-
1
-
-
33750361540
-
A century‐old debate on protein aggregation and neurodegeneration enters the clinic
-
1 Lansbury PT, Jr, Lashuel HA. A century‐old debate on protein aggregation and neurodegeneration enters the clinic. Nature 2006 ; 443: 774–779.
-
(2006)
Nature
, vol.443
, pp. 774-779
-
-
Lansbury, PT1
Lashuel, HA2
-
2
-
-
33749832945
-
Elucidating amyloid β‐protein folding and asembly: a multidisciplinary approach
-
2 Teplow DB, Lazo ND, Bitan G, Bernstein S, Wyttenbach T, Bowers MT, Baumketner A, Shea JE, Urbanc B, Cruz L, Borreguero J, Stanley HE. Elucidating amyloid β‐protein folding and asembly: a multidisciplinary approach. Acc Chem Res 2006 ; 39: 635–645.
-
(2006)
Acc Chem Res
, vol.39
, pp. 635-645
-
-
Teplow, DB1
Lazo, ND2
Bitan, G3
Bernstein, S4
Wyttenbach, T5
Bowers, MT6
Baumketner, A7
Shea, JE8
Urbanc, B9
Cruz, L10
Borreguero, J11
Stanley, HE12
-
3
-
-
33645038471
-
A specific amyloid‐β protein assembly in the brain impairs memory
-
3 Lesné S, Koh MT, Kotilinek L, Kayed R, Glabe CG, Yang A, Gallagher M, Ashe KH. A specific amyloid‐β protein assembly in the brain impairs memory. Nature 2006 ; 440: 352–356.
-
(2006)
Nature
, vol.440
, pp. 352-356
-
-
Lesné, S1
Koh, MT2
Kotilinek, L3
Kayed, R4
Glabe, CG5
Yang, A6
Gallagher, M7
Ashe, KH8
-
4
-
-
1642433249
-
High‐resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy
-
4 Jaroniec CP, MacPhee CE, Bajaj VS, McMahon MT, Dobson CM, Griffin RG. High‐resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. Proc Natl Acad Sci USA 2004 ; 101: 711–716.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 711-716
-
-
Jaroniec, CP1
MacPhee, CE2
Bajaj, VS3
McMahon, MT4
Dobson, CM5
Griffin, RG6
-
5
-
-
28444442999
-
3D structure of Alzheimers amyloid‐(1‐42) fibrils
-
5 Luehrs T, Ritter C, Adrian M, Riek‐Loher D, Bohrmann B, Döbeli H, Schubert D, Riek R. 3D structure of Alzheimers amyloid‐(1‐42) fibrils. Proc Natl Acad Sci USA 2005 ; 102: 17342–17347.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 17342-17347
-
-
Luehrs, T1
Ritter, C2
Adrian, M3
Riek‐Loher, D4
Bohrmann, B5
Döbeli, H6
Schubert, D7
Riek, R8
-
6
-
-
20444440728
-
Structure of the cross‐β spine of amyloid‐like fibrils
-
6 Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross‐β spine of amyloid‐like fibrils. Nature 2005 ; 435: 773–778.
-
(2005)
Nature
, vol.435
, pp. 773-778
-
-
Nelson, R1
Sawaya, MR2
Balbirnie, M3
Madsen, AØ4
Riekel, C5
Grothe, R6
Eisenberg, D7
-
7
-
-
12244285938
-
Molecular basis for amyloid fibril formation and stability
-
7 Makin OS, Atkins E, Sikorski P, Johansson J, Serpell LC. Molecular basis for amyloid fibril formation and stability. Proc Natl Acad Sci USA 2005 ; 102: 315–320.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 315-320
-
-
Makin, OS1
Atkins, E2
Sikorski, P3
Johansson, J4
Serpell, LC5
-
8
-
-
33750365052
-
Are amyloid diseases caused by protein aggregates that mimic bacterial pore‐forming toxins?
-
8 Lashuel HA, Lansbury PT, Jr. Are amyloid diseases caused by protein aggregates that mimic bacterial pore‐forming toxins? Q Rev Biophys 2006 ; 39: 167–201.
-
(2006)
Q Rev Biophys
, vol.39
, pp. 167-201
-
-
Lashuel, HA1
Lansbury, PT2
-
9
-
-
0028670272
-
Beta‐amyloid Ca2+‐channel hypothesis for neuronal death in Alzheimer disease
-
9 Arispe N, Pollard HB, Rojas E. Beta‐amyloid Ca 2+ ‐channel hypothesis for neuronal death in Alzheimer disease. Mol Cell Biochem 1994 ; 140: 119–125.
