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AIMS Molecular Science, 2015, 2(3): 190-210. doi: 10.3934/molsci.2015.3.190.
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Amyloid misfolding, aggregation, and the early onset of protein deposition diseases: insights from AFM experiments and computational analyses
Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
Received date: , Accepted date: , Published date:
Special Issues: Molecular Mechanisms of Neurodegenerative Diseases
Keywords: nanomedicine; nanoimaging; atomic force microscopy; AFM; force spectroscopy;amyloids; Alzheimer's disease; Parkinson's disease; Huntington's disease
Citation: Yuri L. Lyubchenko. Amyloid misfolding, aggregation, and the early onset of protein deposition diseases: insights from AFM experiments and computational analyses. AIMS Molecular Science, 2015, 2(3): 190-210. doi: 10.3934/molsci.2015.3.190
References:
-
1. Dobson CM (2004) Principles of protein folding, misfolding and aggregation. Semin Cell Dev Biol 15: 3-16.
-
2. Fink AL (1998) Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold Des 3: R9-23.
-
3. Demidov VV (2004) Nanobiosensors and molecular diagnostics: a promising partnership. Expert Rev Mol Diagn 4: 267-268.
-
4. Ptitsyn OB (1995) How the molten globule became. Trends Biochem Sci 20: 376-379.
-
5. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269: 2-12.
- 6. Lazo ND, Grant MA, Condron MC, et al. (2005) On the nucleation of amyloid beta-protein monomer folding. Protein Sci 14: 1581-1596.
- 7. Lyubchenko YL, Sherman S, Shlyakhtenko LS, et al. (2006) Nanoimaging for protein misfolding and related diseases. J Cell Biochem 99: 53-70.
-
8. Knowles TP, Fitzpatrick AW, Meehan S, et al. (2007) Role of intermolecular forces in defining material properties of protein nanofibrils. Science 318: 1900-1903.
- 9. Tycko R (2014) Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci23: 1528-1539.
-
10. Balbach JJ, Petkova AT, Oyler NA, et al. (2002) Supramolecular structure in full-length Alzheimer's beta-amyloid fibrils: evidence for a parallel beta-sheet organization from solid-state nuclear magnetic resonance. Biophys J 83: 1205-1216.
-
11. Petkova AT, Ishii Y, Balbach JJ, et al. (2002) A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR. Proc Natl Acad Sci U S A. 99:16742-16747.
-
12. Do TD, LaPointe NE, Sangwan S, et al. (2014) Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants. J Phys Chem B 118: 7247-7256.
-
13. Sawaya MR, Sambashivan S, Nelson R, et al. (2007) Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447: 453-457.
-
14. Baxa U, Wickner RB, Steven AC, et al. (2007) Characterization of beta-sheet structure in Ure2p1-89 yeast prion fibrils by solid-state nuclear magnetic resonance. Biochemistry 46:13149-13162.
-
15. Chan JC, Oyler NA, Yau WM, et al. (2005) Parallel beta-sheets and polar zippers in amyloid fibrils formed by residues 10-39 of the yeast prion protein Ure2p. Biochemistry 44:10669-10680.
-
16. Shewmaker F, Wickner RB, Tycko R (2006) Amyloid of the prion domain of Sup35p has an in-register parallel beta-sheet structure. Proc Natl Acad Sci U S A 103: 19754-19759.
-
17. Farrance OE, Paci E, Radford SE, et al. (2015) Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments. ACS Nano 9: 1315-1324.
-
18. Wickner RB, Dyda F, Tycko R (2008) Amyloid of Rnq1p, the basis of the [PIN+] prion, has a parallel in-register beta-sheet structure. Proc Natl Acad Sci U S A 105: 2403-2408.
-
19. Zhang Y, Lyubchenko YL (2014) The structure of misfolded amyloidogenic dimers: computational analysis of force spectroscopy data. Biophys J 107: 2903-2910.
-
20. Tompa P (2009) Structural disorder in amyloid fibrils: its implication in dynamic interactions of proteins. FEBS J 276: 5406-5415.
