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Alzheimer’s Association. 2012 Alzheimer’s disease facts and figures. Alzheimers Dement. 8, 131–168 (2012).
- 2.
Knowles, T. P. J., Vendruscolo, M. & Dobson, C. M. The amyloid state and its association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15, 384–396 (2014).
- 3.
Selkoe, D. J. Alzheimer’s disease: genes, proteins, and therapy. Physiol. Rev. 81, 741–766 (2001).
- 4.
Haass, C. X. & Selkoe, D. J. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer’s amyloid β-peptide. Nat. Rev. Mol. Cell Biol. 8, 101–112 (2007).
- 5.
Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003).
- 6.
Bieschke, J. Natural compounds may open new routes to treatment of amyloid diseases. Neurotherapeutics 10, 429–439 (2013).
- 7.
Chen, J. X. & Yan, S. S. Role of mitochondrial amyloid-beta in Alzheimer’s disease. J. Alzheimers Dis. 20(Suppl 2), S569–S578 (2010).
- 8.
Kroth, H. et al. Discovery and structure activity relationship of small molecule inhibitors of toxic beta-amyloid-42 fibril formation. J. Biol. Chem. 287, 34786–34800 (2012).
- 9.
Lansbury, P. T. & Lashuel, H. A. A century-old debate on protein aggregation and neurodegeneration enters the clinic. Nature 443, 774–779 (2006).
- 10.
Nie, Q., Du, X. G. & Geng, M. Y. Small molecule inhibitors of amyloid beta peptide aggregation as a potential therapeutic strategy for Alzheimer’s disease. Acta Pharmacol. Sin. 32, 545–551 (2011).
- 11.
Porat, Y., Abramowitz, A. & Gazit, E. Inhibition of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibition mechanism. Chem. Biol. Drug Des. 67, 27–37 (2006).
- 12.
Sinha, S. et al. Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins. J. Am. Chem. Soc. 133, 16958–16969 (2011).
- 13.
Cummings, J. & Zhong, K. Biomarker-driven therapeutic management of alzheimer’s disease: establishing the foundations. Clin. Pharmacol. Ther. 95, 67–77 (2014).
- 14.
Selkoe, D. J. Resolving controversies on the path to Alzheimer’s therapeutics. Nat. Med. 17, 1060–1065 (2011).
- 15.
Arosio, P., Vendruscolo, M., Dobson, C. M. & Knowles, T. P. J. Chemical kinetics for drug discovery to combat protein aggregation diseases. Trends Pharmacol. Sci. 35, 127–135 (2014).
- 16.
Butterfield, S. & Lashuel, H. Amyloidogenic protein-membrane interactions: mechanistic insight from model systems. Angew. Chem. Int. Ed. 49, 5628–5654 (2010).
- 17.
Campioni, S. et al. A causative link between the structure of aberrant protein oligomers and their toxicity. Nat. Chem. Biol. 6, 140–147 (2010).
- 18.
Mannini, B. et al. Toxicity of protein oligomers is rationalized by a function combining size and surface hydrophobicity. ACS Chem. Biol. 9, 2309–2317 (2014).
- 19.
Shankar, G. M. et al. Amyloid-beta protein dimers isolated directly from Alzheimer’s brains impair synaptic plasticity and memory. Nat. Med. 14, 837–842 (2008).
- 20.
Walsh, P., Neudecker, P. & Sharpe, S. Structural properties and dynamic behavior of nonfibrillar oligomers formed by PrP(106-126). J. Am. Chem. Soc. 132, 7684–7695 (2010).
- 21.
Habchi, J. et al. An anticancer drug suppresses the primary nucleation reaction that initiates the production of the toxic Aβ42 aggregates linked with Alzheimer’s disease. Sci. Adv. 2, e1501244 (2016).
- 22.
Cohen, S. I. A. et al. Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism. Proc. Natl Acad. Sci. USA 110, 9758–9763 (2013).
- 23.
Scheidt, T. et al. Secondary nucleation and elongation occur at different sites on Alzheimer’s amyloid-β aggregates. Sci. Adv. 5, eaau3112 (2019).
- 24.
