423
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Modeling structural interconversion in Alzheimers’ amyloid beta peptide with classical and intrinsically disordered protein force fields

ORCID Icon, , & ORCID Icon
Pages 10005-10022 | Received 12 Feb 2021, Accepted 28 May 2021, Published online: 21 Jun 2021

References

  • Adelman, S. (1979). Generalized Langevin theory for many‐body problems in chemical dynamics: General formulation and the equivalent harmonic chain representation. The Journal of Chemical Physics, 71(11), 4471–4486. https://doi.org/10.1063/1.438200
  • Adlard, P. A., & Bush, A. I. (2006). Metals and Alzheimer's disease. Journal of Alzheimer's Disease : JAD, 10(2-3), 145–163. https://doi.org/10.3233/jad-2006-102-303
  • Alves, N. A., & Frigori, R. B. (2018). Structural interconversion in Alzheimer’s Amyloid-β (16–35) peptide in an aqueous solution. The Journal of Physical Chemistry B, 122(6), 1869–1875. https://doi.org/10.1021/acs.jpcb.7b12528
  • Antzutkin, O. N., Leapman, R. D., Balbach, J. J., & Tycko, R. (2002). Supramolecular structural constraints on Alzheimer's beta-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance . Biochemistry, 41(51), 15436–15450. https://doi.org/10.1021/bi0204185
  • Ball, K. A., Phillips, A. H., Wemmer, D. E., & Head-Gordon, T. (2013). Differences in β-strand populations of monomeric Aβ40 and Aβ42. Biophysical Journal, 104(12), 2714–2724. https://doi.org/10.1016/j.bpj.2013.04.056
  • Barz, B., Buell, A. K., & Nath, S. (2021). Compact fibril-like structure of amyloid β-peptide (1-42) monomers. Chemical Communications (Cambridge, England), 57(7), 947–950. https://doi.org/10.1039/d0cc06607a
  • Bhattacharya, S., Xu, L., & Thompson, D. (2019). Molecular simulations reveal terminal group mediated stabilization of helical conformers in both amyloid-β42 and α-synuclein. ACS Chemical Neuroscience, 10(6), 2830–2842. https://doi.org/10.1021/acschemneuro.9b00053
  • Bhattacharya, S., Xu, L., & Thompson, D. (2020). Long-range regulation of partially folded amyloidogenic peptides. Scientific Reports, 10(1), 1–17. https://doi.org/10.1038/s41598-020-64303-x
  • Caliskan, M., Mandaci, S. Y., Uversky, V. N., & Coskuner‐Weber, O. (2021). Secondary structure dependence of Amyloid‐ß (1‐40) on simulation techniques and force field parameters. Chemical Biology & Drug Design, 97(5), 1100–1108. https://doi.org/10.1111/cbdd.13830
  • Carballo‐Pacheco, M., & Strodel, B. (2017). Comparison of force fields for Alzheimer's A: A case study for intrinsically disordered proteins. Protein Science : a Publication of the Protein Society, 26(2), 174–185. https://doi.org/10.1002/pro.3064
  • Case, D., Ben-Shalom, I., Brozell, S., Cerutti, D., Cheatham, T., III, Cruzeiro, V., Darden, T., Duke, R., Ghoreishi, D., & Gilson, M. (2018). AMBER 2018. University of California, San Francisco.
