-
1
-
-
34548729144
-
Ranking the factors that contribute to protein β-sheet folding
-
Parisien M, Major F. Ranking the factors that contribute to protein β-sheet folding. Proteins 2007; 68: 824-829.
-
(2007)
Proteins
, vol.68
, pp. 824-829
-
-
Parisien, M.1
Major, F.2
-
2
-
-
0027998757
-
Context is a major determinant of β-sheet propensity
-
Minor DL, Kim PS. Context is a major determinant of β-sheet propensity. Nature 1994; 371: 264-267.
-
(1994)
Nature
, vol.371
, pp. 264-267
-
-
Minor, D.L.1
Kim, P.S.2
-
3
-
-
4644264473
-
Alanine-scanning mutagenesis of the b-sheet region of T4 lysozyme suggests that tertiary context has a dominant effect on β-sheet propensity
-
He MM, Wood ZA, Baase WA, Xiao H, Matthews BM. Alanine-scanning mutagenesis of the b-sheet region of T4 lysozyme suggests that tertiary context has a dominant effect on β-sheet propensity. Protein Sci 2004; 13: 2716-2724.
-
(2004)
Protein Sci
, vol.13
, pp. 2716-2724
-
-
He, M.M.1
Wood, Z.A.2
Baase, W.A.3
Xiao, H.4
Matthews, B.M.5
-
4
-
-
0347357617
-
Protein folding and misfolding
-
Dobson CM. Protein folding and misfolding. Nature 2003; 426: 884-890.
-
(2003)
Nature
, vol.426
, pp. 884-890
-
-
Dobson, C.M.1
-
5
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75: 333-366.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
6
-
-
0042847751
-
Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing
-
Jiménez JL, naki Guijarro JI, Orlova E, Zurdo J, Dobson CM, Sunde M, Saibil HR. Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. EMBO J 1999; 18: 815-821.
-
(1999)
EMBO J
, vol.18
, pp. 815-821
-
-
Jiménez, J.L.1
naki Guijarro, J.I.2
Orlova, E.3
Zurdo, J.4
Dobson, C.M.5
Sunde, M.6
Saibil, H.R.7
-
7
-
-
0033790878
-
Molecular structure of a fibrillar Alzheimer's Aβ fragment
-
Serpell LC, Blake CCF, Fraser PE. Molecular structure of a fibrillar Alzheimer's Aβ fragment. Biochemistry 2000; 39: 13269-13275.
-
(2000)
Biochemistry
, vol.39
, pp. 13269-13275
-
-
Serpell, L.C.1
Blake, C.C.F.2
Fraser, P.E.3
-
8
-
-
20444440728
-
Structure of the cross-beta spine of amyloid-like fibrils
-
Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature 2005; 435: 773-778.
-
(2005)
Nature
, vol.435
, pp. 773-778
-
-
Nelson, R.1
Sawaya, M.R.2
Balbirnie, M.3
Madsen, A.O.4
Riekel, C.5
Grothe, R.6
Eisenberg, D.7
-
9
-
-
73649140576
-
The common architecture of cross-β amyloid
-
Jahn TR, Makin OS, Morris KL, Marshall KE, Tian P, Sikorski P, Serpell LC. The common architecture of cross-β amyloid. J Mol Biol 2010; 395: 717-727.
-
(2010)
J Mol Biol
, vol.395
, pp. 717-727
-
-
Jahn, T.R.1
Makin, O.S.2
Morris, K.L.3
Marshall, K.E.4
Tian, P.5
Sikorski, P.6
Serpell, L.C.7
-
10
-
-
34249290108
-
Atomic structures of amyloid cross-β spines reveal varied steric zippers
-
Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJW, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 2007; 447: 453-457.
-
(2007)
Nature
, vol.447
, pp. 453-457
-
-
Sawaya, M.R.1
Sambashivan, S.2
Nelson, R.3
Ivanova, M.I.4
Sievers, S.A.5
Apostol, M.I.6
Thompson, M.J.7
Balbirnie, M.8
Wiltzius, J.J.W.9
McFarlane, H.T.10
Madsen, A.11
Riekel, C.12
Eisenberg, D.13
-
11
-
-
50049095633
-
Atomic structure of the cross-β spine of Islet Amyloid Polypeptide (Amylin)
-
Wiltzius JJ, Sievers SA, Sawaya MR, Cascio D, Popov D, Riekel C, Eisenberg D. Atomic structure of the cross-β spine of Islet Amyloid Polypeptide (Amylin). Protein Sci 2008; 17: 1467-1474.