-
(1994)
Mol Cell Biochem
, vol.140
, pp. 119-125
-
-
Arispe, N1
Pollard, HB2
Rojas, E3
-
10
-
-
0034649352
-
Amyloid fibril formation by Aβ16–22, a seven‐residue fragment of the Alzheimer's β‐amyloid peptide, and structural characterization by solid state NMR
-
10 Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Amyloid fibril formation by Aβ 16–22, a seven‐residue fragment of the Alzheimer's β‐amyloid peptide, and structural characterization by solid state NMR. Biochemistry 2000 ; 39: 13748–13759.
-
(2000)
Biochemistry
, vol.39
, pp. 13748-13759
-
-
Balbach, JJ1
Ishii, Y2
Antzutkin, ON3
Leapman, RD4
Rizzo, NW5
Dyda, F6
Reed, J7
Tycko, R8
-
11
-
-
0346057932
-
Increasing the amphiphilicity of an amyloidogenic peptide changes the β‐sheet structure in the fibrils from antiparallel to parallel
-
11 Gordon DJ, Balbach JJ, Tycko R, Meredith SC. Increasing the amphiphilicity of an amyloidogenic peptide changes the β‐sheet structure in the fibrils from antiparallel to parallel. Biophys J 2004 ; 86: 428–434.
-
(2004)
Biophys J
, vol.86
, pp. 428-434
-
-
Gordon, DJ1
Balbach, JJ2
Tycko, R3
Meredith, SC4
-
12
-
-
25844493690
-
Experimental evidence for the reorganization of β‐strands within aggregates of the Aβ16–22 peptide
-
12 Petty SA, Decatur SM. Experimental evidence for the reorganization of β‐strands within aggregates of the Aβ 16–22 peptide. J Am Chem Soc 2005 ; 127: 13488–13489.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 13488-13489
-
-
Petty, SA1
Decatur, SM2
-
13
-
-
0029994633
-
Arrest of β‐amyloid fibril formation by pentapeptide ligand
-
13 Tjernberg LO, Näslund J, Lindqvist F, Johansson J, Karlström AR, Thyberg J, Terenius L, Nordstedt C. Arrest of β‐amyloid fibril formation by pentapeptide ligand. J Biol Chem 1996 ; 271: 8545–8548.
-
(1996)
J Biol Chem
, vol.271
, pp. 8545-8548
-
-
Tjernberg, LO1
Näslund, J2
Lindqvist, F3
Johansson, J4
Karlström, AR5
Thyberg, J6
Terenius, L7
Nordstedt, C8
-
14
-
-
0037195098
-
Stabilities and conformations of Alzheimer's β‐amyloid peptide oligomers (Aβ16–22, Aβ16–35, and Aβ10–35): sequence effects
-
14 Ma B, Nussinov R. Stabilities and conformations of Alzheimer's β‐amyloid peptide oligomers (Aβ 16–22, Aβ 16–35, and Aβ 10–35): sequence effects. Proc Natl Acad Sci USA 2002 ; 99: 14126–14131.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 14126-14131
-
-
Ma, B1
Nussinov, R2
-
15
-
-
0037337271
-
Dissecting the assembly of Aβ16–22 amyloid peptides into antiparallel β sheets
-
15 Klimov DK, Thirumalai D. Dissecting the assembly of Aβ 16–22 amyloid peptides into antiparallel β sheets. Structure 2003 ; 11: 295–307.
-
(2003)
Structure
, vol.11
, pp. 295-307
-
-
Klimov, DK1
Thirumalai, D2
-
16
-
-
10044227276
-
Oligomerization of amyloid Aβ16–22 peptides using hydrogen bonds and hydrophobicity forces
-
16 Favrin G, Irbäck A, Mohanty S. Oligomerization of amyloid Aβ 16–22 peptides using hydrogen bonds and hydrophobicity forces. Biophys J 2004 ; 87: 3657–3664.
