Amino acid substitutions [K16A] and [K28A] distinctly affect amyloid β-protein oligomerization

Selkoe, D.J.: Alzheimer’s disease: genes, proteins, and therapy. Physiol. Rev. 81 (2), 741–766 (2001)

Shaw, L.M., Vanderstichele, H., Knapik-Czajka, M., Clark, C.M., Aisen, P.S., Petersen, R.C., Blennow, K., Soares, H., Simon, A., Lewczuk, P., Dean, R., Siemers, E., Potter, W., Lee, V.M.Y., Trojanowski, J.Q., Initi, A.D.N.: Cerebrospinal fluid biomarker signature in Alzheimer’s disease neuroimaging initiative subjects. Ann. Neurol. 65(4), 403–413 (2009)

Hardy, J.A., Higgins, G.A.: Alzheimer’s disease: the amyloid cascade hypothesis. Science 256, 184–185 (1992)

Hardy, J.: The amyloid hypothesis for Alzheimer’s disease: a critical reappraisal. J. Neurochem. 110, 1129–1134 (2009)

Serpell, L.C.: Alzheimer’s amyloid fibrils: structure and assembly. Biochim. Biophys. Acta 1502(1), 16–30 (2000)

Petkova, A.T., Ishii, Y., Balbach, J.J., Antzutkin, O.N., Leapman, R.D., Delaglio, F., Tycko, R.: A structural model for Alzheimer’s β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl. Acad. Sci. USA 99(26), 16742–16747 (2002)

Petkova, A.T., Leapman, R.D., Guo, Z., Yau, W.M., Mattson, M.P., Tycko, R.: Self-propagating, molecular-level polymorphism in Alzheimer’s β-amyloid fibrils. Science 307, 262–265 (2005)

Sciarretta, K.L., Gordon, D.J., Petkova, A.T., Tycko, R., Meredith, S.C.: A β40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. Biochemistry 44 (16), 6003–6014 (2005)

Paravastu, A., Leapman, R., Yau, W.M., Tycko, R.: Molecular structural basis for polymorphism in Alzheimer’s β-amyloid fibrils. Proc. Natl. Acad. Sci. USA 105, 18349–18354 (2008)

Paravastu, A.K., Qahwash, I., Leapman, R.D., Meredith, S.C., Tycko, R.: Seeded growth of β-amyloid fibrils from Alzheimer’s brain-derived fibrils produces a distinct fibril structure. Proc. Natl. Acad. Sci. USA 106, 7443–7448 (2009)

Tycko, R.: Solid-state NMR studies of amyloid fibril structure. Annu. Rev. Phys. Chem. 62, 279–299 (2011)

Luhrs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Dobeli, H., Schubert, D., Riek, R.: 3D structure of Alzheimer’s amyloid- β(1–42) fibrils. Proc. Natl. Acad. Sci. USA 102, 17342–17347 (2005)

Schmidt, M., Sachse, C., Richter, W., Xu, C., Faendrich, M., Grigorieff, N.: Comparison of Alzheimer A β(1–40) and A β(1–42) amyloid fibrils reveals similar protofilament structures. Proc. Natl. Acad. Sci. USA 106(47), 19813–19818 (2009)

Xiao, Y., Ma, B., McElheny, D., Parthasarathy, S., Long, F., Hoshi, M., Nussinov, R., Ishii, Y.: A β(1–42) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer’s disease. Nat. Struct. Mol. Biol. 22(6), 499–505 (2015)

Schmidt, M., Rohou, A., Lasker, K., Yadav, J.K., Schiene-Fischer, C., Faendrich, M., Grigorieff, N.: Peptide dimer structure in an A β(1–42) fibril visualized with cryo-EM. Proc. Natl. Acad. Sci. USA 112(38), 11858–11863 (2015)

Petkova, A.T., Yau, W.M., Tycko, R.: Experimental constraints on quaternary structure in Alzheimer’s β-amyloid fibrils. Biochemistry 45(2), 498–512 (2006)

Lazo, N.D., Grant, M.A., Condron, M.C., Rigby, A.C., Teplow, D.B.: On the nucleation of amyloid β-protein monomer folding. Protein Sci. 14(6), 1581–1596 (2005)

Grant, M.A., Lazo, N.D., Lomakin, A., Condron, M.M., Arai, H., Yamin, G., Rigby, A.C., Teplow, D.B.: Familial Alzheimer’s disease mutations alter the stability of the amyloid β-protein monomer folding nucleus. Proc. Natl. Acad. Sci. USA 104, 16522–16527 (2007)

Fawzi, N., Phillips, A., Ruscio, J., Doucleff, M., Wemmer, D., Head-Gordon, T.: Structure and dynamics of the A β(21–30) peptide from the interplay of NMR experiments and molecular simulations. J. Am. Chem. Soc. 130, 6145–6158 (2008)