-
21. Welzel AT, Maggio JE, Shankar GM, et al. (2014) Secreted amyloid beta-proteins in a cell culture model include N-terminally extended peptides that impair synaptic plasticity. Biochemistry 53: 3908-3921.
-
22. McGeer PL, McGeer EG (2013) The amyloid cascade-inflammatory hypothesis of Alzheimer disease: implications for therapy. Acta Neuropathologica 126: 479-497.
- 23. Armstrong RA (2014) A critical analysis of the 'amyloid cascade hypothesis'. Folia Neuropathol.52: 211-225.
-
24. Bemporad F, Chiti F (2012) Protein misfolded oligomers: experimental approaches, mechanism of formation, and structure-toxicity relationships. Chem Biol 19: 315-327.
-
25. Deniz AA, Mukhopadhyay S, Lemke EA (2008) Single-molecule biophysics: at the interface of biology, physics and chemistry. J R Soc Interface 5: 15-45.
-
26. Wang H, Duennwald ML, Roberts BE, et al. (2008) Direct and selective elimination of specific prions and amyloids by 4,5-dianilinophthalimide and analogs. Proc Natl Acad Sci U S A 105:7159-7164.
- 27. Ferreon AC, Gambin Y, Lemke EA, et al. (2009) Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence. Proc Natl Acad Sci U S A106: 5645-5650.
-
28. Brucale M, Sandal M, Di Maio S, et al. (2009) Pathogenic mutations shift the equilibria of alpha-synuclein single molecules towards structured conformers. Chembiochem 10: 176-183.
- 29. Sandal M, Valle F, Tessari I, et al. (2008) Conformational equilibria in monomeric alpha-synuclein at the single-molecule level. PLoS Biol 6: e6.
-
30. Straub JE, Thirumalai D (2010) Principles governing oligomer formation in amyloidogenic peptides. Curr Opin Struct Biol 20: 187-195.
-
31. Thirumalai D, Reddy G, Straub JE (2012) Role of water in protein aggregation and amyloid polymorphism. Acc Chem Res 45: 83-92.
-
32. Lyubchenko YL (2011) Preparation of DNA and nucleoprotein samples for AFM imaging. Micron 42: 196-206.
- 33. Lyubchenko YL, Krasnoslobodtsev AV, Luca S (2012) Fibrillogenesis of huntingtin and other glutamine containing proteins. In: Harris JR, editor. Protein Aggregation and Fibrillogenesis in Cerebral and Systemic Amyloid Disease. 2012/12/12 ed: Springer Netherlands. pp. 225-251.
- 34. Eibl RH, Moy VT (2005) Atomic force microscopy measurements of protein-ligand interactions on living cells. Methods Mol Biol 305: 439-450.
-
35. Lee GU, Chrisey LA, Colton RJ (1994) Direct measurement of the forces between complementary strands of DNA. Science 266: 771-773.
-
36. Florin EL, Moy VT, Gaub HE (1994) Adhesion forces between individual ligand-receptor pairs. Science 264: 415-417.
-
37. McAllister C, Karymov MA, Kawano Y, et al. (2005) Protein interactions and misfolding analyzed by AFM force spectroscopy. J Mol Biol 354: 1028-1042.
-
38. Kransnoslobodtsev AV, Shlyakhtenko LS, Ukraintsev E, et al. (2005) Nanomedicine and Protein Misfolding Diseases. Nanomedicine 1: 300-305.
-
39. Yu J, Lyubchenko YL (2009) Early stages for Parkinson's development: alpha-synuclein misfolding and aggregation. J Neuroimmune Pharmacol 4: 10-16.
-
40. Yu J, Malkova S, Lyubchenko YL (2008) alpha-Synuclein misfolding: single molecule AFM force spectroscopy study. J Mol Biol 384: 992-1001.
-
41. Lyubchenko YL, Kim BH, Krasnoslobodtsev AV, et al. (2010) Nanoimaging for protein misfolding diseases. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2: 526-543.