  • Caughey, B., & Lansbury, P. T. (2003). Protofibrils, pores, fibrils, and neurodegeneration: separating the responsible protein aggregates from the innocent bystanders. Annual Review of Neuroscience, 26(1), 267–298. https://doi.org/10.1146/annurev.neuro.26.010302.081142
  • Chakraborty, D., Straub, J. E., & Thirumalai, D. (2020). Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities. Proceedings of the National Academy of Sciences of the United States of America, 117(33), 19926–19937. https://doi.org/10.1073/pnas.2002570117
  • Chiti, F., & Dobson, C. M. (2017). Protein misfolding, amyloid formation, and human disease: A summary of progress over the last decade. Annual Review of Biochemistry, 86, 27–68. https://doi.org/10.1146/annurev-biochem-061516-045115
  • Cline, E. N., Bicca, M. A., Viola, K. L., & Klein, W. L. (2018). The amyloid-β oligomer hypothesis: Beginning of the third decade. Journal of Alzheimer's Disease : JAD, 64(s1), S567–S610. https://doi.org/10.3233/JAD-179941
  • Cohen, S. I. A., Arosio, P., Presto, J., Kurudenkandy, F. R., Biverstål, H., Dolfe, L., Dunning, C., Yang, X., Frohm, B., Vendruscolo, M., Johansson, J., Dobson, C. M., Fisahn, A., Knowles, T. P. J., & Linse, S. (2015). A molecular chaperone breaks the catalytic cycle that generates toxic Aβ oligomers. Nature Structural & Molecular Biology, 22(3), 207–213. https://doi.org/10.1038/nsmb.2971
  • Dan, A., & Chen, H. F. (2019). Secondary structures transition of tau protein with intrinsically disordered proteins specific force field. Chemical Biology & Drug Design, 93(3), 242–253. https://doi.org/10.1111/cbdd.13407
  • Doll, J., & Dion, D. (1976). Generalized Langevin equation approach for atom/solid–surface scattering: Numerical techniques for Gaussian generalized Langevin dynamics. The Journal of Chemical Physics, 65(9), 3762–3766. https://doi.org/10.1063/1.433565
  • Doshi, U., & Hamelberg, D. (2015). Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics. Biochimica et Biophysica Acta, 1850(5), 878–888. https://doi.org/10.1016/j.bbagen.2014.08.003
  • Duan, S., Guan, X., Lin, R., Liu, X., Yan, Y., Lin, R., Zhang, T., Chen, X., Huang, J., Sun, X., Li, Q., Fang, S., Xu, J., Yao, Z., & Gu, H. (2015). Silibinin inhibits acetylcholinesterase activity and amyloid β peptide aggregation: A dual-target drug for the treatment of Alzheimer's disease. Neurobiology of Aging, 36(5), 1792–1807. https://doi.org/10.1016/j.neurobiolaging.2015.02.002
  • Duong, V. T., Chen, Z., Thapa, M. T., & Luo, R. (2018). Computational studies of intrinsically disordered proteins. The Journal of Physical Chemistry. B, 122(46), 10455–10469. https://doi.org/10.1021/acs.jpcb.8b09029
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
  • Finder, V. H., Vodopivec, I., Nitsch, R. M., Glockshuber, R., & Forel-Strasse, A. (2010). The recombinant amyloid-beta peptide Abeta1-42 aggregates faster and is more neurotoxic than synthetic Abeta1-42 . Journal of Molecular Biology, 396(1), 9–18. https://doi.org/10.1016/j.jmb.2009.12.016
  • Gerben, S. R., Lemkul, J. A., Brown, A. M., & Bevan, D. R. (2014). Comparing atomistic molecular mechanics force fields for a difficult target: A case study on the Alzheimer’s amyloid β-peptide. Journal of Biomolecular Structure & Dynamics, 32(11), 1817–1832. https://doi.org/10.1080/07391102.2013.838518