-
(2004)
Biophys J
, vol.87
, pp. 3657-3664
-
-
Favrin, G1
Irbäck, A2
Mohanty, S3
-
17
-
-
4544283591
-
In silico assembly of Alzheimer's Aβ16–22 peptide into β‐sheets
-
17 Santini S, Mousseau N, Derreumaux P. In silico assembly of Alzheimer's Aβ 16–22 peptide into β‐sheets. J Am Chem Soc 2004 ; 126: 11509–11516.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 11509-11516
-
-
Santini, S1
Mousseau, N2
Derreumaux, P3
-
18
-
-
4444346811
-
Kinetic control of dimer structure formation in amyloid fibrillogenesis
-
18 Hwang W, Zhang S, Kamm RD, Karplus M. Kinetic control of dimer structure formation in amyloid fibrillogenesis. Proc Natl Acad Sci USA 2004 ; 101: 12916–12921.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 12916-12921
-
-
Hwang, W1
Zhang, S2
Kamm, RD3
Karplus, M4
-
19
-
-
6944241424
-
Aqeous urea solution destabilizes Aβ16–22 oligomers
-
19 Klimov DK, Straub JE, Thirumalai D. Aqeous urea solution destabilizes Aβ 16–22 oligomers. Proc Natl Acad Sci USA 2004 ; 101: 14760–14765.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 14760-14765
-
-
Klimov, DK1
Straub, JE2
Thirumalai, D3
-
20
-
-
33751248251
-
Stability and structure of oligomers of the Alzheimer peptide Aβ16–22: from the dimer to the 32‐mer
-
20 Röhrig UF, Laio A, Tantalo N, Parrinello M, Petronzio R. Stability and structure of oligomers of the Alzheimer peptide Aβ 16–22: from the dimer to the 32‐mer. Biophys J 2006 ; 91: 3217–3229.
-
(2006)
Biophys J
, vol.91
, pp. 3217-3229
-
-
Röhrig, UF1
Laio, A2
Tantalo, N3
Parrinello, M4
Petronzio, R5
-
21
-
-
33846088432
-
Aggregation of β‐amyloid fragments
-
21 Meinke JH, Hansmann UHE. Aggregation of β‐amyloid fragments. J Chem Phys 2007 ; 126: 014706.
-
(2007)
J Chem Phys
, vol.126
, pp. 014706
-
-
Meinke, JH1
Hansmann, UHE2
-
22
-
-
33846036362
-
Monomer adds to preformed structured oligomers of Aβ‐peptides by a two‐stage dock‐lock mechanism
-
22 Nguyen PH, Li MS, Stock G, Straub JE, Thirumalai D. Monomer adds to preformed structured oligomers of Aβ‐peptides by a two‐stage dock‐lock mechanism. Proc Natl Acad Sci USA 2007 ; 104: 111–116.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 111-116
-
-
Nguyen, PH1
Li, MS2
Stock, G3
Straub, JE4
Thirumalai, D5
-
23
-
-
33644536691
-
Atomic‐level description of amyloid β‐dimer formation
-
23 Gnanakaran S, Nussinov R, García AE. Atomic‐level description of amyloid β‐dimer formation. J Am Chem Soc 2006 ; 128: 2158–2159.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 2158-2159
-
-
Gnanakaran, S1
Nussinov, R2
García, AE3
-
24
-
-
1942470951
-
Self‐assembly of peptides into a β‐barrel motif
-
24 Friedel M ; Shea JE. Self‐assembly of peptides into a β‐barrel motif. J Chem Phys 2004 ; 120: 5809–5823.
-
(2004)
J Chem Phys
, vol.120
, pp. 5809-5823
-
-
Friedel, M1
Shea, JE2
-
25
-
-
33747032067
-
Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides
-
25 Marchut AJ, Hall CK. Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides. Comput Biol Chem 2006 ; 30: 215–218.
-
(2006)
Comput Biol Chem
, vol.30
, pp. 215-218
-
-
Marchut, AJ1
Hall, CK2
-
26
-
-
10044289451
-
Sampling the self‐assembly pathways of KFFE hexamers
-
26 Wei G, Mousseau N, Derreumaux P. Sampling the self‐assembly pathways of KFFE hexamers. Biophys J 2004 ; 87: 3648–3656.
-
(2004)
Biophys J
, vol.87
, pp. 3648-3656
-
-
Wei, G1
Mousseau, N2
Derreumaux, P3
-
27
-
-
33748278029
-
Structures of soluble amyloid oligomers from computer simulations
-
27 Melquiond A, Mousseau N, Derreumaux P. Structures of soluble amyloid oligomers from computer simulations. Proteins 2006 ; 65: 180–191.
-
(2006)
Proteins
, vol.65
, pp. 180-191
-
-
Melquiond, A1
Mousseau, N2
Derreumaux, P3
-
28
-
-
33748689799
-
Simulations as analytical tools to understand protein aggregation and predict amyloid formation
-
28 Ma B, Nussinov R. Simulations as analytical tools to understand protein aggregation and predict amyloid formation. Curr Opin Chem Biol 2006 ; 10: 1–8.
