-
1
-
-
0037135111
-
The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics
-
Hardy J, Selkoe DJ. The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics. Science 2002;297:353-356.
-
(2002)
Science
, vol.297
, pp. 353-356
-
-
Hardy, J.1
Selkoe, D.J.2
-
2
-
-
33750731675
-
100 years and counting: prospects for defeating Alzheimer's disease
-
Roberson ED, Mucke L. 100 years and counting: prospects for defeating Alzheimer's disease. Science 2006;314:781-784.
-
(2006)
Science
, vol.314
, pp. 781-784
-
-
Roberson, E.D.1
Mucke, L.2
-
3
-
-
84867477898
-
The amyloid β peptide: a chemist's perspective. Role in Alzheimer's and fibrillization
-
Hamley IW. The amyloid β peptide: a chemist's perspective. Role in Alzheimer's and fibrillization. Chem Rev 2012;112:5147-5192.
-
(2012)
Chem Rev
, vol.112
, pp. 5147-5192
-
-
Hamley, I.W.1
-
4
-
-
70350153272
-
The chemistry of Alzheimer's disease
-
Rauk A. The chemistry of Alzheimer's disease. Chem Soc Rev 2009;38:2698-2715.
-
(2009)
Chem Soc Rev
, vol.38
, pp. 2698-2715
-
-
Rauk, A.1
-
5
-
-
84893869490
-
Amyloid fibrils: formation, polymorphism, and inhibition
-
Härd T. Amyloid fibrils: formation, polymorphism, and inhibition. J Phys Chem Lett 2014;5:607-614.
-
(2014)
J Phys Chem Lett
, vol.5
, pp. 607-614
-
-
Härd, T.1
-
6
-
-
28444442999
-
3D structure of Alzheimer's amyloid β(1-42) fibrils
-
Lührs 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 2005;102:17342-17347.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 17342-17347
-
-
Lührs, T.1
Ritter, C.2
Adrian, M.3
Riek-Loher, D.4
Bohrmann, B.5
Dobeli, H.6
Schubert, D.7
Riek, R.8
-
7
-
-
0037168655
-
A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR
-
Petkova AT, Ishii Y, Balbach JJ, Antzutkin ON, Leapman RD, 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 2002;99:16742-16747.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16742-16747
-
-
Petkova, A.T.1
Ishii, Y.2
Balbach, J.J.3
Antzutkin, O.N.4
Leapman, R.D.5
Delaglio, F.6
Tycko, R.7
-
8
-
-
70349923038
-
Alzheimer's disease: from pathology to therapeutic approaches
-
Jakob-Roetne R, Jacobsen H. Alzheimer's disease: from pathology to therapeutic approaches. Angew Chem Int Ed 2009;48:3030-3059.
-
(2009)
Angew Chem Int Ed
, vol.48
, pp. 3030-3059
-
-
Jakob-Roetne, R.1
Jacobsen, H.2
-
9
-
-
84954358028
-
Amyloid β-Protein monomer folding: free-energy surfaces reveal alloform-specific differences
-
Yang MF, Teplow DB. Amyloid β-Protein monomer folding: free-energy surfaces reveal alloform-specific differences. J Mol Biol 2008;384:450-464.
-
(2008)
J Mol Biol
, vol.384
, pp. 450-464
-
-
Yang, M.F.1
Teplow, D.B.2
-
10
-
-
78650863624
-
Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms
-
Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. J Mol Biol 2011;405:570-583.
-
(2011)
J Mol Biol
, vol.405
, pp. 570-583
-
-
Sgourakis, N.G.1
Merced-Serrano, M.2
Boutsidis, C.3
Drineas, P.4
Du, Z.5
Wang, C.6
Garcia, A.E.7
-
11
-
-
84883297832
-
Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach
-
Rosenman DJ, Connors CR, Chen W, Wang C, García AE. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. J Mol Biol 2013;425:3338-3359.
-
(2013)
J Mol Biol
, vol.425
, pp. 3338-3359
-
-
Rosenman, D.J.1
Connors, C.R.2
Chen, W.3
Wang, C.4
García, A.E.5
-
12
-
-
61649098771
-
The structure of Aβ42 C-terminal fragments probed by a combined experimental and theoretical study
-
Wu C, Murray MM, Bernstein SL, Condron MM, Bitan G, Shea J-E, Bowers MT. The structure of Aβ42 C-terminal fragments probed by a combined experimental and theoretical study. J Mol Biol 2009;387:492-501.
-
(2009)
J Mol Biol
, vol.387
, pp. 492-501
-
-
Wu, C.1
Murray, M.M.2
Bernstein, S.L.3
Condron, M.M.4
Bitan, G.5
Shea, J.-E.6
Bowers, M.T.7
-
13
-
-
82555173714
-
Amyloid-β peptide structure in aqueous solution varies with fragment size
-
Wise-Scira O, Xu L, Kitahara T, Perry G, Coskuner O. Amyloid-β peptide structure in aqueous solution varies with fragment size. J Chem Phys 2011;135:205101.