  • Grasso, G., Rebella, M., Morbiducci, U., Tuszynski, J. A., Danani, A., & Deriu, M. A. (2019). The role of structural polymorphism in driving the mechanical performance of the Alzheimer's beta amyloid fibrils. Frontiers in Bioengineering and Biotechnology, 7(April), 83–11. https://doi.org/10.3389/fbioe.2019.00083
  • Hamelberg, D., Mongan, J., & McCammon, J. A. (2004). Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. The Journal of Chemical Physics, 120(24), 11919–11929. https://doi.org/10.1063/1.1755656
  • Han, X., & He, G. (2018). Toward a rational design to regulate β-amyloid fibrillation for alzheimer’s disease treatment. ACS Chemical Neuroscience, 9(2), 198–210. https://doi.org/10.1021/acschemneuro.7b00477
  • Han, B., Liu, Y., Ginzinger, S. W., & Wishart, D. S. (2011). SHIFTX2: Significantly improved protein chemical shift prediction. Journal of Biomolecular NMR, 50(1), 43–57. https://doi.org/10.1007/s10858-011-9478-4
  • Hashemi, M., Zhang, Y., Lv, Z., & Lyubchenko, Y. L. (2019). Spontaneous self-assembly of amyloid β (1–40) into dimers. Nanoscale Advances, 1(10), 3892–3899. https://doi.org/10.1039/C9NA00380K
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65(3), 712–725. https://doi.org/10.1002/prot.21123
  • Hou, L., Shao, H., Zhang, Y., Li, H., Menon, N. K., Neuhaus, E. B., Brewer, J. M., Byeon, I.-J L., Ray, D. G., Vitek, M. P., Iwashita, T., Makula, R. A., Przybyla, A. B., & Zagorski, M. G. (2004). Solution NMR studies of the Aβ (1 − 40) and Aβ (1 − 42) peptides establish that the Met35 oxidation state affects the mechanism of amyloid formation. Journal of the American Chemical Society, 126(7), 1992–2005. https://doi.org/10.1021/ja036813f
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Huy, P. D. Q., Vuong, Q. V., La Penna, G., Faller, P., & Li, M. S. (2016). Impact of Cu(II) binding on structures and dynamics of Aβ42 monomer and dimer: Molecular dynamics study. ACS Chemical Neuroscience, 7(10), 1348–1363. https://doi.org/10.1021/acschemneuro.6b00109
  • Ilie, I. M., & Caflisch, A. (2018). Disorder at the tips of a disease-relevant Aβ42 amyloid fibril: A molecular dynamics study. The Journal of Physical Chemistry. B, 122(49), 11072–11082. https://doi.org/10.1021/acs.jpcb.8b05236
  • Ilie, I. M., & Caflisch, A. (2019). Simulation studies of amyloidogenic polypeptides and their aggregates. Chemical Reviews, 119(12), 6956–6993. https://doi.org/10.1021/acs.chemrev.8b00731
  • Jia, Z., Schmit, J. D., & Chen, J. (2020). Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape. Proceedings of the National Academy of Sciences of the United States of America, 117(19), 10322–10328. https://doi.org/10.1073/pnas.1911153117
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Kheterpal, I., Zhou, S., Cook, K. D., & Wetzel, R. (2000). Aβ amyloid fibrils possess a core structure highly resistant to hydrogen exchange. Proceedings of the National Academy of Sciences, 97(25), 13597–13601. https://doi.org/10.1073/pnas.250288897
  • Kirkitadze, M. D., Condron, M. M., & Teplow, D. B. (2001). Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis. Journal of Molecular Biology, 312(5), 1103–1119. https://doi.org/10.1006/jmbi.2001.4970
  • Kirschner, D. A., Abraham, C., & Selkoe, D. (1986). X-ray diffraction from intraneuronal paired helical filaments and extraneuronal amyloid fibers in Alzheimer disease indicates cross-beta conformation. Proceedings of the National Academy of Sciences, 83(2), 503–507. https://doi.org/10.1073/pnas.83.2.503
