Residual structure, backbone dynamics, and interactions within the synuclein family. J Mol Biol 2007, 372 (3), 689-707.
71. Frishman, D.; Argos, P. Knowledge-based protein secondary structure assignment. Proteins 1995, 23 (4), 566-579.
72. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J Mol Graphics 1996, 14 (1), 33-38.
73. Mirza, U. A.; Cohen, S. L.; Chait, B. T. Heat-induced conformational-changes in proteins studied by electrospray ionization mass-spectrometry. Anal Chem 1993, 65 (1), 1-6.
74. Kaltashov, I. A.; Eyles, S. J. Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom Rev 2002, 21 (1), 37-71.
75. Sabbagh, M. N. Drug development for Alzheimer’s disease: Where are we now and where are we headed? Am J Geriatr Pharmacother 2009, 7 (3), 167-185.
76. Coskuner, O.; Jarvis, E. A. A.; Allison, T. C. Water dissociation in the presence of metal ions. Angew Chem Int Ed 2007, 46 (41), 7853-7855.