-
(2006)
Curr Opin Chem Biol
, vol.10
, pp. 1-8
-
-
Ma, B1
Nussinov, R2
-
29
-
-
33645513980
-
Theoretical approaches to protein aggregation
-
29 Gsponer J, Vendruscolo M. Theoretical approaches to protein aggregation. Protein Pept Lett 2006 ; 13: 287–293.
-
(2006)
Protein Pept Lett
, vol.13
, pp. 287-293
-
-
Gsponer, J1
Vendruscolo, M2
-
30
-
-
0041629626
-
Thermodynamics of α‐ and β‐structure formation in proteins
-
30 Irbäck A, Samuelsson B, Sjunnesson F, Wallin S. Thermodynamics of α‐ and β‐structure formation in proteins. Biophys J 2003 ; 85: 1466–1473.
-
(2003)
Biophys J
, vol.85
, pp. 1466-1473
-
-
Irbäck, A1
Samuelsson, B2
Sjunnesson, F3
Wallin, S4
-
31
-
-
21244495332
-
Folding thermodynamics of peptides
-
31 Irbäck A, Mohanty S. Folding thermodynamics of peptides. Biophys J 2005 ; 88: 1560–1569.
-
(2005)
Biophys J
, vol.88
, pp. 1560-1569
-
-
Irbäck, A1
Mohanty, S2
-
32
-
-
26444577856
-
Dissecting the mechanical unfolding of ubiquitin
-
32 Irbäck A, Mitternacht S, Mohanty S. Dissecting the mechanical unfolding of ubiquitin. Proc Natl Acad Sci USA 2005 ; 102: 13427–13432.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13427-13432
-
-
Irbäck, A1
Mitternacht, S2
Mohanty, S3
-
33
-
-
33750073182
-
Thermal versus mechanical unfolding of ubiquitin
-
33 Irbäck A, Mitternacht S. Thermal versus mechanical unfolding of ubiquitin. Proteins 2006 ; 65: 759–766.
-
(2006)
Proteins
, vol.65
, pp. 759-766
-
-
Irbäck, A1
Mitternacht, S2
-
35
-
-
84953648015
-
New approach to Monte Carlo calculation of the free energy: method of expanded ensembles
-
35 Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov‐Velyaminov PN. New approach to Monte Carlo calculation of the free energy: method of expanded ensembles. J Chem Phys 1992 ; 96: 1776–1783.
-
(1992)
J Chem Phys
, vol.96
, pp. 1776-1783
-
-
Lyubartsev, AP1
Martsinovski, AA2
Shevkunov, SV3
Vorontsov‐Velyaminov, PN4
-
36
-
-
33644899039
-
Simulated tempering: a new Monte Carlo scheme
-
36 Marinari E, Parisi G. Simulated tempering: a new Monte Carlo scheme. Europhys Lett 1992 ; 19: 451–458.
-
(1992)
Europhys Lett
, vol.19
, pp. 451-458
-
-
Marinari, E1
Parisi, G2
-
37
-
-
0000773431
-
Studies of an off‐lattice model for protein folding: sequence dependence and improved sampling at finite temperature
-
37 Irbäck A, Potthast F. Studies of an off‐lattice model for protein folding: sequence dependence and improved sampling at finite temperature. J Chem Phys 1995 ; 103: 10298–10305.
-
(1995)
J Chem Phys
, vol.103
, pp. 10298-10305
-
-
Irbäck, A1
Potthast, F2
-
38
-
-
0039924671
-
Monte Carlo study of the interacting self‐avoiding walk model in three dimensions
-
38 Tesi MC, van Rensburg EJJ, Orlandini E, Whittington SG. Monte Carlo study of the interacting self‐avoiding walk model in three dimensions. J Stat Phys 1996 ; 82: 155–181.
-
(1996)
J Stat Phys
, vol.82
, pp. 155-181
-
-
Tesi, MC1
van Rensburg, EJJ2
Orlandini, E3
Whittington, SG4
-
39
-
-
0030516672
-
Exchange Monte Carlo method and application to spin glass simulations
-
39 Hukushima K, Nemoto K. Exchange Monte Carlo method and application to spin glass simulations. J Phys Soc Jpn 1996 ; 65: 1604–1608.
-
(1996)
J Phys Soc Jpn
, vol.65
, pp. 1604-1608
-
-
Hukushima, K1
Nemoto, K2
-
40
-
-
0031578972
-
Parallel tempering algorithm for conformational studies of biological molecules
-
40 Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 1997 ; 281: 140–150.