  • Krupa, P., Quoc Huy, P. D., & Li, M. S. (2019). Properties of monomeric A β 42 probed by different sampling methods and force fields: Role of energy components. The Journal of Chemical Physics, 151(5), 055101. https://doi.org/10.1063/1.5093184
  • Lee, S. J. C., Nam, E., Lee, H. J., Savelieff, M. G., & Lim, M. H. (2017). Towards an understanding of amyloid-β oligomers: Characterization, toxicity mechanisms, and inhibitors. Chemical Society Reviews, 46(2), 310–323. https://doi.org/10.1039/C6CS00731G
  • Liao, Q., Owen, M. C., Olubiyi, O. O., Barz, B., & Strodel, B. (2017). Conformational transitions of the Amyloid‐β peptide upon copper (II) binding and pH changes. Israel Journal of Chemistry, 57(7-8), 771–784. https://doi.org/10.1002/ijch.201600108
  • Lin, Y., Im, H., Diem, L. T., & Ham, S. (2019). Characterizing the structural and thermodynamic properties of Aβ42 and Aβ40. Biochemical and Biophysical Research Communications, 510(3), 442–448. https://doi.org/10.1016/j.bbrc.2019.01.124
  • Lincoff, J., Sasmal, S., & Head-Gordon, T. (2019). The combined force field-sampling problem in simulations of disordered amyloid-β peptides. The Journal of Chemical Physics, 150(10), 104108. https://doi.org/10.1063/1.5078615
  • Liu, R., McAllister, C., Lyubchenko, Y., & Sierks, M. R. (2004). Residues 17-20 and 30-35 of beta-amyloid play critical roles in aggregation. Journal of Neuroscience Research, 75(2), 162–171. https://doi.org/10.1002/jnr.10859
  • Liu, H., Song, D., Lu, H., Luo, R., & Chen, H. F. (2018). Intrinsically disordered protein-specific force field CHARMM36IDPSFF. Chemical Biology & Drug Design, 92(4), 1722–1735. https://doi.org/10.1111/cbdd.13342
  • Luhrs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Do, H., Schubert, D., & Riek, R. (2005). 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proceedings of the National Academy of Sciences of the United States of America, 102(48), 17342–17347. https://doi.org/10.1073/pnas.0506723102
  • Man, V. H., He, X., Derreumaux, P., Ji, B., Xie, X.-Q., Nguyen, P. H., & Wang, J. (2019). Effects of all-atom molecular mechanics force fields on amyloid peptide assembly: The case of Aβ16-22 Dimer. Journal of Chemical Theory and Computation, 15(2), 1440–1452. https://doi.org/10.1021/acs.jctc.8b01107
  • Man, V. H., Nguyen, P. H., & Derreumaux, P. (2017). High-resolution structures of the amyloid-β 1-42 Dimers from the comparison of four atomistic force fields. The Journal of Physical Chemistry. B, 121(24), 5977–5987. https://doi.org/10.1021/acs.jpcb.7b04689
  • Markwick, P. R., Bouvignies, G., & Blackledge, M. (2007). Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. Journal of the American Chemical Society, 129(15), 4724–4730. https://doi.org/10.1021/ja0687668
  • Masuda, Y., Uemura, S., Nakanishi, A., Ohashi, R., Takegoshi, K., Shimizu, T., Shirasawa, T., & Irie, K. (2008). Verification of the C-terminal intramolecular β-sheet in Aβ42 aggregates using solid-state NMR: Implications for potent neurotoxicity through the formation of radicals. Bioorganic & Medicinal Chemistry Letters, 18(11), 3206–3210. https://doi.org/10.1016/j.bmcl.2008.04.060
  • Masutani, K., Yamamori, Y., Kim, K., & Matubayasi, N. (2019). Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. The Journal of Chemical Physics, 150(14), 145101. https://doi.org/10.1063/1.5088395