-
(2011)
J Chem Phys
, vol.135
, pp. 205101
-
-
Wise-Scira, O.1
Xu, L.2
Kitahara, T.3
Perry, G.4
Coskuner, O.5
-
14
-
-
80052231359
-
Homogeneous and heterogeneous tertiary structure ensembles of amyloid β peptides
-
Ball KA, Phillips AH, Nerenberg PS, Fawzi NL, Wemmer DE, Head-Gordon T. Homogeneous and heterogeneous tertiary structure ensembles of amyloid β peptides. Biochemistry 2011;50:7612-7628.
-
(2011)
Biochemistry
, vol.50
, pp. 7612-7628
-
-
Ball, K.A.1
Phillips, A.H.2
Nerenberg, P.S.3
Fawzi, N.L.4
Wemmer, D.E.5
Head-Gordon, T.6
-
15
-
-
17244372981
-
Conformational transition of amyloid β-peptide
-
Xu YC, Shen JH, Luo XM, Zhu WL, Chen KX, Ma JP, Jiang, HL. Conformational transition of amyloid β-peptide. Proc Natl Acad Sci USA 2005;102:5403-5407.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 5403-5407
-
-
Xu, Y.C.1
Shen, J.H.2
Luo, X.M.3
Zhu, W.L.4
Chen, K.X.5
Ma, J.P.6
Jiang, H.L.7
-
16
-
-
84872113583
-
C-terminal turn stability determines assembly differences between Aβ40 and Aβ42
-
Roychaudhuri R, Yang MF, Deshpande A, Cole GM, Frautschy S, Lomakin A, Benedek GB, Teplow DB. C-terminal turn stability determines assembly differences between Aβ40 and Aβ42. J Mol Biol 2013;425:292-308.
-
(2013)
J Mol Biol
, vol.425
, pp. 292-308
-
-
Roychaudhuri, R.1
Yang, M.F.2
Deshpande, A.3
Cole, G.M.4
Frautschy, S.5
Lomakin, A.6
Benedek, G.B.7
Teplow, D.B.8
-
17
-
-
33644526613
-
Amyloid β-protein monomer structure: a computational and experimental study
-
Baumketner A. Amyloid β-protein monomer structure: a computational and experimental study. Protein Sci 2006;15:420-428.
-
(2006)
Protein Sci
, vol.15
, pp. 420-428
-
-
Baumketner, A.1
-
19
-
-
43249091143
-
Structure and dynamics of the Aβ21-30 peptide from the interplay of NMR experiments and molecular simulations
-
L Fawzi N, Phillips AH, Ruscio JZ, Doucleff M, Wemmer DE, Head-Gordon T. Structure and dynamics of the Aβ21-30 peptide from the interplay of NMR experiments and molecular simulations. J Am Chem Soc 2008;130:6145-6158.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 6145-6158
-
-
Fawzi, L.N.1
Phillips, A.H.2
Ruscio, J.Z.3
Doucleff, M.4
Wemmer, D.E.5
Head-Gordon, T.6
-
20
-
-
79958703402
-
Structural basis for Aβ1-42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study
-
Urbanc B, Betnel M, Cruz L, Li H, Fradinger EA, Monien BH, Bitan G. Structural basis for Aβ1-42 toxicity inhibition by Aβ C-terminal fragments: discrete molecular dynamics study. J Mol Biol 2011;410:316-328.
-
(2011)
J Mol Biol
, vol.410
, pp. 316-328
-
-
Urbanc, B.1
Betnel, M.2
Cruz, L.3
Li, H.4
Fradinger, E.A.5
Monien, B.H.6
Bitan, G.7
-
21
-
-
84885616825
-
Revealing hidden helix propensity in Aβ peptides by molecular dynamics simulations
-
Lockhart C, Klimov DK. Revealing hidden helix propensity in Aβ peptides by molecular dynamics simulations. J Phys Chem B 2013;117:12030-12038.
-
(2013)
J Phys Chem B
, vol.117
, pp. 12030-12038
-
-
Lockhart, C.1
Klimov, D.K.2
-
22
-
-
84902953466
-
Comparison of structure determination methods for intrinsically disordered amyloid β peptides
-
Ball KA, Wemmer DE, Head-Gordon T. Comparison of structure determination methods for intrinsically disordered amyloid β peptides. J Phys Chem B 2014; 118:6405-6416.
-
(2014)
J Phys Chem B
, vol.118
, pp. 6405-6416
-
-
Ball, K.A.1
Wemmer, D.E.2
Head-Gordon, T.3
-
23
-
-
84892777680
-
Familial Alzheimer A2V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer
-
Nguyen PH, Tarus B, Derreumaux P. Familial Alzheimer A2V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer. J Phys Chem B 2014;118:501-510.