-
(2008)
Protein Sci
, vol.17
, pp. 1467-1474
-
-
Wiltzius, J.J.1
Sievers, S.A.2
Sawaya, M.R.3
Cascio, D.4
Popov, D.5
Riekel, C.6
Eisenberg, D.7
-
12
-
-
47249110199
-
The fold of {alpha}-synuclein fibrils
-
Vilar M, Chou HT, Luhrs T, Maji SK, Riek-Loher D, Verel R, Manning G, Stahlberg H, Riek R. The fold of {alpha}-synuclein fibrils. Proc Natl Acad Sci USA 2008; 105: 8637.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 8637
-
-
Vilar, M.1
Chou, H.T.2
Luhrs, T.3
Maji, S.K.4
Riek-Loher, D.5
Verel, R.6
Manning, G.7
Stahlberg, H.8
Riek, R.9
-
13
-
-
0029861772
-
Membrane disruption by Alzheimer beta-amyloid peptides mediated through specific binding to either phospholipids or gangliosides
-
McLaurin JA, Chakrabartty A. Membrane disruption by Alzheimer beta-amyloid peptides mediated through specific binding to either phospholipids or gangliosides. J Biol Chem 1996; 280: 30001-30008.
-
(1996)
J Biol Chem
, vol.280
, pp. 30001-30008
-
-
McLaurin, J.A.1
Chakrabartty, A.2
-
14
-
-
67650325176
-
The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes
-
Hebda JA, Miranker AD. The interplay of catalysis and toxicity by amyloid intermediates on lipid bilayers: insights from type II diabetes. Annu Rev Biophys 2009; 38: 125-152.
-
(2009)
Annu Rev Biophys
, vol.38
, pp. 125-152
-
-
Hebda, J.A.1
Miranker, A.D.2
-
15
-
-
0035800097
-
Vesicle permeabilization by protofibrillar α-synuclein: implications for the pathogenesis and treatment of Parkinson's disease
-
Volles MJ, Lee SJ, Rochet JC, Shtilerman MD, Ding TT, Kessler JC, Lansbury PT, Jr. Vesicle permeabilization by protofibrillar α-synuclein: implications for the pathogenesis and treatment of Parkinson's disease. Biochemistry 2001; 40: 7812-7819.
-
(2001)
Biochemistry
, vol.40
, pp. 7812-7819
-
-
Volles, M.J.1
Lee, S.J.2
Rochet, J.C.3
Shtilerman, M.D.4
Ding, T.T.5
Kessler, J.C.6
Lansbury Jr, P.T.7
-
16
-
-
0037930855
-
Lipid binding inhibits alpha-synuclein fibril formation
-
Zhu M, Fink AL. Lipid binding inhibits alpha-synuclein fibril formation. J Biol Chem 2003; 278: 16873-16877.
-
(2003)
J Biol Chem
, vol.278
, pp. 16873-16877
-
-
Zhu, M.1
Fink, A.L.2
-
17
-
-
37349043948
-
Amyloid toxicity is independent of polypeptide sequence, length, and chirality
-
Pastor MT, Kümmerer N, Schubert V, Esteras-Chopo A, Dotti CG, López de la Paz M, Serrano L. Amyloid toxicity is independent of polypeptide sequence, length, and chirality. J Mol Biol 2008; 375: 695-707.
-
(2008)
J Mol Biol
, vol.375
, pp. 695-707
-
-
Pastor, M.T.1
Kümmerer, N.2
Schubert, V.3
Esteras-Chopo, A.4
Dotti, C.G.5
López de la Paz, M.6
Serrano, L.7
-
18
-
-
0037016741
-
Membrane-bound α-synuclein has a high aggregation propensity and the ability to seed the aggregation of the cytosolic form
-
Lee HJ, Choi C, Lee SJ. Membrane-bound α-synuclein has a high aggregation propensity and the ability to seed the aggregation of the cytosolic form. J Biol Chem 2002; 277: 671-678.