  • Maynard, C. J., Bush, A. I., Masters, C. L., Cappai, R., & Li, Q. X. (2005). Metals and amyloid-beta in Alzheimer's disease . International Journal of Experimental Pathology, 86(3), 147–159. https://doi.org/10.1111/j.0959-9673.2005.00434.x
  • Meisl, G., Yang, X., Hellstrand, E., Frohm, B., Kirkegaard, J. B., Cohen, S. I. A., Dobson, C. M., Linse, S., & Knowles, T. P. J. (2014). Differences in nucleation behavior underlie the contrasting aggregation kinetics of the Aβ40 and Aβ42 peptides. Proceedings of the National Academy of Sciences, 111(26), 9384–9389. https://doi.org/10.1073/pnas.1401564111
  • Meng, F., Bellaiche, M. M., Kim, J.-Y., Zerze, G. H., Best, R. B., & Chung, H. S. (2018). Highly disordered amyloid-β monomer probed by single-molecule FRET and MD simulation. Biophysical Journal, 114(4), 870–884. https://doi.org/10.1016/j.bpj.2017.12.025
  • Nasica-Labouze, J., Nguyen, P. H., Sterpone, F., Berthoumieu, O., Buchete, N.-V., Coté, S., De Simone, A., Doig, A. J., Faller, P., Garcia, A., Laio, A., Li, M. S., Melchionna, S., Mousseau, N., Mu, Y., Paravastu, A., Pasquali, S., Rosenman, D. J., Strodel, B., … Derreumaux, P. (2015). Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies. Chemical Reviews, 115(9), 3518–3563. https://doi.org/10.1021/cr500638n
  • Nguyen, P. H., Campanera, J. M., Ngo, S. T., Loquet, A., & Derreumaux, P. (2019). Tetrameric Aβ40 and Aβ42 β-barrel structures by extensive atomistic simulations. i. in a bilayer mimicking a neuronal membrane. The Journal of Physical Chemistry. B, 123(17), 3643–3648. https://doi.org/10.1021/acs.jpcb.9b01206
  • Nguyen, P. H., & Derreumaux, P. (2020). Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations. Biophysical Chemistry, 264, 106421. https://doi.org/10.1016/j.bpc.2020.106421
  • Nguyen, H. L., Krupa, P., Hai, N. M., Linh, H. Q., & Li, M. S. (2019). Structure and physicochemical properties of the Aβ42 tetramer: Multiscale molecular dynamics simulations. The Journal of Physical Chemistry. B, 123(34), 7253–7269. https://doi.org/10.1021/acs.jpcb.9b04208
  • Nguyen, P. H., Ramamoorthy, A., Sahoo, B. R., Zheng, J., Faller, P., Straub, J. E., Dominguez, L., Shea, J.-E., Dokholyan, N. V., De Simone, A., Ma, B., Nussinov, R., Najafi, S., Ngo, S. T., Loquet, A., Chiricotto, M., Ganguly, P., McCarty, J., Li, M. S., … Derreumaux, P. (2021). Amyloid oligomers: A joint experimental/computational perspective on Alzheimer’s disease, Parkinson’s disease, Type II diabetes, and amyotrophic lateral sclerosis. Chemical Reviews, 121(4), 2545–2647. https://doi.org/10.1021/acs.chemrev.0c01122
  • Nguyen, P. H., Sterpone, F., & Derreumaux, P. (2020). Aggregation of disease-related peptides. Progress in Molecular Biology and Translational Science, 170, 435–460. https://doi.org/10.1016/bs.pmbts.2019.12.002
  • Olofsson, A., Lindhagen-Persson, M., Sauer-Eriksson, A. E., & Ohman, A. (2007). Amide solvent protection analysis demonstrates that amyloid-beta(1-40) and amyloid-beta(1-42) form different fibrillar structures under identical conditions. The Biochemical Journal, 404(1), 63–70. https://doi.org/10.1042/BJ20061561
  • Olubiyi, O. O., & Strodel, B. (2012). Structures of the amyloid β-peptides Aβ1-40 and Aβ1-42 as influenced by pH and a D-peptide. The Journal of Physical Chemistry. B, 116(10), 3280–3291. https://doi.org/10.1021/jp2076337