-
(2014)
J Phys Chem B
, vol.118
, pp. 501-510
-
-
Nguyen, P.H.1
Tarus, B.2
Derreumaux, P.3
-
24
-
-
84884902112
-
Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations
-
Xu L, Wang X, Shan S, Wang X. Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations. J Comput Chem 2013;34:2524-2536.
-
(2013)
J Comput Chem
, vol.34
, pp. 2524-2536
-
-
Xu, L.1
Wang, X.2
Shan, S.3
Wang, X.4
-
25
-
-
84888339056
-
Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42
-
Viet MH, Nguyen PH, Ngo ST, Li MS, Derreumaux P. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2013;4:1446-1457.
-
(2013)
ACS Chem Neurosci
, vol.4
, pp. 1446-1457
-
-
Viet, M.H.1
Nguyen, P.H.2
Ngo, S.T.3
Li, M.S.4
Derreumaux, P.5
-
26
-
-
77954927651
-
Effects of the English (H6R) and Tottori (D7N) familial Alzheimer disease mutations on amyloid β-protein assembly and toxicity
-
Ono K, Condron MM, Teplow DB. Effects of the English (H6R) and Tottori (D7N) familial Alzheimer disease mutations on amyloid β-protein assembly and toxicity. J Biol Chem 2010;285:23184-23195.
-
(2010)
J Biol Chem
, vol.285
, pp. 23184-23195
-
-
Ono, K.1
Condron, M.M.2
Teplow, D.B.3
-
27
-
-
84860434786
-
Amyloid-β(Aβ) D7H mutation increases oligomeric Aβ42 and alters properties of Aβ zinc/copper assemblies
-
Chen WT, Hong CJ, Lin YT, Chang WH, Huang HT, Liao JY, Chang YJ, Hsieh YF, Cheng CY, Liu HC, Chen YR, Cheng IH. Amyloid-β(Aβ) D7H mutation increases oligomeric Aβ42 and alters properties of Aβ zinc/copper assemblies. PLoS One 2012;7:e35807.
-
(2012)
PLoS One
, vol.7
, pp. e35807
-
-
Chen, W.T.1
Hong, C.J.2
Lin, Y.T.3
Chang, W.H.4
Huang, H.T.5
Liao, J.Y.6
Chang, Y.J.7
Hsieh, Y.F.8
Cheng, C.Y.9
Liu, H.C.10
Chen, Y.R.11
Cheng, I.H.12
-
28
-
-
84862848514
-
A Key A key role for lysine residues in amyloid β-protein folding, assembly, and toxicity
-
Sinha S, Lopes DHJ, Bitan G. A Key A key role for lysine residues in amyloid β-protein folding, assembly, and toxicity. ACS Chem Neurosci 2012;3:473-481.
-
(2012)
ACS Chem Neurosci
, vol.3
, pp. 473-481
-
-
Sinha, S.1
Lopes, D.H.J.2
Bitan, G.3
-
29
-
-
70349295278
-
Structure-neurotoxicity relationships of amyloid β-protein oligomers
-
Ono K, Condron MM, Teplow DB. Structure-neurotoxicity relationships of amyloid β-protein oligomers. Proc Natl Acad Sci USA 2009;106:14745-14750.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 14745-14750
-
-
Ono, K.1
Condron, M.M.2
Teplow, D.B.3
-
30
-
-
77954892793
-
Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape
-
Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010;110:4820-4838.
-
(2010)
Chem Rev
, vol.110
, pp. 4820-4838
-
-
Miller, Y.1
Ma, B.2
Nussinov, R.3
-
31
-
-
77953113490
-
Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states
-
Miller Y, Ma BY, Nussinov R. Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states. Proc Natl Acad Sci USA 2010;107:9490-9495.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 9490-9495
-
-
Miller, Y.1
Ma, B.Y.2
Nussinov, R.3
-
32
-
-
34247234602
-
The Alzheimer's peptides Aβ40 and 42 adopt distinct conformations in water: A combined MD/NMR study
-
Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. The Alzheimer's peptides Aβ40 and 42 adopt distinct conformations in water: A combined MD/NMR study. J Mol Biol 2007;368:1448-1457.
-
(2007)
J Mol Biol
, vol.368
, pp. 1448-1457
-
-
Sgourakis, N.G.1
Yan, Y.2
McCallum, S.A.3
Wang, C.4
Garcia, A.E.5
-
33
-
-
84867460758
-
Bioinorganic chemistry of Alzheimer's disease
-
Kepp KP. Bioinorganic chemistry of Alzheimer's disease. Chem Rev 2012;112:5193-5239.