Cramer, P. E. et al. ApoE-directed therapeutics rapidly clear β-amyloid and reverse deficits in AD mouse models. Science 335, 1503–1506 (2012).
- 25.
Ruggeri, F. S. et al. Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation. Nat. Commun. 6, 7831 (2015).
- 26.
Muller, T. et al. Nanoscale spatially resolved infrared spectra from single microdroplets. Lab Chip 14, 1315–1319 (2014).
- 27.
Qamar, S. et al. FUS phase separation is modulated by a molecular chaperone and methylation of arginine cation-π interactions. Cell 173, 720–734 (2018).
- 28.
Ruggeri, F. S. et al. Identification of oxidative stress in red blood cells with nanoscale chemical resolution by infrared nanospectroscopy. Int. J. Mol. Sci. 19, 2582 (2018).
- 29.
Volpatti, L. R. et al. Micro- and nanoscale hierarchical structure of core-shell protein microgels. J. Mater. Chem. B 4, 7989–7999 (2016).
- 30.
Ruggeri, F. S. et al. Nanoscale studies link amyloid maturity with polyglutamine diseases onset. Sci. Rep. 6, 31155 (2016).
- 31.
Ruggeri, F. S. et al. Concentration-dependent and surface-assisted self-assembly properties of a bioactive estrogen receptor alpha-derived peptide. J. Pept. Sci. 21, 95–104 (2015).
- 32.
Dazzi, A. & Prater, C. B. AFM-IR: technology and applications in nanoscale infrared spectroscopy and chemical imaging. Chem. Rev. 117, 5146–5173 (2017).
- 33.
Centrone, A. in Annual Review of Analytical Chemistry Vol 8. (eds Cooks, R. G. & Pemberton, J. E.) 101–126 (Annual Reviews, 2015).
- 34.
Galante, D. et al. A critical concentration of N-terminal pyroglutamylated amyloid beta drives the misfolding of Ab1-42 into more toxic aggregates. Int J. Biochem. Cell Biol. 79, 261–270 (2016).
- 35.
Ruggeri, F. S., Habchi, J., Cerreta, A. & Dietler, G. AFM-based single molecule techniques: unraveling the amyloid pathogenic species. Curr. Pharm. Des. 22, 3950–3970 (2016).
- 36.
Ramer, G., Ruggeri, F. S., Levin, A., Knowles, T. P. J. & Centrone, A. Determination of polypeptide conformation with nanoscale resolution in water. ACS Nano 12, 6612–6619 (2018).
- 37.
Lu, F., Jin, M. Z. & Belkin, M. A. Tip-enhanced infrared nanospectroscopy via molecular expansion force detection. Nat. Photonics 8, 307–312 (2014).
- 38.
Ruggeri, F. S., Mannini, B., Schmid, R., Vendruscolo, M. & Knowles, T. P. J. Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy. Nat. Commun. 11, 2945 (2020).
- 39.
Hellstrand, E., Boland, B., Walsh, D. M. & Linse, S. Amyloid beta-protein aggregation produces highly reproducible kinetic data and occurs by a two-phase process. Acs Chem. Neurosci. 1, 13–18 (2010).
- 40.
Chia, S. et al. SAR by kinetics for drug discovery in protein misfolding diseases. Proc. Natl Acad. Sci. USA 115, 10245–10250 (2018).
- 41.
Zanjani, A. A. H. et al. Amyloid evolution: antiparallel replaced by parallel. Biophys. J. 118, 2526–2536 (2020).
- 42.
Habchi, J. et al. Cholesterol catalyses Abeta42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes. Nat. Chem. 10, 673–683 (2018).
- 43.
Okada, Y. et al. Toxic amyloid tape: a novel mixed antiparallel/parallel β-sheet structure formed by amyloid β-protein on GM1 clusters. ACS Chem. Neurosci. 10, 563–572 (2019).
- 44.
Moran, S. D. & Zanni, M. T. How to get insight into amyloid structure and formation from infrared spectroscopy. J. Phys. Chem. Lett. 5, 1984–1993 (2014).
- 45.
Michaels, T. C. T. et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nat. Chem. 12, 445–451 (2020).