  • Ono, K., Condron, M. M., & Teplow, D. B. (2009). Structure-neurotoxicity relationships of amyloid beta-protein oligomers. Proceedings of the National Academy of Sciences of the United States of America, 106(35), 14745–14750. https://doi.org/10.1073/pnas.0905127106
  • Panza, F., Lozupone, M., Logroscino, G., & Imbimbo, B. P. (2019). A critical appraisal of amyloid-β-targeting therapies for Alzheimer disease. Nature Reviews. Neurology, 15(2), 73–88. https://doi.org/10.1038/s41582-018-0116-6
  • Petkova, A. T., Ishii, Y., Balbach, J. J., Antzutkin, O. N., Leapman, R. D., Delaglio, F., & Tycko, R. (2002). A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR. Proceedings of the National Academy of Sciences of the United States of America, 99(26), 16742–16747. https://doi.org/10.1073/pnas.262663499
  • Petkova, A. T., Yau, W-m., & Tycko, R. (2006). Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochemistry, 45(2), 498–512. https://doi.org/10.1021/bi051952q
  • Qiang, W., Yau, W.-M., Lu, J.-X., Collinge, J., & Tycko, R. (2017). Structural variation in amyloid-β fibrils from Alzheimer's disease clinical subtypes. Nature, 541(7636), 217–221. https://doi.org/10.1038/nature20814
  • Rahman, M. U., Rehman, A. U., Liu, H., & Chen, H.-F. (2020). Comparison and evaluation of force fields for intrinsically disordered proteins. Journal of Chemical Information and Modeling, 60(10), 4912–4923. https://doi.org/10.1021/acs.jcim.0c00762
  • Reddy, G., Straub, J. E., & Thirumalai, D. (2009). Influence of preformed Asp23-Lys28 salt bridge on the conformational fluctuations of monomers and dimers of Abeta peptides with implications for rates of fibril formation. The Journal of Physical Chemistry. B, 113(4), 1162–1172. https://doi.org/10.1021/jp808914c
  • Roberts, B. R., Ryan, T. M., Bush, A. I., Masters, C. L., & Duce, J. A. (2012). The role of metallobiology and amyloid‐β peptides in Alzheimer’s disease. Journal of Neurochemistry, 120, 149–166. https://doi.org/10.1111/j.1471-4159.2011.07500.x
  • Robustelli, P., Piana, S., & Shaw, D. E. (2018). Developing a molecular dynamics force field for both folded and disordered protein states. Proceedings of the National Academy of Sciences of the United States of America, 115(21), E4758–E4766. https://doi.org/10.1073/pnas.1800690115
  • Roche, J., Shen, Y., Lee, J. H., Ying, J., & Bax, A. (2016). Monomeric Aβ(1-40) and Aβ(1-42) peptides in solution adopt very similar Ramachandran map distributions that closely resemble random coil. Biochemistry, 55(5), 762–775. https://doi.org/10.1021/acs.biochem.5b01259
  • Rodriguez‐Bussey, I. G., Doshi, U., & Hamelberg, D. (2016). Enhanced molecular dynamics sampling of drug target conformations. Biopolymers, 105(1), 35–42. https://doi.org/10.1002/bip.22740
  • Rosenman, D. J., Wang, C., & García, A. E. (2016). Characterization of Aβ monomers through the convergence of ensemble properties among simulations with multiple force fields. The Journal of Physical Chemistry. B, 120(2), 259–277. https://doi.org/10.1021/acs.jpcb.5b09379
  • Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
  • Schmidt, M., Rohou, A., Lasker, K., Yadav, J. K., Schiene-Fischer, C., Fändrich, M., & Grigorieff, N. (2015). Peptide dimer structure in an A β (1-42) fibril visualized with cryo-EM. Proceedings of the National Academy of Sciences, 112(38), 11858–11863. https://doi.org/10.1073/pnas.1503455112
  • Sciarretta, K. L., Gordon, D. J., Petkova, A. T., Tycko, R., & Meredith, S. C. (2005). Abeta40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry, 44(16), 6003–6014. https://doi.org/10.1021/bi0474867