Borreguero, J.M., Urbanc, B., Lazo, N.D., Buldyrev, S.V., Teplow, D.B., Stanley, H.E.: Folding events in the 21–30 region of amyloid β-protein (A β) studied in silico. Proc. Natl. Acad. Sci. USA 102(17), 6015–6020 (2005)

Cruz, L., Urbanc, B., Borreguero, J.M., Lazo, N.D., Teplow, D.B., Stanley, H.E.: Solvent and mutation effects on the nucleation of amyloid β-protein folding. Proc. Natl. Acad. Sci. USA 102(51), 18258–18263 (2005)

Baumketner, A., Bernstein, S.L., Wyttenbach, T., Lazo, N.D., Teplow, D.B., Bowers, M.T., Shea, J.E.: Structure of the 21–30 fragment of amyloid β-protein. Protein Sci. 15(6), 1239–1247 (2006)

Chen, W., Mousseau, N., Derreumaux, P.: The conformations of the amyloid- β (21–30) fragment can be described by three families in solution. J. Chem. Phys. 125 (8), 084911 (2006)

Tarus, B., Straub, J.E., Thirumalai, D.: Structures and Free-Energy Landscapes of the wild type and mutants of the A β 21−30 peptide are determined by an interplay between intrapeptide electrostatic and hydrophobic interactions. J. Mol. Biol. 379(4), 815–829 (2008)

Krone, M.G., Baumketner, A., Bernstein, S.L., Wyttenbach, T., Lazo, N.D., Teplow, D.B., Bowers, M.T., Shea, J.E.: Effects of familial mutations on the folding nucleation of the Alzheimer amyloid β-protein. J. Mol. Biol. 381, 221–228 (2008)

Cruz, L., Rao, J.S., Teplow, D.B., Urbanc, B.: Dynamics of metastable β-hairpin structures in the folding nucleus of amyloid β-protein. J. Phys. Chem. B 116, 6311–6325 (2012)

Keshet, B., Gray, J.J., Good, T.A.: Structurally distinct toxicity inhibitors bind at common loci on β-amyloid fibril. Protein Sci. 19, 2291–2304 (2010)

Esler, W.P., Stimson, E.R., Ghilardi, J.R., Lu, Y.A., Felix, A.M., Vinters, H.V., Mantyh, P.W., Lee, J.P., Maggio, J.E.: Point substitution in the central hydrophobic cluster of a human β-amyloid congener disrupts peptide folding and abolishes plaque competence. Biochemistry 35 (44), 13914–13921 (1996)

de Groot, N.S., Aviles, F.X., Vendrell, J., Ventura, S.: Mutagenesis of the central hydrophobic cluster in A β42 Alzheimer’s peptide. Side-chain properties correlate with aggregation propensities. FEBS J. 273, 658–668 (2006)

Levy, E., Carman, M.D., Fernandez-Madrid, I.J., Power, M.D., Lieberburg, I., van Duinen, S.G., Bots, G.T.A.M., Luyendijk, W., Frangione, B.: Mutation of the Alzheimer’s disease amyloid gene in hereditary cerebral hemorrhage, Dutch-type. Science 248, 1124–1126 (1990)

Tycko, R., Sciarretta, K., Orgel, J., Meredith, S.: Evidence for novel β-sheet structures in Iowa mutant β-amyloid fibrils. Biochemistry 48, 6072–6084 (2009)

Zhang, S.S., Casey, N., Lee, J.P.: Residual structure in the Alzheimer’s disease peptide—probing the origin of a central hydrophobic cluster. Fold. Des. 3, 413–422 (1998)

Zhang, S., Iwata, K., Lachenmann, M.J., Peng, J.W., Li, S., Stimson, E.R., Lu, Y., Felix, A.M., Maggio, J.E., Lee, J.P.: The Alzheimer’s peptide A β adopts a collapsed coil structure in water. J. Struct. Biol. 130(2–3), 130–141 (2000)

Chen, Z., Krause, G., Reif, B.: Structure and orientation of peptide inhibitors bound to β-amyloid fibrils. J. Mol. Biol. 354, 760–776 (2005)

Terzi, E., Hölzemann, G., Seelig, J.: Reversible random coil- β-sheet transition of the Alzheimer β-amyloid fragment (25–35). Biochemistry 33, 1345–1350 (1994)

Hertel, C., Terzi, E., Hauser, N., Jakob-Rotne, R., Seelig, J., Kemp, J.A.: Inhibition of electrostatic interaction between β-amyloid peptide and membranes prevents β-amyloid-induced toxicity. Proc. Natl. Acad. Sci. USA 94, 9412–9416 (1997)