-
42. Kim BH, Palermo NY, Lovas S, et al. (2011) Single-molecule atomic force microscopy force spectroscopy study of Abeta-40 interactions. Biochemistry 50: 5154-5162.
-
43. Kim BH, Lyubchenko YL (2014) Nanoprobing of misfolding and interactions of amyloid beta 42 protein. Nanomedicine 10: 871-878.
-
44. Lv Z, Condron MM, Teplow DB, et al. (2013) Nanoprobing of the effect of Cu(2+) cations on misfolding, interaction and aggregation of amyloid beta peptide. J Neuroimmune Pharmacol 8:262-273.
- 45. Lv Z, Roychaudhuri R, Condron MM, et al. (2013) Mechanism of amyloid beta-protein dimerization determined using single-molecule AFM force spectroscopy. Sci Rep 3: 2880.
-
46. Yu J, Lyubchenko YL (2009) Early stages for Parkinson's development: alpha-synuclein misfolding and aggregation. J Neuroimmune Pharmacol 4: 10-16.
-
47. Yu J, Malkova S, Lyubchenko YL (2008) alpha-Synuclein misfolding: single molecule AFM force spectroscopy study. J Mol Biol 384: 992-1001.
-
48. Lyubchenko Y, Kim B-H, Krasnoslobodtsev A, et al. (2010) Nanoimaging for protein misfolding diseases. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2:526-543.
-
49. Tong Z, Mikheikin A, Krasnoslobodtsev A, et al. (2013) Novel polymer linkers for single molecule AFM force spectroscopy. Methods 60: 161-168.
-
50. Urbanc B, Betnel M, Cruz L, et al. (2010) Elucidation of amyloid beta-protein oligomerization mechanisms: discrete molecular dynamics study. J Am Chem Soc 132: 4266-4280.
-
51. Gu L, Liu C, Guo Z (2013) Structural insights into Abeta42 oligomers using site-directed spin labeling. J Biol Chem 288: 18673-18683.
-
52. Ball KA, Phillips AH, Wemmer DE, et al. (2013) Differences in beta-strand Populations of Monomeric Abeta40 and Abeta42. Biophys J 104: 2714-2724.
-
53. Maji SK, Ogorzalek Loo RR, Inayathullah M, et al. (2009) Amino acid position-specific contributions to amyloid beta-protein oligomerization. J Biol Chem 284: 23580-23591.
- 54. Krasnoslobodtsev AV, Volkov IL, Asiago JM, et al. (2013) alpha-Synuclein Misfolding Assessed with Single Molecule AFM Force Spectroscopy: Effect of Pathogenic Mutations. Biochemistry52: 7377-7386.
-
55. Heise H, Celej MS, Becker S, et al. (2008) Solid-state NMR reveals structural differences between fibrils of wild-type and disease-related A53T mutant alpha-synuclein. J Mol Biol 380:444-450.
-
56. Comellas G, Lemkau LR, Nieuwkoop AJ, et al. (2011) Structured Regions of α-Synuclein Fibrils Include the Early-Onset Parkinson's Disease Mutation Sites. J Mol Biol 411: 881-895.
-
57. Haupt C, Leppert J, Ronicke R, et al. (2012) Structural basis of beta-amyloid-dependent synaptic dysfunctions. Angew Chem Int Ed Engl 51: 1576-1579.
-
58. Yu J, Warnke J, Lyubchenko YL (2011) Nanoprobing of alpha-synuclein misfolding and aggregation with atomic force microscopy. Nanomedicine 7: 146-152.
-
59. Krasnoslobodtsev AV, Peng J, Asiago JM, et al. (2012) Effect of spermidine on misfolding and interactions of alpha-synuclein. PloS One 7: e38099.
-
60. Bertoncini CW, Fernandez CO, Griesinger C, et al. (2005) Familial mutants of alpha-synuclein with increased neurotoxicity have a destabilized conformation. J Biol Chem 280: 30649-30652.
-
61. Brucale M, Sandal M, Di Maio S, et al. (2009) Pathogenic mutations shift the equilibria of alpha-synuclein single molecules towards structured conformers. Chembiochem 10: 176-183.