  • Sgourakis, N. G., Merced-Serrano, M., Boutsidis, C., Drineas, P., Du, Z., Wang, C., & Garcia, A. E. (2011). Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. Journal of Molecular Biology, 405(2), 570–583. https://doi.org/10.1016/j.jmb.2010.10.015
  • Shao, J., Tanner, S. W., Thompson, N., & Cheatham, T. E. (2007). Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. Journal of Chemical Theory and Computation, 3(6), 2312–2334. https://doi.org/10.1021/ct700119m
  • Siwy, C. M., Lockhart, C., & Klimov, D. K. (2017). Is the Conformational ensemble of Alzheimer's Aβ10-40 peptide force field dependent? PLoS Computational Biology, 13(1), e1005314. https://doi.org/10.1371/journal.pcbi.1005314
  • Smith, M. D., Rao, J. S., Segelken, E., & Cruz, L. (2015). Force-field induced bias in the structure of Aβ21-30: A comparison of OPLS, AMBER, CHARMM, and GROMOS force fields. Journal of Chemical Information and Modeling, 55(12), 2587–2595. https://doi.org/10.1021/acs.jcim.5b00308
  • Song, D., Luo, R., & Chen, H. F. (2017). The IDP-specific force field ff14IDPSFF improves the conformer sampling of intrinsically disordered proteins. Journal of Chemical Information and Modeling, 57(5), 1166–1178. https://doi.org/10.1021/acs.jcim.7b00135
  • Song, D., Wang, W., Ye, W., Ji, D., Luo, R., & Chen, H. F. (2017). ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. Chemical Biology & Drug Design, 89(1), 5–15. https://doi.org/10.1111/cbdd.12832
  • Strodel, B. (2021). Amyloid aggregation simulations: Challenges, advances and perspectives. Current Opinion in Structural Biology, 67, 145–152. https://doi.org/10.1016/j.sbi.2020.10.019
  • Thu, T. T. M., Co, N. T., Tu, L. A., & Li, M. S. (2019). Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state. The Journal of Chemical Physics, 150(22), 225101. https://doi.org/10.1063/1.5096379
  • Tomaselli, S., Esposito, V., Vangone, P., Nuland, N. A. J. V., Bonvin, A. M. J. J., Guerrini, R., Tancredi, T., Temussi, P. A., & Picone, D. (2006). The α -to- β c onformational transition of Alzheimer's A β -(1–42) peptide in aqueous media is reversible: A step by step conformational analysis suggests the location of β c onformation seeding. Chembiochem., 7(2), 257–267. https://doi.org/10.1002/cbic.200500223
  • Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y. E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C. F., Tolmie, D. E., Kent Wenger, R., Yao, H., & Markley, J. L. (2008). BioMagResBank. Nucleic Acids Research, 36(Database issue), D402–D408. https://doi.org/10.1093/nar/gkm957
  • Vivekanandan, S., Brender, J. R., Lee, S. Y., & Ramamoorthy, A. (2011). A partially folded structure of amyloid-beta(1-40) in an aqueous environment. Biochemical and Biophysical Research Communications, 411(2), 312–316. https://doi.org/10.1016/j.bbrc.2011.06.133
  • Wälti, M. A., Ravotti, F., Arai, H., Glabe, C. G., Wall, J. S., Böckmann, A., Güntert, P., Meier, B. H., & Riek, R. (2016). Atomic-resolution structure of a disease-relevant Aβ(1-42) amyloid fibril. Proceedings of the National Academy of Sciences of the United States of America, 113(34), E4976–84. https://doi.org/10.1073/pnas.1600749113
  • Wang, W., Ye, W., Jiang, C., Luo, R., & Chen, H. F. (2014). New force field on modeling intrinsically disordered proteins. Chemical Biology & Drug Design, 84(3), 253–269. https://doi.org/10.1111/cbdd.12314