-
(2012)
Chem Rev
, vol.112
, pp. 5193-5239
-
-
Kepp, K.P.1
-
34
-
-
84859651929
-
Metal-associated amyloid-β species in Alzheimer's disease
-
Pithadia AS, Lim MH. Metal-associated amyloid-β species in Alzheimer's disease. Curr Opin Chem Biol 2012;16:67-73.
-
(2012)
Curr Opin Chem Biol
, vol.16
, pp. 67-73
-
-
Pithadia, A.S.1
Lim, M.H.2
-
35
-
-
79952513228
-
Interactions of Zn(II) and Cu(II) ions with Alzheimer's amyloid-β peptide Metal ion binding, contribution to fibrillization and toxicity
-
Tougu V, Tiiman A, Palumaa P. Interactions of Zn(II) and Cu(II) ions with Alzheimer's amyloid-β peptide Metal ion binding, contribution to fibrillization and toxicity. Metallomics 2011;3:250-261.
-
(2011)
Metallomics
, vol.3
, pp. 250-261
-
-
Tougu, V.1
Tiiman, A.2
Palumaa, P.3
-
36
-
-
84864551223
-
Metal binding sites in amyloid oligomers: Complexes and mechanisms
-
Miller Y, Ma B, Nussinov R. Metal binding sites in amyloid oligomers: Complexes and mechanisms. Coord Chem Rev 2012;256:2245-2252.
-
(2012)
Coord Chem Rev
, vol.256
, pp. 2245-2252
-
-
Miller, Y.1
Ma, B.2
Nussinov, R.3
-
37
-
-
84872562074
-
The metal theory of Alzheimer's disease
-
Bush AI. The metal theory of Alzheimer's disease. J Alzheimers Dis 2013;33(Suppl 1):S277-S281.
-
(2013)
J Alzheimers Dis
, vol.33
, Issue.SUPPL 1
, pp. S277-S281
-
-
Bush, A.I.1
-
38
-
-
59449097016
-
Bioinorganic chemistry of copper and zinc ions coordinated to amyloid-beta peptide
-
Faller P, Hureau C. Bioinorganic chemistry of copper and zinc ions coordinated to amyloid-beta peptide. Dalton Trans 2009;7:1080-1094.
-
(2009)
Dalton Trans
, vol.7
, pp. 1080-1094
-
-
Faller, P.1
Hureau, C.2
-
40
-
-
80052489511
-
Effect of zinc binding on β-amyloid structure and dynamics: implications for Aβ aggregation
-
Rezaei-Ghaleh N, Giller K, Becker S, Zweckstetter M. Effect of zinc binding on β-amyloid structure and dynamics: implications for Aβ aggregation. Biophys J 2011;101:1202-1211.
-
(2011)
Biophys J
, vol.101
, pp. 1202-1211
-
-
Rezaei-Ghaleh, N.1
Giller, K.2
Becker, S.3
Zweckstetter, M.4
-
41
-
-
38049136879
-
Effects of zinc binding on the conformational distribution of the amyloid β peptide based on molecular dynamics simulations
-
Li W, Zhang J, Su Y, Wang J, Qin M, Wang W. Effects of zinc binding on the conformational distribution of the amyloid β peptide based on molecular dynamics simulations. J Phys Chem B 2007;111:13814-13821.
-
(2007)
J Phys Chem B
, vol.111
, pp. 13814-13821
-
-
Li, W.1
Zhang, J.2
Su, Y.3
Wang, J.4
Qin, M.5
Wang, W.6
-
42
-
-
84865652373
-
Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics
-
Wise-Scira O, Xu L, Perry G, Coskuner O. Structures and free energy landscapes of aqueous zinc(II)-bound amyloid-β(1-40) and zinc(II)-bound amyloid-β(1-42) with dynamics. J Biol Inorg Chem 2012;17:927-938.
-
(2012)
J Biol Inorg Chem
, vol.17
, pp. 927-938
-
-
Wise-Scira, O.1
Xu, L.2
Perry, G.3
Coskuner, O.4
-
43
-
-
84867333336
-
Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules
-
Xu L, Gao K, Bao C, Wang X. Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules. J Comput Aided Mol Des 2012;26:963-976.
-
(2012)
J Comput Aided Mol Des
, vol.26
, pp. 963-976
-
-
Xu, L.1
Gao, K.2
Bao, C.3
Wang, X.4
-
44
-
-
38649112930
-
Zinc-amyloid β interactions on a millisecond time-scale stabilize non-fibrillar Alzheimer-related species
-
Noy D, Solomonov I, Sinkevich O, Arad T, Kjaer K, Sagi I. Zinc-amyloid β interactions on a millisecond time-scale stabilize non-fibrillar Alzheimer-related species. J Am Chem Soc 2008;130:1376-1383.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 1376-1383
-
-
Noy, D.1
Solomonov, I.2
Sinkevich, O.3
Arad, T.4
Kjaer, K.5
Sagi, I.6
-
45
-
-
84888354585
-
Effects of Zn2+binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1or Glu11?