- 46.
Abrosimova, K. V., Shulenina, O. V. & Paston, S. V. FTIR study of secondary structure of bovine serum albumin and ovalbumin. J. Phys. Conf. Ser. 769, 12016 (2016).
- 47.
Nie, B., Stutzman, J. & Xie, A. A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Biophys. J. 88, 2833–2847 (2005).
- 48.
Mirza, Z. & Beg, M. A. Possible molecular interactions of bexarotene—a retinoid drug and Alzheimer’s Aβ peptide: a docking study. Curr. Alzheimer Res. 14, 327–334 (2017).
- 49.
Patrick, G. L. An Introduction to Medicinal Chemistry (Oxford University Press, 2017).
- 50.
Cohen, S. I. A., Vendruscolo, M., Dobson, C. M. & Knowles, T. P. J. From macroscopic measurements to microscopic mechanisms of protein aggregation. J. Mol. Biol. 421, 160–171 (2012).
- 51.
Miller, M. S., Ferrato, M.-A., Niec, A., Biesinger, M. C. & Carmichael, T. B. Ultrasmooth gold surfaces prepared by chemical mechanical polishing for applications in nanoscience. Langmuir 30, 14171–14178 (2014).
- 52.
Ruggeri, F. S., Sneideris, T., Chia, S., Vendruscolo, M. & Knowles, T. P. J. Characterizing individual protein aggregates by infrared nanospectroscopy and atomic force microscopy. J. Vis. Exp. https://doi.org/10.3791/60108 (2019).
- 53.
Ramer, G., Reisenbauer, F., Steindl, B., Tomischko, W. & Lendl, B. Implementation of resonance tracking for assuring reliability in resonance enhanced photothermal infrared spectroscopy and imaging. Appl. Spectrosc. 71, 2013–2020 (2017).
- 54.
Shimanovich, U. et al. Silk micrococoons for protein stabilisation and molecular encapsulation. Nat. Commun. 8, 15902 (2017).
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Source: https://www.nature.com/articles/s41467-020-20782-0
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Original Text (This is the original text for your reference.)
- 1.
Alzheimer’s Association. 2012 Alzheimer’s disease facts and figures. Alzheimers Dement. 8, 131–168 (2012).
- 2.
Knowles, T. P. J., Vendruscolo, M. & Dobson, C. M. The amyloid state and its association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15, 384–396 (2014).
- 3.
Selkoe, D. J. Alzheimer’s disease: genes, proteins, and therapy. Physiol. Rev. 81, 741–766 (2001).
- 4.
Haass, C. X. & Selkoe, D. J. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer’s amyloid β-peptide. Nat. Rev. Mol. Cell Biol. 8, 101–112 (2007).
- 5.
Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003).
- 6.
Bieschke, J. Natural compounds may open new routes to treatment of amyloid diseases. Neurotherapeutics 10, 429–439 (2013).
- 7.
Chen, J. X. & Yan, S. S. Role of mitochondrial amyloid-beta in Alzheimer’s disease. J. Alzheimers Dis. 20(Suppl 2), S569–S578 (2010).
- 8.
Kroth, H. et al. Discovery and structure activity relationship of small molecule inhibitors of toxic beta-amyloid-42 fibril formation. J. Biol. Chem. 287, 34786–34800 (2012).
- 9.
Lansbury, P. T. & Lashuel, H. A. A century-old debate on protein aggregation and neurodegeneration enters the clinic. Nature 443, 774–779 (2006).
- 10.
Nie, Q., Du, X. G. & Geng, M. Y. Small molecule inhibitors of amyloid beta peptide aggregation as a potential therapeutic strategy for Alzheimer’s disease. Acta Pharmacol. Sin. 32, 545–551 (2011).
- 11.
Porat, Y., Abramowitz, A. & Gazit, E. Inhibition of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibition mechanism. Chem. Biol. Drug Des. 67, 27–37 (2006).
- 12.
Sinha, S. et al. Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins. J. Am. Chem. Soc. 133, 16958–16969 (2011).
- 13.
Cummings, J. & Zhong, K. Biomarker-driven therapeutic management of alzheimer’s disease: establishing the foundations. Clin. Pharmacol. Ther. 95, 67–77 (2014).
