Molecular dynamics simulations of copper binding to N-terminus mutants of amyloid-β

References

• Alies, B., Eury, H., Bijani, C., Rechignat, L., Faller, P., & Hureau, C. (2011). PH-dependent Cu(II) coordination to amyloid-β peptide: Impact of sequence alterations, including the H6R and D7N familial mutations. Inorganic Chemistry, 50(21), 11192–11201. doi:10.1021/ic201739n
   PubMed Web of Science ®Google Scholar
• Alí-Torres, J., Maréchal, J. D., Rodríguez-Santiago, L., & Sodupe, M. (2011). Three dimensional models of Cu 2+-Aβ(1-16) complexes from computational approaches. Journal of the American Chemical Society, 133(38), 15008–15014. doi:10.1021/ja203407v
   PubMed Web of Science ®Google Scholar
• Alzforum.org (2018). Retrieved November 17, 2018, from https://www.alzforum.org/mutations/app
   Google Scholar
• Alzheimer’s Association. (2018). What is Alzheimer’s Retrieved November 14, 2018, from https://alz.org/alzheimers-dementia/what-is-alzheimers
   Google Scholar
• Atrián-Blasco, E., Del Barrio, M., Faller, P., & Hureau, C. (2018). Ascorbate oxidation by Cu(Amyloid-β) complexes: Determination of the intrinsic rate as a function of alterations in the peptide sequence revealing key residues for reactive oxygen species production. Analytical Chemistry, 90(9), 5909–5915. doi:10.1021/acs.analchem.8b00740
   PubMed Web of Science ®Google Scholar
• Balland, V., Hureau, C., & Savéant, J.-M. (2010). Electrochemical and homogeneous electron transfers to the Alzheimer amyloid-β copper complex follow a preorganization mechanism. Proceedings of the National Academy of Sciences, 107(40), 17113–17118. doi:10.1073/pnas.1011315107
   PubMed Web of Science ®Google Scholar
• Ballard, C., Gauthier, S., Corbett, A., Brayne, C., Aarsland, D., & Jones, E. (2011). Alzheimer's disease. Lancet (London, England)), 377(9770), 1019–1031. doi:10.1016/S0140-6736(10)61349-9
   PubMed Web of Science ®Google Scholar
• Bannwarth, C., Ehlert, S., & Grimme, S. (2019). GFN2-xTB - An accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions [Research-article]. Journal of Chemical Theory and Computation, 15(3), 1652–1671. doi:10.1021/acs.jctc.8b01176
   PubMed Web of Science ®Google Scholar
• Bush, A. I. (2003). The metallobiology of Alzheimer’s disease. Trends in Neurosciences, 26(4), 207–214. doi:10.1016/S0166-2236(03)00067-5
   PubMed Web of Science ®Google Scholar
• Bush, A. I., & Tanzi, R. E. (2008). Therapeutics for Alzheimer’s disease based on the metal hypothesis. Neurotherapeutics, 5(3), 421–432.
   PubMed Web of Science ®Google Scholar
• Case, D. A., Betz, R. M., Cerutti, D. S., Darden, T. A., Duke, R. E., Giese, T. J., Gohlke, H., Goetz, A. W., Homeyer, N., Izadi, S., Janowski, P., Kaus, J., Kovalenko, A., Lee, T. S., LeGrand, S., Li, P., Lin, C., Luchko, T., Luo, R., … Kollman, P. A. (2016). AMBER 2016 (Version 2016) [Computer software].