-
(1997)
Chem Phys Lett
, vol.281
, pp. 140-150
-
-
Hansmann, UHE1
-
41
-
-
33748604047
-
PROFASI: a Monte Carlo simulation package for protein folding and aggregation
-
41 Irbäck A, Mohanty S. PROFASI: a Monte Carlo simulation package for protein folding and aggregation. J Comput Chem 2006 ; 27: 1548–1555.
-
(2006)
J Comput Chem
, vol.27
, pp. 1548-1555
-
-
Irbäck, A1
Mohanty, S2
-
42
-
-
0035826575
-
Monte Carlo update for chain molecules: biased Gaussian steps in torsional space
-
42 Favrin G, Irbäck A, Sjunnesson F. Monte Carlo update for chain molecules: biased Gaussian steps in torsional space. J Chem Phys 2001 ; 114: 8154–8158.
-
(2001)
J Chem Phys
, vol.114
, pp. 8154-8158
-
-
Favrin, G1
Irbäck, A2
Sjunnesson, F3
-
43
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
43 Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1989 ; 63: 1195–1198.
-
(1989)
Phys Rev Lett
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, AM1
Swendsen, RH2
-
44
-
-
0015971972
-
The jackknife—a review
-
44 Miller, R.G. The jackknife—a review. Biometrika 1974 ; 61: 1–15.
-
(1974)
Biometrika
, vol.61
, pp. 1-15
-
-
Miller, R.G.1
-
45
-
-
0003845223
-
The PyMOL molecular graphics system
-
45 DeLano WL. The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific ; 2002.
-
(2002)
-
-
DeLano, WL1
-
46
-
-
0018350099
-
Gene duplication in the structural evolution of chymotrypsin
-
46 McLachlan AD. Gene duplication in the structural evolution of chymotrypsin. J Mol Biol 1979 ; 128: 49–79.
-
(1979)
J Mol Biol
, vol.128
, pp. 49-79
-
-
McLachlan, AD1
-
47
-
-
85120592111
-
Conformational and geometrical properties of idealized β‐barrels in proteins
-
47 Chou KC, Carlacci L, Maggiora GG. Conformational and geometrical properties of idealized β‐barrels in proteins. J Mol Biol 1990 ; 168: 389–407.
-
(1990)
J Mol Biol
, vol.168
, pp. 389-407
-
-
Chou, KC1
Carlacci, L2
Maggiora, GG3
-
48
-
-
0028348081
-
Principles determining the structure of β‐sheet barrels in proteins. I. A theoretical analysis
-
48 Murzin AG, Lesk AM, Chothia C. Principles determining the structure of β‐sheet barrels in proteins. I. A theoretical analysis. J Mol Biol 1994 ; 236: 1369–1381.
-
(1994)
J Mol Biol
, vol.236
, pp. 1369-1381
-
-
Murzin, AG1
Lesk, AM2
Chothia, C3
-
49
-
-
0028330220
-
Principles determining the structure of β‐sheet barrels in proteins. II. The observed structures
-
49 Murzin AG, Lesk AM, Chothia C. Principles determining the structure of β‐sheet barrels in proteins. II. The observed structures. J Mol Biol 1994 ; 236: 1382–1400.
-
(1994)
J Mol Biol
, vol.236
, pp. 1382-1400
-
-
Murzin, AG1
Lesk, AM2
Chothia, C3
-
50
-
-
0032579317
-
Shear numbers of protein β‐barrels: definition refinements and statistics
-
50 Liu WM. Shear numbers of protein β‐barrels: definition refinements and statistics. J Mol Biol 1998 ; 275: 541–545.
-
(1998)
J Mol Biol
, vol.275
, pp. 541-545
-
-
Liu, WM1
-
51
-
-
33845958636
-
Encapsulation and NMR on an aggregating peptide before fibrillogenesis
-
51 Lazar KL, Kurutz JW, Tycko R, Meredith SC. Encapsulation and NMR on an aggregating peptide before fibrillogenesis. J Am Chem Soc 2006 ; 128: 16460–16461.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 16460-16461
-
-
Lazar, KL1
Kurutz, JW2
Tycko, R3
Meredith, SC4
-
52
-
-
8844247180
-
Mechanism of prion propagation: amyloid growth occurs by monomer addition
-
52 Collins SR, Douglas A, Vale RD, Weissman JS. Mechanism of prion propagation: amyloid growth occurs by monomer addition. PLoS Biol 2004 ; 2: 1582–1590.
-
(2004)
PLoS Biol
, vol.2
, pp. 1582-1590
-
-
Collins, SR1
Douglas, A2
Vale, RD3
Weissman, JS4
|