-
Xu L, Wang X, Wang X. Effects of Zn2+binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1or Glu11? ACS Chem Neurosci 2013;4:1458-1468.
-
(2013)
ACS Chem Neurosci
, vol.4
, pp. 1458-1468
-
-
Xu, L.1
Wang, X.2
Wang, X.3
-
46
-
-
77953113490
-
Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states
-
Miller Y, Ma B, Nussinov R. Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states Proc Natl Acad Sci USA 2010;107:9490-9495.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 9490-9495
-
-
Miller, Y.1
Ma, B.2
Nussinov, R.3
-
47
-
-
2542424288
-
Novel amyloid precursor protein gene missense mutation (D678N) in probable familial Alzheimer's disease
-
Wakutani Y, Watanabe K, Adachi Y, Wada-Isoe K, Urakami K, Ninomiya H, Saido TC, Hashimoto T, Iwatsubo T, Nakashima K. Novel amyloid precursor protein gene missense mutation (D678N) in probable familial Alzheimer's disease. J Neurol Neurosurg Psychiatry 2004;75:1039-1042.
-
(2004)
J Neurol Neurosurg Psychiatry
, vol.75
, pp. 1039-1042
-
-
Wakutani, Y.1
Watanabe, K.2
Adachi, Y.3
Wada-Isoe, K.4
Urakami, K.5
Ninomiya, H.6
Saido, T.C.7
Hashimoto, T.8
Iwatsubo, T.9
Nakashima, K.10
-
48
-
-
0037469171
-
Early onset familial Alzheimer's disease-mutation frequency in 31 families
-
Janssen JC, Beck JA, Campbell TA, Dickinson A, Fox NC, Harvey RJ, Houlden H, Rossor MN, Collinge J. Early onset familial Alzheimer's disease-mutation frequency in 31 families. Neurology 2003;60:235-239.
-
(2003)
Neurology
, vol.60
, pp. 235-239
-
-
Janssen, J.C.1
Beck, J.A.2
Campbell, T.A.3
Dickinson, A.4
Fox, N.C.5
Harvey, R.J.6
Houlden, H.7
Rossor, M.N.8
Collinge, J.9
-
49
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
-
(1999)
Chem Phys Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
50
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 2001;60:96-123.
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
51
-
-
33947505097
-
The Tottori (D7N) and English (H6R) familial Alzheimer disease mutations accelerate A beta fibril formation without increasing protofibril formation
-
Hori Y, Hashimoto T, Wakutani Y, Urakami K, Nakashima K, Condron MM, Tsubuki S, Saido TC, Teplow DB, Iwatsubo T. The Tottori (D7N) and English (H6R) familial Alzheimer disease mutations accelerate A beta fibril formation without increasing protofibril formation. J Biol Chem 2007;282:4916-4923.
-
(2007)
J Biol Chem
, vol.282
, pp. 4916-4923
-
-
Hori, Y.1
Hashimoto, T.2
Wakutani, Y.3
Urakami, K.4
Nakashima, K.5
Condron, M.M.6
Tsubuki, S.7
Saido, T.C.8
Teplow, D.B.9
Iwatsubo, T.10
-
52
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.H.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
53
-
-
77953976984
-
An MM/3D-RISM approach for ligand binding affinities
-
Genheden S, Luchko T, Gusarov S, Kovalenko A, Ryde U. An MM/3D-RISM approach for ligand binding affinities. J Phys Chem B 2010;114:8505-8516.
-
(2010)
J Phys Chem B
, vol.114
, pp. 8505-8516
-
-
Genheden, S.1
Luchko, T.2
Gusarov, S.3
Kovalenko, A.4
Ryde, U.5
-
54
-
-
32344451179
-
The α-to-β conformational transition of Alzheimer's Aβ(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of β conformation seeding
-
Tomaselli S, Esposito V, Vangone P, van Nuland NA, Bonvin AM, Guerrini R, Tancredi T, Temussi PA, Picone D. The α-to-β conformational transition of Alzheimer's Aβ(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of β conformation seeding. ChemBioChem 2006;7:257-267.
-
(2006)
ChemBioChem
, vol.7
, pp. 257-267
-
-
Tomaselli, S.1
Esposito, V.2
Vangone, P.3
van Nuland, N.A.4
Bonvin, A.M.5
Guerrini, R.6
Tancredi, T.7
Temussi, P.A.8
Picone, D.9
-
56
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006;65:712-725.