   Google Scholar
• Cheignon, C., Jones, M., Atrián-Blasco, E., Kieffer, I., Faller, P., Collin, F., & Hureau, C. (2017). Identification of key structural features of the elusive Cu-Aβ complex that generates ROS in Alzheimer’s disease. Chemical Science, 8(7), 5107–5118. doi:10.1039/C7SC00809K
   PubMed Web of Science ®Google Scholar
• Constanciel, R., & Contreras, R. (1984). Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution. Theoretica Chimica Acta, 65(1), 1–11. doi:10.1007/BF02427575
   Google Scholar
• Deeth, R. J., Fey, N., & Williams–Hubbard, B. (2005). DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment. Journal of Computational Chemistry, 26(2), 123–130. doi:10.1002/jcc.20137
   PubMed Web of Science ®Google Scholar
• Di Fede, G., Catania, M., Morbin, M., Rossi, G., Suardi, S., Mazzoleni, G., Merlin, M., Giovagnoli, A. R., Prioni, S., Erbetta, A., Falcone, C., Gobbi, M., Colombo, L., Bastone, A., Beeg, M., Manzoni, C., Francescucci, B., Spagnoli, A., Cantù, L., … Tagliavini, F. (2009). A recessive mutation in the APP gene with dominant-negative effect on amyloidogenesis. Science (Science), 323(5920), 1473–1477. doi:10.1126/science.1168979
   PubMed Web of Science ®Google Scholar
• Drew, S. C., Noble, C. J., Masters, C. L., Hanson, G. R., & Barnham, K. J. (2009). Pleomorphic copper coordination by Alzheimer’s disease amyloid-β peptide. Journal of the American Chemical Society, 131(3), 1195–1207. doi:10.1021/ja808073b
   PubMed Web of Science ®Google Scholar
• Duce, J. A., & Bush, A. I. (2010). Biological metals and Alzheimer’s disease: Implications for therapeutics and diagnostics. Progress in Neurobiology, 92(1), 1–18. doi:10.1016/j.pneurobio.2010.04.003
   PubMed Web of Science ®Google Scholar
• Eckman, C. B., & Eckman, E. A. (2007). An Update on the Amyloid hypothesis Christopher. Neurologic Clinics, 25(3), 669–679. doi:10.1016/j.ncl.2007.03.007
   PubMed Web of Science ®Google Scholar
• Ferri, C. P., Prince, M., Brayne C., Brodaty, H., Fratiglioni L., Ganguli, M., Hall, K., Hasegawa, K., Hendrie, H., Huang, Y., Jorm, A., Mathers, C., Menezes, P. R., Rimmer, E., & Scazufca, M. (2005). Global prevalence of dementia: A Delphi consensus study. The Lancet), 366(9503), 2112–2117., doi:10.1016/S0140-6736(05)67889-0
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., & Sonnenber, D. J. (2009). Gaussian09. Wallingford, CT: Gaussian Inc.
   Google Scholar
• Furlan, S., Hureau, C., Faller, P., & La Penna, G. (2010). Modeling the Cu + binding in the 1-16 region of the amyloid-β peptide involved in Alzheimer’s disease. The Journal of Physical Chemistry. B, 114(46), 15119–15133. doi:10.1021/jp102928h
   PubMed Web of Science ®Google Scholar
• GitHub (2019). Retrieved November 14, 2019, from https://github.com/grimme-lab/xtb/
   Google Scholar
• Glenner, G. G., & Wong, C. W. (1984). Alzheimer’s disease: Initial report of the purification and characterization of a novel cerebrovascular amyloid protein. Biochemical and Biophysical Research Communications, 120(3), 885–890.(84)80190-4 doi:10.1016/S0006-291X(84)80190-4
   PubMed Web of Science ®Google Scholar
• Greene, D., Po, T., Pan, J., Tabibian, T., & Luo, R. (2018). Computational analysis for the rational design of anti-amyloid beta (Aβ) antibodies. The Journal of Physical Chemistry. B, 122(16), 4521–4536. doi:10.1021/acs.jpcb.8b01837
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Karplus, P. A. (2010). A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. BioMolecular Concepts, 1(3-4), 271–283. doi:10.1515/bmc.2010.022
   PubMedGoogle Scholar
• Hori, Y., Hashimoto, T., Wakutani, Y., Urakami, K., Nakashima, K., Condron, M. M., Tsubuki, S., Saido, T. C., Teplow, D. B., & Iwatsubo, T. (2007). The Tottori (D7N) and English (H6R) familial Alzheimer disease mutations accelerate Abeta fibril formation without increasing protofibril formation. The Journal of Biological Chemistry, 282(7), 4916–4923. doi:10.1074/jbc.M608220200
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. ( doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Hung, Y. H., Bush, A. I., & Cherny, R. A. (2010). Copper in the brain and Alzheimer’s disease. Jbic Journal of Biological Inorganic Chemistry, 15(1), 61–76. doi:10.1007/s00775-009-0600-y
   PubMed Web of Science ®Google Scholar
• Huy, P. D. Q., Vuong, Q., Van, La Penna, G., Faller, P., & Li, M. S. (2016). Impact of Cu(II) binding on structures and dynamics of Aβ42Monomer and dimer: Molecular dynamics study. ACS Chemical Neuroscience, 7(10), 1348–1363. doi:10.1021/acschemneuro.6b00109
   PubMed Web of Science ®Google Scholar