Chauhan, A., Ray, I., Chauhan, V.P.: Interaction of amyloid β-protein with anionic phospholipids: possible involvement of Lys28 and C-terminus aliphatic amino acids. Neurochem. Res. 25, 423–429 (2000)

Bokvist, M., Lindstrom, F., Watts, A., Grobner, G.: Two types of Alzheimer’s β-amyloid (1–40) peptide membrane interactions: aggregation preventing transmembrane anchoring versus accelerated surface fibril formation. J. Mol. Biol. 335, 1039–1049 (2004)

Williamson, M., Suzuki, Y., Bourne, N., Asakura, T.: Binding of amyloid β-peptide to ganglioside micelles is dependent on histidine-13. Biochem. J. 397, 483–490 (2006)

Yoshiike, Y., Akagi, T., Takashima, A.: Surface structure of amyloid- β fibrils contributes to cytotoxicity. Biochemistry 46, 9805–9812 (2007)

Sinha, S., Lopes, D.H.J., Du, Z., Pang, E.S., Shanmugam, A., Lomakin, A., Talbiersky, P., Tennstaedt, A., McDaniel, K., Bakshi, R., Kuo, P.Y., Ehrmann, M., Benedek, G.B., Loo, J.A., Klärner, F.G., Schrader, T., Wang, C., Bitan, G.: Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins. J. Am. Chem. Soc. 133(42), 16958–16969 (2011)

Sinha, S., Lopes, D.H.J., Bitan, G.: A key role for lysine residues in amyloid β-protein folding, assembly, and toxicity. ACS Chem. Neurosci. 3(6), 473–481 (2012)

Bitan, G., Kirkitadze, M.D., Lomakin, A., Vollers, S.S., Benedek, G.B., Teplow, D.B.: Amyloid β-protein (A β) assembly: A β40 and A β42 oligomerize through distinct pathways. Proc. Natl. Acad. Sci. USA 100(1), 330–335 (2003)

Urbanc, B., Cruz, L., Yun, S., Buldyrev, S.V., Bitan, G., Teplow, D.B., Stanley, H.E.: In silico study of amyloid β-protein folding and oligomerization. Proc. Natl. Acad. Sci. USA 101(50), 17345–17350 (2004)

Urbanc, B., Betnel, M., Cruz, L., Bitan, G., Teplow, D.B.: Elucidation of amyloid β-protein oligomerization mechanisms: discrete molecular dynamics study. J. Am. Chem. Soc. 132, 4266–4280 (2010)

Meral, D., Urbanc, B.: Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J. Mol. Biol. 425, 2260–2275 (2013)

Barz, B., Urbanc, B.: Dimer formation enhances structural differences between amyloid β-protein (1–40) and (1–42): an explicit-solvent molecular dynamics study. PLoS One 7(4), e34345 (2012)

Urbanc, B., Betnel, M., Cruz, L., Li, H., Fradinger, E., Monien, B.H., Bitan, G.: Structural basis of A β 1−42 toxicity inhibition by A β C-terminal fragments: discrete molecular dynamics study. J. Mol. Biol. 410, 316–328 (2011)

Lam, A., Teplow, D.B., Stanley, H.E., Urbanc, B.: Effects of the Arctic (E22 →G) mutation on amyloid β-protein folding: discrete molecular dynamics study. J. Am. Chem. Soc. 130, 17413–17422 (2008)

žganec, M., žerovnik, E., Urbanc, B.: Self-assembly of globular protein stefin B into polymorphic oligomers probed by discrete molecular dynamics. J. Chem. Theory Comput. 11, 2355–2366 (2015)

Yun, S., Urbanc, B., Cruz, L., Bitan, G., Teplow, D.B., Stanley, H.E.: Role of electrostatic interactions in amyloid β-protein (A β) oligomer formation: a discrete molecular dynamics study. Biophys. J. 92, 4064–4077 (2007)

Meral, D., Urbanc, B.: Erratum to discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J. Mol. Biol. 427, 2726–2729 (2015)

Williams, T.L., Johnson, B.J., Urbanc, B., Jenkins, T.A., Connell, S.D., Serpell, L.C.: Alzheimer’s A β42 oligomers but not fibrils simultaneously bind to and cause damage to ganglioside containing lipid membranes. Biochem. J. 439, 67–77 (2011)

Williams, T.L., Urbanc, B., Marshall, K.E., Vadukul, D.M., Jenkins, A.T.A., Serpell, L.C.: Europium as an inhibitor of amyloid β(1–42) induced membrane permeation. FEBS Lett. 589, 3228–3236 (2015)

Williams, T.L., Serpell, L.C., Urbanc, B.: Stabilization of native amyloid β-protein oligomers by Copper and Hydrogen peroxide Induced Cross-linking of Unmodified Proteins (CHICUP). Biochim. Biophys. Acta 1864, 249–259 (2016)