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
57
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 2004;55:383-394.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
58
-
-
36749079289
-
Linking folding with aggregation in Alzheimer's β-amyloid peptides
-
Khandogin J, Brooks CL, 3rd. Linking folding with aggregation in Alzheimer's β-amyloid peptides. Proc Natl Acad Sci USA 2007;104:16880-16885.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 16880-16885
-
-
Khandogin, J.1
Brooks, C.L.2
-
59
-
-
84878079536
-
Single point mutation alters the microstate dynamics of amyloid β-protein Aβ42 as revealed by dihedral dynamics analyses
-
Xu L, Shan S, Wang X. Single point mutation alters the microstate dynamics of amyloid β-protein Aβ42 as revealed by dihedral dynamics analyses. J Phys Chem B 2013;117:6206-6216.
-
(2013)
J Phys Chem B
, vol.117
, pp. 6206-6216
-
-
Xu, L.1
Shan, S.2
Wang, X.3
-
61
-
-
0038407231
-
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
-
Neal S, Nip AM, Zhang H, Wishart DS. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 2003;26:215-240.
-
(2003)
J Biomol NMR
, vol.26
, pp. 215-240
-
-
Neal, S.1
Nip, A.M.2
Zhang, H.3
Wishart, D.S.4
-
62
-
-
10744219665
-
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
-
Hou L, Shao H, Zhang Y, Li H, Menon NK, Neuhaus EB, Brewer JM, Byeon IJ, Ray DG, Vitek MP, Iwashita T, Makula RA, Przybyla AB, Zagorski MG. 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. J Am Chem Soc 2004;126:1992-2005.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 1992-2005
-
-
Hou, L.1
Shao, H.2
Zhang, Y.3
Li, H.4
Menon, N.K.5
Neuhaus, E.B.6
Brewer, J.M.7
Byeon, I.J.8
Ray, D.G.9
Vitek, M.P.10
Iwashita, T.11
Makula, R.A.12
Przybyla, A.B.13
Zagorski, M.G.14
-
63
-
-
33750014578
-
A criterion for orbital hybridization and charge distribution in chemical bonds
-
Karplus M, Grant DM. A criterion for orbital hybridization and charge distribution in chemical bonds. Proc Natl Acad Sci USA 1959;45:1269-1273.
-
(1959)
Proc Natl Acad Sci USA
, vol.45
, pp. 1269-1273
-
-
Karplus, M.1
Grant, D.M.2
-
64
-
-
12044259775
-
α coupling constants in 15N-enriched proteins
-
α coupling constants in 15N-enriched proteins. J Am Chem Soc 1993;115:7772-7777.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 7772-7777
-
-
Vuister, G.W.1
Bax, A.2
-
65
-
-
42949166112
-
M35 oxidation induces Aβ40-like structural and dynamical changes in Aβ42
-
Yan Y, McCallum SA, Wang C. M35 oxidation induces Aβ40-like structural and dynamical changes in Aβ42. J Am Chem Soc 2008;130:5394-5395.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 5394-5395
-
-
Yan, Y.1
McCallum, S.A.2
Wang, C.3
-
66
-
-
84937602381
-
-
III TEC, AMBER12. San Francisco, CA: University of California; 2012.
-
Case DA, Darden TA, III TEC, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, A. Roitberg, Seabra G, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA. AMBER12. San Francisco, CA: University of California; 2012.
-
-
-
Case, D.A.1
Darden, T.A.2
Simmerling, C.L.3
Wang, J.4
Duke, R.E.5
Luo, R.6
Walker, R.C.7
Zhang, W.8
Merz, K.M.9
Roberts, B.10
Hayik, S.11
Roitberg, A.12
Seabra, G.13
Swails, J.14
Goetz, A.W.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wolf, R.M.20
Liu, J.21
Wu, X.22
Brozell, S.R.23
Steinbrecher, T.24
Gohlke, H.25
Cai, Q.26
Ye, X.27
Wang, J.28
Hsieh, M.-J.29
Cui, G.30
Roe, D.R.31
Mathews, D.H.32
Seetin, M.G.33
Salomon-Ferrer, R.34
Sagui, C.35
Babin, V.36
Luchko, T.37
Gusarov, S.38
Kovalenko, A.39
Kollman, P.A.40
more..
-
67
-
-
0001324288
-
Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model
-
Kovalenko A, Hirata F. Self-consistent description of a metal-water interface by the Kohn-Sham density functional theory and the three-dimensional reference interaction site model. J Chem Phys 1999;110:10095.
-
(1999)
J Chem Phys
, vol.110
, pp. 10095
-
-
Kovalenko, A.1
Hirata, F.2
-
68
-
-
0033691158
-
Potentials of mean force of simple ions in ambient aqueous solution I Three-dimensional reference interaction site model approach
-
Kovalenko A, Hirata F. Potentials of mean force of simple ions in ambient aqueous solution I Three-dimensional reference interaction site model approach. J Chem Phys 2000;112:10391.