• Jiao, B., Tang, B., Liu, X., Xu, J., Wang, Y., Zhou, L., Zhang, F., Yan, X., Zhou, Y., & Shen, L. (2014). Mutational analysis in early-onset familial Alzheimer’s disease in Mainland China. Neurobiology of Aging, 35(8), 1957.e1–1957.e6. doi:10.1016/j.neurobiolaging.2014.02.014
   Web of Science ®Google Scholar
• Kaden, D., Harmeier, A., Weise, C., Munter, L. M., Althoff, V., Rost, B. R., Hildebrand, P. W., Schmitz, D., Schaefer, M., Lurz, R., Skodda, S., Yamamoto, R., Arlt, S., Finckh, U., & Multhaup, G. (2012). Novel APP/Aβ mutation K16N produces highly toxic heteromeric Aβ oligomers. EMBO Molecular Medicine, 4(7), 647–659. doi:10.1002/emmm.201200239
   PubMed Web of Science ®Google Scholar
• Karantzoulis, S., & Galvin, J. E. (2011). Distinguishing Alzheimer’s disease from other major forms of dementia. Expert Review of Neurotherapeutics, 11(11), 1579–1591. doi:10.1586/ern.11.155
   PubMed Web of Science ®Google Scholar
• Kepp, K. P. (2017). Alzheimer’s disease: How metal ions define β-amyloid function. Coordination Chemistry Reviews, 351, 127–159. doi:10.1016/j.ccr.2017.05.007
   Web of Science ®Google Scholar
• Labute, P. (2010). LowModeMD - Implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops. Journal of Chemical Information and Modeling, 50(5), 792–800. doi:10.1021/ci900508k
   PubMed Web of Science ®Google Scholar
• Li, P., & Merz, K. M. (2016). MCPB.py: A Python Based Metal Center Parameter Builder. Journal of Chemical Information and Modeling, 56(4), 599–604. doi:10.1021/acs.jcim.5b00674
   PubMed Web of Science ®Google Scholar
• Lovell, M. A., Robertson, J. D., Teesdale, W. J., Campbell, J. L., & Markesbery, W. R. (1998). Copper, iron and zinc in Alzheimer’s disease senile plaques. Journal of the Neurological Sciences, 158(1), 47–52.(98)00092-6 doi:10.1016/S0022-510X(98)00092-6
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi:10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Maloney, J. A., Bainbridge, T., Gustafson, A., Zhang, S., Kyauk, R., Steiner, P., Van Der Brug, M., Liu, Y., Ernst, J. A., Watts, R. J., & Atwal, J. K. (2014). Molecular mechanisms of Alzheimer disease protection by the A673T allele of amyloid precursor protein. The Journal of Biological Chemistry, 289(45), 30990–31000. doi:10.1074/jbc.M114.589069
   PubMed Web of Science ®Google Scholar
• Margreitter, C., & Oostenbrink, C. (2017). MDplot: Visualise molecular dynamics. The R Journal, 9(1), 164–186.
   PubMedGoogle Scholar
• McKhann, G., Drachman, D., Folstein, M., Katzman, R., Price, D., & Stadlan, E. (1984). Table 1. Criteria for clinical diagnosis of Alzheimer’s disease. Neurology, 34(7), 939–944. doi:10.1212/WNL.34.7.939
   PubMed Web of Science ®Google Scholar
• Murray, B., Sorci, M., Rosenthal, J., Lippens, J., Isaacson, D., Das, P., Fabris, D., Li, S., & Belfort, G. (2016). A2T and A2V Aβ peptides exhibit different aggregation kinetics, primary nucleation, morphology, structure, and LTP inhibition. Proteins, 84(4), 488–500. doi:10.1002/prot.24995
   PubMed Web of Science ®Google Scholar
• Ono, K., Condron, M. M., & Teplow, D. B. (2010). Effects of the english (H6R) and tottori (D7N) familial alzheimer disease mutations on amyloid β-protein assembly and toxicity. The Journal of Biological Chemistry, 285(30), 23186–23197. doi:10.1074/jbc.M109.086496
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Polshakov, V. I., Mantsyzov, A. B., Kozin, S. A., Adzhubei, A. A., Zhokhov, S. S., van Beek, W., Kulikova, A. A., Indeykina, M. I., Mitkevich, V. A., & Makarov, A. A. (2017). A binuclear zinc interaction fold discovered in the homodimer of Alzheimer’s amyloid-β fragment with Taiwanese mutation D7H. Angewandte Chemie International Edition), 56(39), 11734–11739. doi:10.1002/anie.201704615
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. doi:10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (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.(77)90098-5 doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Schaefer, M., & Karplus, M. (1996). A comprehensive analytical treatment of continuum electrostatics. The Journal of Physical Chemistry, 100(5), 1578–1599. doi:10.1021/jp9521621
   Web of Science ®Google Scholar
• Silva, K. I., Michael, B. C., Geib, S. J., & Saxena, S. (2014). ESEEM analysis of multi-histidine Cu(II)-coordination in model complexes, peptides, and amyloid-β. The Journal of Physical Chemistry. B, 118(30), 8935–8944. doi:10.1021/jp500767n
   PubMed Web of Science ®Google Scholar
• Simmons, L. K., May, P. C., Tomaselli, K. J., Rydel, R. E., Fuson, K. S., Brigham, E. F., Wright, S., Lieberburg, I., Becker, G. W., & Brems, D. N. (1994). Secondary structure of amyloid beta peptide correlates with neurotoxic activity in vitro. Molecular Pharmacology, 45(3), 373–379.