-
62. Losasso V, Pietropaolo A, Zannoni C, et al. (2011) Structural role of compensatory amino acid replacements in the alpha-synuclein protein. Biochemistry 50: 6994-7001.
- 63. Roede JR, Uppal K, Park Y, et al. (2013) Serum metabolomics of slow vs. rapid motor progression Parkinson's disease: a pilot study. PloS One 8: e77629.
-
64. Evans E (2001) Probing the relation between force--lifetime--and chemistry in single molecular bonds. Annu Rev Biophys Biomol Struct 30: 105-128.
-
65. Lv Z, Krasnoslobodtsev AV, Zhang Y, et al. (2015) Direct Detection of alpha-Synuclein Dimerization Dynamics: Single-Molecule Fluorescence Analysis. Biophys J 108: 2038-2047.
- 66. Kim BH, Lyubchenko YL (2013) Nanoprobing of misfolding and interactions of amyloid beta 42 protein. Nanomedicine 10: 871-878.
-
67. Lovas S, Zhang Y, Yu J, et al. (2013) Molecular mechanism of misfolding and aggregation of Abeta(13-23). J Phys Chem B 117: 6175-6186.
-
68. Portillo AM, Krasnoslobodtsev AV, Lyubchenko YL (2012) Effect of electrostatics on aggregation of prion protein Sup35 peptide. J Phys Condens Matter 24: 164205.
- 69. Lovas S, Zhang Y, Lyubchenko YL (2012) Insight into Aß misfolding and aggregation. In: Kokotos G, Copnstantinou-Kokotou, V and Matsoukas, J., editor. Peptides 2012. Proceedings of the 32nd European Peptide Symposium ed. Athens, Greece: European Peptide Society, University of Athens, Laboratory of Organic Chemistry. pp. 56-57.
- 70. Tjernberg LO, Tjernberg A, Bark N, et al. (2002) Assembling amyloid fibrils from designed structures containing a significant amyloid beta-peptide fragment. Biochem J 366: 343-351.
-
71. Balbach JJ, Ishii Y, Antzutkin ON, et al. (2000) Amyloid fibril formation by A beta 16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Biochemistry 39: 13748-13759.
-
72. Booth DR, Sunde M, Bellotti V, et al. (1997) Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis. Nature 385: 787-793.
-
73. Uversky VN (2015) Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins. Biotechnol J 10: 356-366.
-
74. Castillo V, Ventura S (2009) Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases. PLoS Comput Biol 5: e1000476.
- 75. Lakowicz JR (2006) Principles of Fluorescence Spectroscopy. Singapore: Springer. 954 p.
-
76. Piana S, Klepeis JL, Shaw DE (2014) Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol 24: 98-105.
-
77. Basak S, Chattopadhyay K (2014) Studies of protein folding and dynamics using single molecule fluorescence spectroscopy. Phys Chem Chem Phys 16: 11139-11149.
-
78. Gedeon PC, Thomas JR, Madura JD (2015) Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter. Methods Mol Biol 1215: 253-287.
-
79. Ono K, Condron MM, Teplow DB (2009) Structure-neurotoxicity relationships of amyloid beta-protein oligomers. Proc Natl Acad Sci U S A 106: 14745-14750.
-
80. Shankar GM, Li S, Mehta TH, et al. (2008) Amyloid-beta protein dimers isolated directly from Alzheimer's brains impair synaptic plasticity and memory. Nat Med 14: 837-842.
-
81. Shankar GM, Bloodgood BL, Townsend M, et al. (2007) Natural oligomers of the Alzheimer amyloid-beta protein induce reversible synapse loss by modulating an NMDA-type glutamate receptor-dependent signaling pathway. J Neurosci 27: 2866-2875.
-
82. Yankner BA, Lu T, Loerch P (2008) The aging brain. Annu Rev Pathol 3: 41-66.
- 83. He X, Giurleo JT, Talaga DS (2009) Role of small oligomers on the amyloidogenic aggregation free-energy landscape. J Mol Biol 395: 134-154.
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