  • Watts, C. R., Gregory, A. J., Frisbie, C. P., & Lovas, S. (2017). Structural properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins, 85(6), 1024–1045. https://doi.org/10.1002/prot.25270
  • Weber, O. C., & Uversky, V. N. (2017). How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42 in water. Intrinsically Disordered Proteins, 5(1), e1377813. https://doi.org/10.1080/21690707.2017.1377813
  • Whittemore, N. A., Mishra, R., Kheterpal, I., Williams, A. D., Wetzel, R., & Serpersu, E. H. (2005). Hydrogen − Deuterium (H/D) exchange mapping of Aβ1-40 amyloid fibril secondary structure using nuclear magnetic resonance spectroscopy. Biochemistry, 44(11), 4434–4441. https://doi.org/10.1021/bi048292u
  • Wu, C., Murray, M. M., Bernstein, S. L., Condron, M. M., Bitan, G., Shea, J.-E., & Bowers, M. T. (2009). The structure of Aβ42 C-terminal fragments probed by a combined experimental and theoretical study. Journal of Molecular Biology, 387(2), 492–501. https://doi.org/10.1016/j.jmb.2009.01.029
  • Xu, Y., Shen, J., Luo, X., Zhu, W., Chen, K., Ma, J., & Jiang, H. (2005). Conformational transition of amyloid beta-peptide. Proceedings of the National Academy of Sciences of the United States of America, 102(15), 5403–5407. https://doi.org/10.1073/pnas.0501218102
  • Yan, Y., & Wang, C. (2006). Aβ42 is more rigid than Aβ40 at the C terminus: Implications for Aβ aggregation and toxicity. Journal of Molecular Biology, 364(5), 853–862. https://doi.org/10.1016/j.jmb.2006.09.046
  • Yang, S., Liu, H., Zhang, Y., Lu, H., & Chen, H. (2019). Residue-specific force field improving the sample of intrinsically disordered proteins and folded proteins. Journal of Chemical Information and Modeling, 59(11), 4793–4805. https://doi.org/10.1021/acs.jcim.9b00647
  • You, W., & Chang, C. E. A. (2018). Role of molecular interactions and protein rearrangement in the dissociation kinetics of p38α MAP kinase Type-I/II/III inhibitors. Journal of Chemical Information and Modeling, 58(5), 968–981. https://doi.org/10.1021/acs.jcim.7b00640
  • Yu, L., Li, D.-W., & Bruschweiler, R. (2020). Balanced amino-acid specific molecular dynamics force field for the realistic simulation of both folded and disordered proteins. Journal of Chemical Theory and Computation, 16(2), 1311–1318. https://doi.org/10.1021/acs.jctc.9b01062
  • Zhang, Y., Hashemi, M., Lv, Z., & Lyubchenko, Y. L. (2016). Self-assembly of the full-length amyloid Aβ42 protein in dimers. Nanoscale, 8(45), 18928–18937. https://doi.org/10.1039/c6nr06850b
  • Zhang, M., Ren, B., Chen, H., Sun, Y., Ma, J., Jiang, B., & Zheng, J. (2017). Molecular simulations of amyloid structures, toxicity, and inhibition. Israel Journal of Chemistry, 57(7-8), 586–601. https://doi.org/10.1002/ijch.201600075
  • Zheng, W., Tsai, M.-Y., Chen, M., & Wolynes, P. G. (2016). Exploring the aggregation free energy landscape of the amyloid-β protein (1-40). Proceedings of the National Academy of Sciences of the United States of America, 113(42), 11835–11840. https://doi.org/10.1073/pnas.1612362113
  • Zheng, W., Tsai, M.-Y., & Wolynes, P. G. (2017). Comparing the aggregation free energy landscapes of amyloid Beta(1-42) and Amyloid Beta(1-40). Journal of the American Chemical Society, 139(46), 16666–16676. https://doi.org/10.1021/jacs.7b08089

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.