- 14.
Selkoe, D. J. Resolving controversies on the path to Alzheimer’s therapeutics. Nat. Med. 17, 1060–1065 (2011).
- 15.
Arosio, P., Vendruscolo, M., Dobson, C. M. & Knowles, T. P. J. Chemical kinetics for drug discovery to combat protein aggregation diseases. Trends Pharmacol. Sci. 35, 127–135 (2014).
- 16.
Butterfield, S. & Lashuel, H. Amyloidogenic protein-membrane interactions: mechanistic insight from model systems. Angew. Chem. Int. Ed. 49, 5628–5654 (2010).
- 17.
Campioni, S. et al. A causative link between the structure of aberrant protein oligomers and their toxicity. Nat. Chem. Biol. 6, 140–147 (2010).
- 18.
Mannini, B. et al. Toxicity of protein oligomers is rationalized by a function combining size and surface hydrophobicity. ACS Chem. Biol. 9, 2309–2317 (2014).
- 19.
Shankar, G. M. et al. Amyloid-beta protein dimers isolated directly from Alzheimer’s brains impair synaptic plasticity and memory. Nat. Med. 14, 837–842 (2008).
- 20.
Walsh, P., Neudecker, P. & Sharpe, S. Structural properties and dynamic behavior of nonfibrillar oligomers formed by PrP(106-126). J. Am. Chem. Soc. 132, 7684–7695 (2010).
- 21.
Habchi, J. et al. An anticancer drug suppresses the primary nucleation reaction that initiates the production of the toxic Aβ42 aggregates linked with Alzheimer’s disease. Sci. Adv. 2, e1501244 (2016).
- 22.
Cohen, S. I. A. et al. Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism. Proc. Natl Acad. Sci. USA 110, 9758–9763 (2013).
- 23.
Scheidt, T. et al. Secondary nucleation and elongation occur at different sites on Alzheimer’s amyloid-β aggregates. Sci. Adv. 5, eaau3112 (2019).
- 24.
Cramer, P. E. et al. ApoE-directed therapeutics rapidly clear β-amyloid and reverse deficits in AD mouse models. Science 335, 1503–1506 (2012).
- 25.
Ruggeri, F. S. et al. Infrared nanospectroscopy characterization of oligomeric and fibrillar aggregates during amyloid formation. Nat. Commun. 6, 7831 (2015).
- 26.
Muller, T. et al. Nanoscale spatially resolved infrared spectra from single microdroplets. Lab Chip 14, 1315–1319 (2014).
- 27.
Qamar, S. et al. FUS phase separation is modulated by a molecular chaperone and methylation of arginine cation-π interactions. Cell 173, 720–734 (2018).
- 28.
Ruggeri, F. S. et al. Identification of oxidative stress in red blood cells with nanoscale chemical resolution by infrared nanospectroscopy. Int. J. Mol. Sci. 19, 2582 (2018).
- 29.
Volpatti, L. R. et al. Micro- and nanoscale hierarchical structure of core-shell protein microgels. J. Mater. Chem. B 4, 7989–7999 (2016).
- 30.
Ruggeri, F. S. et al. Nanoscale studies link amyloid maturity with polyglutamine diseases onset. Sci. Rep. 6, 31155 (2016).
- 31.
Ruggeri, F. S. et al. Concentration-dependent and surface-assisted self-assembly properties of a bioactive estrogen receptor alpha-derived peptide. J. Pept. Sci. 21, 95–104 (2015).
- 32.
Dazzi, A. & Prater, C. B. AFM-IR: technology and applications in nanoscale infrared spectroscopy and chemical imaging. Chem. Rev. 117, 5146–5173 (2017).
- 33.
Centrone, A. in Annual Review of Analytical Chemistry Vol 8. (eds Cooks, R. G. & Pemberton, J. E.) 101–126 (Annual Reviews, 2015).
- 34.
Galante, D. et al. A critical concentration of N-terminal pyroglutamylated amyloid beta drives the misfolding of Ab1-42 into more toxic aggregates. Int J. Biochem. Cell Biol. 79, 261–270 (2016).