-
(2002)
J Biol Chem
, vol.277
, pp. 671-678
-
-
Lee, H.J.1
Choi, C.2
Lee, S.J.3
-
19
-
-
0034602296
-
George-Hyslop P, Fraser PE. α-Synuclein membrane interactions and lipid specificity
-
Jo E, McLaurin JA, Yip CM, St. George-Hyslop P, Fraser PE. α-Synuclein membrane interactions and lipid specificity. J Biol Chem 2000; 275: 34328-34334.
-
(2000)
J Biol Chem
, vol.275
, pp. 34328-34334
-
-
Jo, E.1
McLaurin, J.A.2
Yip St, C.M.3
-
20
-
-
58149277415
-
Soluble amyloid β-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity
-
Valincius G, Heinrich F, Budvytyte R, Vanderah DJ, Sokolov Y, Hall JE, Lösche M. Soluble amyloid β-oligomers affect dielectric membrane properties by bilayer insertion and domain formation: implications for cell toxicity. Biophys J 2008; 95: 4845-4861.
-
(2008)
Biophys J
, vol.95
, pp. 4845-4861
-
-
Valincius, G.1
Heinrich, F.2
Budvytyte, R.3
Vanderah, D.J.4
Sokolov, Y.5
Hall, J.E.6
Lösche, M.7
-
21
-
-
7544245555
-
Islet amyloid polypeptide-induced membrane leakage involves uptake of lipids by forming amyloid fibers
-
Sparr E, Engel MFM, Sakharov DV, Sprong M, Jacobs J, de Kruijff B, Höppener JWM, Killian JA. Islet amyloid polypeptide-induced membrane leakage involves uptake of lipids by forming amyloid fibers. FEBS Lett 2004; 577: 117-120.
-
(2004)
FEBS Lett
, vol.577
, pp. 117-120
-
-
Sparr, E.1
Engel, M.F.M.2
Sakharov, D.V.3
Sprong, M.4
Jacobs, J.5
de Kruijff, B.6
Höppener, J.W.M.7
Killian, J.A.8
-
22
-
-
33845395215
-
Natively folded HypF-N and its early amyloid aggregates interact with phospholipid monolayers and destabilize supported phospholipid bilayers
-
Canale C, Torrassa S, Rispoli P, Relini A, Rolandi R, Bucciantini M, Stefani M, Gliozzi A. Natively folded HypF-N and its early amyloid aggregates interact with phospholipid monolayers and destabilize supported phospholipid bilayers. Biophys J 2006; 91: 4575.
-
(2006)
Biophys J
, vol.91
, pp. 4575
-
-
Canale, C.1
Torrassa, S.2
Rispoli, P.3
Relini, A.4
Rolandi, R.5
Bucciantini, M.6
Stefani, M.7
Gliozzi, A.8
-
23
-
-
4043100348
-
Formation of amyloid fibers triggered by phosphatidylserine-containing membranes
-
Zhao H, Tuominen EKJ, Kinnunen PKJ. Formation of amyloid fibers triggered by phosphatidylserine-containing membranes. Biochemistry 2004; 43: 10302-10307.
-
(2004)
Biochemistry
, vol.43
, pp. 10302-10307
-
-
Zhao, H.1
Tuominen, E.K.J.2
Kinnunen, P.K.J.3
-
24
-
-
0037185013
-
Surface-catalyzed amyloid fibril formation
-
Zhu M, Souillac PO, Ionescu-Zanetti C, Carter SA, Fink AL. Surface-catalyzed amyloid fibril formation. J Biol Chem 2002; 277: 50914-50922.
-
(2002)
J Biol Chem
, vol.277
, pp. 50914-50922
-
-
Zhu, M.1
Souillac, P.O.2
Ionescu-Zanetti, C.3
Carter, S.A.4
Fink, A.L.5
-
26
-
-
61949248657
-
Effect of dehydration on the aggregation kinetics of two amyloid peptides
-
Mukherjee S, Chowdhury P, Gai F. Effect of dehydration on the aggregation kinetics of two amyloid peptides. J Phys Chem B 2009; 113: 531-535.
-
(2009)
J Phys Chem B
, vol.113
, pp. 531-535
-
-
Mukherjee, S.1
Chowdhury, P.2
Gai, F.3
-
27
-
-
47749146102
-
Instantaneous amyloid fibril formation of α-synuclein from the oligomeric granular structures in the presence of hexane
-
Lee J, Bhak G, Lee SG, Paik SR. Instantaneous amyloid fibril formation of α-synuclein from the oligomeric granular structures in the presence of hexane. Biophys J 2008; 95: L16-L18.