-
(2000)
J Chem Phys
, vol.112
, pp. 10391
-
-
Kovalenko, A.1
Hirata, F.2
-
69
-
-
79952360229
-
Configurational entropy of protein: A combined approach based on molecular simulation and integral-equation theory of liquids
-
Chong S-H, Ham S. Configurational entropy of protein: A combined approach based on molecular simulation and integral-equation theory of liquids. Chem Phys Lett 2011;504:225-229.
-
(2011)
Chem Phys Lett
, vol.504
, pp. 225-229
-
-
Chong, S.-H.1
Ham, S.2
-
70
-
-
84877694532
-
Conformational entropy of intrinsically disordered protein
-
Chong S-H, Ham S. Conformational entropy of intrinsically disordered protein. J Phys Chem B 2013;117:5503-5509.
-
(2013)
J Phys Chem B
, vol.117
, pp. 5503-5509
-
-
Chong, S.-H.1
Ham, S.2
-
71
-
-
84861217855
-
Impact of chemical heterogeneity on protein self-assembly in water
-
Chong SH, Ham S. Impact of chemical heterogeneity on protein self-assembly in water. Proc Natl Acad Sci USA 2012;109:7636-7641.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 7636-7641
-
-
Chong, S.H.1
Ham, S.2
-
72
-
-
84878960082
-
Characterization of the internal dynamics and conformational space of zinc-bound amyloid beta peptides by replica-exchange molecular dynamics simulations
-
Xu L, Wang XJ, Wang XC. Characterization of the internal dynamics and conformational space of zinc-bound amyloid beta peptides by replica-exchange molecular dynamics simulations. Eur Biophys J 2013;42:575-586.
-
(2013)
Eur Biophys J
, vol.42
, pp. 575-586
-
-
Xu, L.1
Wang, X.J.2
Wang, X.C.3
-
73
-
-
84881666267
-
Buried and accessible surface area control intrinsic protein flexibility
-
Marsh JA. Buried and accessible surface area control intrinsic protein flexibility. J Mol Biol 2013;425:3250-3263.
-
(2013)
J Mol Biol
, vol.425
, pp. 3250-3263
-
-
Marsh, J.A.1
-
74
-
-
79958093841
-
Relative solvent accessible surface area predicts protein conformational changes upon binding
-
Marsh Joseph A, Teichmann Sarah A. Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure 2011;19:859-867.
-
(2011)
Structure
, vol.19
, pp. 859-867
-
-
Marsh Joseph, A.1
Teichmann Sarah, A.2
-
75
-
-
0033556236
-
Peptide folding: when simulation meets experiment
-
Daura X, Gademann K, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Peptide folding: when simulation meets experiment. Angew Chem Int Ed 1999;38:236-240.
-
(1999)
Angew Chem Int Ed
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
van Gunsteren, W.F.5
Mark, A.E.6
-
76
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
77
-
-
46749127364
-
Are current molecular dynamics force fields too helical?
-
Best RB, Buchete N-V, Hummer G. Are current molecular dynamics force fields too helical? Biophys J 2008;95:L07-L09.
-
(2008)
Biophys J
, vol.95
, pp. L07-L09
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
78
-
-
79955622216
-
Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16-22 dimer and trimer
-
Nguyen PH, Li MS, Derreumaux P. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16-22 dimer and trimer. Phys Chem Chem Phys 2011;13:9778-9788.
-
(2011)
Phys Chem Chem Phys
, vol.13
, pp. 9778-9788
-
-
Nguyen, P.H.1
Li, M.S.2
Derreumaux, P.3
-
79
-
-
0033855845
-
The Alzheimer's peptide Aβ adopts a collapsed coil structure in water
-
Zhang S, Iwata K, Lachenmann MJ, Peng JW, Li S, Stimson ER, Lu YA, Felix AM, Maggio JE, Lee JP. The Alzheimer's peptide Aβ adopts a collapsed coil structure in water. J Struct Biol 2000;130:130-141.
-
(2000)
J Struct Biol
, vol.130
, pp. 130-141
-
-
Zhang, S.1
Iwata, K.2
Lachenmann, M.J.3
Peng, J.W.4
Li, S.5
Stimson, E.R.6
Lu, Y.A.7
Felix, A.M.8
Maggio, J.E.9
Lee, J.P.10
-
80
-
-
84884507134
-
A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms
-
Camilloni C, Vendruscolo M. A relationship between the aggregation rates of α-synuclein variants and the β-sheet populations in their monomeric forms. J Phys Chem B 2013;117:10737-10741.