- 35.
Ruggeri, F. S., Habchi, J., Cerreta, A. & Dietler, G. AFM-based single molecule techniques: unraveling the amyloid pathogenic species. Curr. Pharm. Des. 22, 3950–3970 (2016).
- 36.
Ramer, G., Ruggeri, F. S., Levin, A., Knowles, T. P. J. & Centrone, A. Determination of polypeptide conformation with nanoscale resolution in water. ACS Nano 12, 6612–6619 (2018).
- 37.
Lu, F., Jin, M. Z. & Belkin, M. A. Tip-enhanced infrared nanospectroscopy via molecular expansion force detection. Nat. Photonics 8, 307–312 (2014).
- 38.
Ruggeri, F. S., Mannini, B., Schmid, R., Vendruscolo, M. & Knowles, T. P. J. Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy. Nat. Commun. 11, 2945 (2020).
- 39.
Hellstrand, E., Boland, B., Walsh, D. M. & Linse, S. Amyloid beta-protein aggregation produces highly reproducible kinetic data and occurs by a two-phase process. Acs Chem. Neurosci. 1, 13–18 (2010).
- 40.
Chia, S. et al. SAR by kinetics for drug discovery in protein misfolding diseases. Proc. Natl Acad. Sci. USA 115, 10245–10250 (2018).
- 41.
Zanjani, A. A. H. et al. Amyloid evolution: antiparallel replaced by parallel. Biophys. J. 118, 2526–2536 (2020).
- 42.
Habchi, J. et al. Cholesterol catalyses Abeta42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes. Nat. Chem. 10, 673–683 (2018).
- 43.
Okada, Y. et al. Toxic amyloid tape: a novel mixed antiparallel/parallel β-sheet structure formed by amyloid β-protein on GM1 clusters. ACS Chem. Neurosci. 10, 563–572 (2019).
- 44.
Moran, S. D. & Zanni, M. T. How to get insight into amyloid structure and formation from infrared spectroscopy. J. Phys. Chem. Lett. 5, 1984–1993 (2014).
- 45.
Michaels, T. C. T. et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nat. Chem. 12, 445–451 (2020).
- 46.
Abrosimova, K. V., Shulenina, O. V. & Paston, S. V. FTIR study of secondary structure of bovine serum albumin and ovalbumin. J. Phys. Conf. Ser. 769, 12016 (2016).
- 47.
Nie, B., Stutzman, J. & Xie, A. A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Biophys. J. 88, 2833–2847 (2005).
- 48.
Mirza, Z. & Beg, M. A. Possible molecular interactions of bexarotene—a retinoid drug and Alzheimer’s Aβ peptide: a docking study. Curr. Alzheimer Res. 14, 327–334 (2017).
- 49.
Patrick, G. L. An Introduction to Medicinal Chemistry (Oxford University Press, 2017).
- 50.
Cohen, S. I. A., Vendruscolo, M., Dobson, C. M. & Knowles, T. P. J. From macroscopic measurements to microscopic mechanisms of protein aggregation. J. Mol. Biol. 421, 160–171 (2012).
- 51.
Miller, M. S., Ferrato, M.-A., Niec, A., Biesinger, M. C. & Carmichael, T. B. Ultrasmooth gold surfaces prepared by chemical mechanical polishing for applications in nanoscience. Langmuir 30, 14171–14178 (2014).
- 52.
Ruggeri, F. S., Sneideris, T., Chia, S., Vendruscolo, M. & Knowles, T. P. J. Characterizing individual protein aggregates by infrared nanospectroscopy and atomic force microscopy. J. Vis. Exp. https://doi.org/10.3791/60108 (2019).
- 53.
Ramer, G., Reisenbauer, F., Steindl, B., Tomischko, W. & Lendl, B. Implementation of resonance tracking for assuring reliability in resonance enhanced photothermal infrared spectroscopy and imaging. Appl. Spectrosc. 71, 2013–2020 (2017).
- 54.
Shimanovich, U. et al. Silk micrococoons for protein stabilisation and molecular encapsulation. Nat. Commun. 8, 15902 (2017).
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