   PubMed Web of Science ®Google Scholar
• Stelzmann, R. A., Schnitzlein, H. N., & Murtagh, F. R. (1995). An English translation of Alzheimer’s 1907 paper “Über eine eigenartige Erkrankung der Hirnrinde. Clinical Anatomy, 8(6), 429–443. doi:10.1002/ca.980080612
   PubMedGoogle Scholar
• Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. (1990). Semianalytical treatment of solvation for molecular mechanics and dynamics. Journal of the American Chemical Society, 112(16), 6127–6129. doi:10.1021/ja00172a038
   Web of Science ®Google Scholar
• Teich, A. F., & Arancio, O. (2012). Is the amyloid hypothesis of Alzheimer’s disease therapeutically relevant? The Biochemical Journal, 446(2), 165–177. doi:10.1042/BJ20120653
   PubMed Web of Science ®Google Scholar
• Tõugu, V., Karafin, A., Zovo, K., Chung, R. S., Howells, C., West, A. K., & Palumaa, P. (2009). Zn(II)- and Cu(II)-induced non-fibrillar aggregates of amyloid-β (1-42) peptide are transformed to amyloid fibrils, both spontaneously and under the influence of metal chelators. Journal of Neurochemistry, 110(6), 1784–1795. doi:10.1111/j.1471-4159.2009.06269.x
   PubMed Web of Science ®Google Scholar
• Viet, M. H., Nguyen, P. H., Ngo, S. T., Li, M. S., & Derreumaux, P. (2013). Effect of the tottori familial disease mutation (D7N) on the monomers and dimers of A beta(40) and A beta(42). ACS Chemical Neuroscience, 4(11), 1446–1457. doi:10.1021/cn400110d
   PubMed Web of Science ®Google Scholar
• Wärmländer, S., Tiiman, A., Abelein, A., Luo, J., Jarvet, J., Söderberg, K. L., Danielsson, J., & Gräslund, A. (2013). Biophysical studies of the amyloid β-peptide: Interactions with metal ions and small molecules. Chembiochem : a European Journal of Chemical Biology, 14(14), 1692–1704. doi:10.1002/cbic.201300262
   PubMed Web of Science ®Google Scholar
• Weggen, S., & Beher, D. (2012). Molecular consequences of amyloid precursor protein and presenilin mutations causing autosomal-dominant Alzheimer’s disease. Alzheimer’s Research and Therapy, 4(2), 9. 10.1186/alzrt107
   PubMed Web of Science ®Google Scholar
• Xu, L., Chen, Y., & Wang, X. (2014). Dual effects of familial Alzheimer’s disease mutations (D7H, D7N, and H6R) on amyloid β peptide: Correlation dynamics and zinc binding. Proteins: Structure, Function, and Bioinformatics, 82(12), 3286–3297. doi:10.1002/prot.24669
   PubMed Web of Science ®Google Scholar
• Zhou, L., Brouwers, N., Benilova, I., Vandersteen, A., Mercken, M., Van Laere, K., Van Damme, P., Demedts, D., Van Leuven, F., Sleegers, K., Broersen, K., Van Broeckhoven, C., Vandenberghe, R., & De Strooper, B. (2011). Amyloid precursor protein mutation E682K at the alternative β-secretase cleavage β’-site increases Aβ generation. EMBO Molecular Medicine, 3(5), 291–302. doi:10.1002/emmm.201100138
   PubMed Web of Science ®Google Scholar