-
(2013)
J Phys Chem B
, vol.117
, pp. 10737-10741
-
-
Camilloni, C.1
Vendruscolo, M.2
-
81
-
-
84901786895
-
Gly25-Ser26 amyloid β-protein structural isomorphs produce distinct Aβ42 conformational dynamics and assembly characteristics
-
Roychaudhuri R, Lomakin A, Bernstein S, Zheng X, Condron MM, Benedek GB, Bowers M, Teplow DB. Gly25-Ser26 amyloid β-protein structural isomorphs produce distinct Aβ42 conformational dynamics and assembly characteristics. J Mol Biol 2014;426:2422-2441.
-
(2014)
J Mol Biol
, vol.426
, pp. 2422-2441
-
-
Roychaudhuri, R.1
Lomakin, A.2
Bernstein, S.3
Zheng, X.4
Condron, M.M.5
Benedek, G.B.6
Bowers, M.7
Teplow, D.B.8
-
82
-
-
84874091627
-
The Structures of the E22X mutant-type amyloid-β alloforms and the impact of E22Δ mutation on the structures of the wild-type amyloid-β alloforms
-
Coskuner O, Wise-Scira O, Perry G, Kitahara T. The Structures of the E22X mutant-type amyloid-β alloforms and the impact of E22Δ mutation on the structures of the wild-type amyloid-β alloforms. ACS Chem Neurosci 2013;4:310-320.
-
(2013)
ACS Chem Neurosci
, vol.4
, pp. 310-320
-
-
Coskuner, O.1
Wise-Scira, O.2
Perry, G.3
Kitahara, T.4
-
83
-
-
46849090552
-
Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid β-protein
-
Krone MG, Baumketner A, Bernstein SL, Wyttenbach T, Lazo ND, Teplow DB, Bowers MT, Shea J-E. Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid β-protein. J Mol Biol 2008;381:221-228.
-
(2008)
J Mol Biol
, vol.381
, pp. 221-228
-
-
Krone, M.G.1
Baumketner, A.2
Bernstein, S.L.3
Wyttenbach, T.4
Lazo, N.D.5
Teplow, D.B.6
Bowers, M.T.7
Shea, J.-E.8
-
84
-
-
67849095816
-
Effects of the Arctic (E22→G) mutation on amyloid β-protein folding: discrete molecular dynamics study
-
Lam AR, Teplow DB, Stanley HE, Urbanc B. Effects of the Arctic (E22→G) mutation on amyloid β-protein folding: discrete molecular dynamics study. J Am Chem Soc 2008;130:17413-17422.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 17413-17422
-
-
Lam, A.R.1
Teplow, D.B.2
Stanley, H.E.3
Urbanc, B.4
-
85
-
-
80051658781
-
Distinct morphologies for amyloid beta protein monomer: Aβ1-40, Aβ1-42, and Aβ1-40(D23N)
-
Côté S, Derreumaux P, Mousseau N. Distinct morphologies for amyloid beta protein monomer: Aβ1-40, Aβ1-42, and Aβ1-40(D23N). J Chem Theory Comput 2011;7:2584-2592.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2584-2592
-
-
Côté, S.1
Derreumaux, P.2
Mousseau, N.3
-
86
-
-
84862909284
-
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer
-
Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J 2012;102:315-324.
-
(2012)
Biophys J
, vol.102
, pp. 315-324
-
-
Lin, Y.S.1
Bowman, G.R.2
Beauchamp, K.A.3
Pande, V.S.4
-
87
-
-
84871347622
-
Effects of familial mutations on the monomer structure of Aβ42
-
Lin Y-S, Pande VS. Effects of familial mutations on the monomer structure of Aβ42. Biophys J 2012;103:L47-L49.
-
(2012)
Biophys J
, vol.103
, pp. L47-L49
-
-
Lin, Y.-S.1
Pande, V.S.2
-
88
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5:789-796.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
89
-
-
44849096899
-
Identifying the minimal copper- and zinc-binding site sequence in amyloid-β peptides
-
Minicozzi V, Stellato F, Comai M, Dalla Serra M, Potrich C, Meyer-Klaucke W, Morante S. Identifying the minimal copper- and zinc-binding site sequence in amyloid-β peptides. J Biol Chem 2008;283:10784-10792.
-
(2008)
J Biol Chem
, vol.283
, pp. 10784-10792
-
-
Minicozzi, V.1
Stellato, F.2
Comai, M.3
Dalla Serra, M.4
Potrich, C.5
Meyer-Klaucke, W.6
Morante, S.7
-
90
-
-
84874330804
-
Bapineuzumab captures the N-terminus of the Alzheimer's disease amyloid-beta peptide in a helical conformation
-
Miles LA, Crespi GAN, Doughty L, Parker MW. Bapineuzumab captures the N-terminus of the Alzheimer's disease amyloid-beta peptide in a helical conformation. Sci Rep 2013;3:1302.
-
(2013)
Sci Rep
, vol.3
, pp. 1302
-
-
Miles, L.A.1
Crespi, G.A.N.2
Doughty, L.3
Parker, M.W.4
|