MODELIZATION OF AMYLOID FIBRIL SELF-ASSEMBLY
Keywords:
amyloid fibrils, misfolding, mathematical models, amyloid diseases, nanomaterials
Abstract
Intermolecular noncovalent interactions between protein molecules result in the formation of a wide spectrum of supramolecular assemblies the structure of which varies from disordered amorphous aggregates to the crystals with strictly defined translational symmetry in three directions. One-dimensional protein aggregates (amyloid fibrils) represent highly ordered semiflexible polymers with unique mesoscopic properties which can be tuned by both intrinsic physicochemical characteristics of polypeptide chain and milieu conditions. In the present work the molecular mechanisms of amyloid formation are discussed and mathematical description of the existing models of protein fibrillization are given. For disease-related amyloids, deeper understanding of fibril growth process may shed light on the pathogenesis and molecular mechanisms of the disorders, as well as on the strategies of amyloidosis prevention at atomistic level. In the context of nanotechnology and functional material science, knowing the details of amyloid formation is crucially required for the design of novel nanomaterials with unprecedented qualities.
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References
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4. Maji S., Schubert D., Rivier C., Lee S., Rivier J., Riek R. Amyloid as a depot for the formulation of long-acting drugs // PLoS Biol. – 2008. – Vol. 6. - P. e17.
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6. Luthey-Schulten Z., Wolynes P. Theory of protein folding: the energy landscape perspective // Annu. Rev. Phys. Chem. – 1997. – Vol. 48. – P. 545-600.
7. Ferreiro D., Hegler J., Komives E., Wolynes P. On the role of frustration in the energy landscapes of allosteric proteins // Proc. Natl. Acad. Sci. USA. – 2011. – Vol. 108. – P. 3499-3503.
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9. Bowerman C., Ryan D., Nissan D., Nilsson B. The effect of increasing hydrophobicity on the self-assembly of amphipathic beta-sheet peptides // Mol. Biosyst. – 2009. – Vol. 5. – P. 1058-1069.
10. Doran T., Kamens A., Byrnes N., Nilsson B. Role of amino acid hydrophobicity, aromaticity, and molecular volume on IAPP (20-29) amyloid self-assembly // Proteins. – 2012. – Vol. 80. – P. 1053-1065.
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13. Marek P., Abedini A., Song B., Kanungo M., Johnson M., Gupta R., Zaman W., Wong S., Raleigh D. Aromatic interactions are not required for amyloid fibril formation by islet amyloid polypeptide but do influence the rate of fibril formation and fibril morphology // Biochemistry. – 2007. – Vol. 46. – P. 3255-3261.
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15. Marshall K., Morris K., Charlton D., O’Reilly N., Lewis L., Walden H., Serpell L.C. Hydrophobic, aromatic, and electrostatic interactions play a central role in amyloid fibril formation and stability // Biochemistry. – 2011. – Vol. 50. – P. 2061-2071.
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21. Jarrett J., Lansbury P. Seeding “one-dimensional crystallization” of amyloid: a pathogenic mechanism in Alzheimer’s disease and scrapie? // Cell. – 1993. – Vol. 73. – P. 1055-1058.
22. Flyvbjerg H., Jobs E., Leibler S. Kinetics of self-assembling microtubules: an “inverse problem” in biochemistry // Proc. Natl. Acad. Sci. USA. – 1996. – Vol. 93. – P. 5975-5979.
23. Lomakin A., Chung D., Benedek G., Kirschner D., Teplow D. On the nucleation and growth of amyloid β-protein fibrils: detection of nuclei and quantification of rate constants // Proc. Natl. Acad. Sci. USA. – 1996. – Vol. 93. – P. 1125-1129.
24. Griffith J. Self-replication and scrapie // Nature. – 1967. – Vol. 215. – P. 1043-1044.
25. Ferrone F., Hofrichter J., Ferrone F.A., Hofrichter J., Sunshine H.R., Eaton W.A. Kinetic studies on photolysis-induced gelation of sickle cell hemoglobin suggest a new mechanism // Biophys. J. – 1980. – Vol. 32. – P. 361-377.
26. Prusiner S. Molecular biology of prion diseases // Science. – 1991. – Vol. 252. – P. 1515-1522.
27. Kodaka M. Requirements for generating sigmoidal time-course aggregation in nucleation-dependent polymerization model // Biophys. Chem. – 2004. – Vol. 107. – P. 243-253.
28. Ferrone F. Analysis of protein aggregation kinetics // Methods Enzymol. – 1999. – Vol. 309. – P. 256-274.
29. Serio T., Cashikar A., Kowal A., Sawicki G., Moslehi J., Serpell L., Arnsdorf M., Lindquist S. Nucleated conformational conversion and the replication of conformational information by a prion determinant // Science. – 2000. – Vol. 289. – P. 1317 1321.
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34. van Gestel J., de Leeuw S. A statistical-mechanical theory of fibril formation in dilute protein solutions // Biophys. J. – 2006. – Vol. 90. – P. 3134-3145.
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36. Schmit J., Ghosh K., Dill K. What drives amyloid molecules to assemble into oligomers and fibrils? // Biophys. J. – 2011. – Vol. 100. – P. 450-458.
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38. Di Michele L., Eiser E., Foderà V. Minimal model for self-catalysis in the formation of amyloid-like elongated fibrils // J. Phys. Chem. Lett. – 2013. – Vol. 4. – P. 3158-3164.
39. Auer S. Amyloid fibril nucleation: effect of amino acid hydrophobicity // J. Phys. Chem. B. – 2014. – Vol. 118. – P. 5289-5299.
Citations
Chitosan Oligosaccharides Attenuate Amyloid Formation of hIAPP and Protect Pancreatic β-Cells from Cytotoxicity
Meng Qin-Yu, Wang Hua, Cui Zi-Bo, Yu Wen-Gong & Lu Xin-Zhi (2020) Molecules
Crossref
Published
2018-04-03
How to Cite
Trusova, V., & Gorbenko, G. (2018). MODELIZATION OF AMYLOID FIBRIL SELF-ASSEMBLY. East European Journal of Physics, 5(1), 47-54. https://doi.org/10.26565/2312-4334-2018-1-05
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