-
(2008)
Biophys J
, vol.95
-
-
Lee, J.1
Bhak, G.2
Lee, S.G.3
Paik, S.R.4
-
28
-
-
34547454920
-
Nucleation of protein fibrillation by nanoparticles
-
Linse S, Cabaleiro-Lago C, Xue WF, Lynch I, Lindman S, Thulin E, Radford SE, Dawson KA. Nucleation of protein fibrillation by nanoparticles. Proc Natl Acad Sci USA 2007; 104: 8691-8696.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8691-8696
-
-
Linse, S.1
Cabaleiro-Lago, C.2
Xue, W.F.3
Lynch, I.4
Lindman, S.5
Thulin, E.6
Radford, S.E.7
Dawson, K.A.8
-
29
-
-
34547481020
-
Nanoparticles as catalysts for protein fibrillation
-
Colvin VL, Kulinowski KM. Nanoparticles as catalysts for protein fibrillation. Proc Natl Acad Sci USA 2007; 104: 8679-8680.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 8679-8680
-
-
Colvin, V.L.1
Kulinowski, K.M.2
-
30
-
-
11844249291
-
Rapid assembly of amyloid-beta peptide at a liquid/liquid interface produces unstable beta-sheet fibers
-
Nichols MR, Moss MA, Reed DK, Hoh JH, Rosenberry TL. Rapid assembly of amyloid-beta peptide at a liquid/liquid interface produces unstable beta-sheet fibers. Biochemistry 2005; 44: 165-173.
-
(2005)
Biochemistry
, vol.44
, pp. 165-173
-
-
Nichols, M.R.1
Moss, M.A.2
Reed, D.K.3
Hoh, J.H.4
Rosenberry, T.L.5
-
32
-
-
33750331994
-
Two-dimensional ordered β-sheet lipopeptide monolayers
-
Cavalli S, Handgraaf JW, Tellers EE, Popescu DC, Overhand M, Kjaer K, Vaiser V, Sommerdijk NA, Rapaport H, Kros A. Two-dimensional ordered β-sheet lipopeptide monolayers. J Am Chem Soc 2006; 128: 13959-13966.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 13959-13966
-
-
Cavalli, S.1
Handgraaf, J.W.2
Tellers, E.E.3
Popescu, D.C.4
Overhand, M.5
Kjaer, K.6
Vaiser, V.7
Sommerdijk, N.A.8
Rapaport, H.9
Kros, A.10
-
33
-
-
67651093773
-
Surface properties and conformation of Nephila clavipes spider recombinant silk proteins at the air-water interface
-
Renault A, Rioux-Dubé JF, Lefèvre T, Pezennec S, Beaufils S, Vié V, Tremblay M, Pézolet M. Surface properties and conformation of Nephila clavipes spider recombinant silk proteins at the air-water interface. Langmuir 2009; 25: 8170-8180.
-
(2009)
Langmuir
, vol.25
, pp. 8170-8180
-
-
Renault, A.1
Rioux-Dubé, J.F.2
Lefèvre, T.3
Pezennec, S.4
Beaufils, S.5
Vié, V.6
Tremblay, M.7
Pézolet, M.8
-
34
-
-
75149180052
-
Competing discrete interfacial effects are critical for amyloidogenesis
-
Jean L, Lee CF, Lee C, Shaw M, Vaux DJ. Competing discrete interfacial effects are critical for amyloidogenesis. FASEB J 2010; 24: 309-317.
-
(2010)
FASEB J
, vol.24
, pp. 309-317
-
-
Jean, L.1
Lee, C.F.2
Lee, C.3
Shaw, M.4
Vaux, D.J.5
-
35
-
-
58149216444
-
Protein folding and misfolding on surfaces
-
Stefani M. Protein folding and misfolding on surfaces. Int J Mol Sci 2008; 9: 2515-2542.
-
(2008)
Int J Mol Sci
, vol.9
, pp. 2515-2542
-
-
Stefani, M.1
-
36
-
-
33749642847
-
Computational approaches to fibril structure and formation
-
Hall CK, Wagoner VA. Computational approaches to fibril structure and formation. Meth Enzymol 2006; 412: 338-365.
-
(2006)
Meth Enzymol
, vol.412
, pp. 338-365
-
-
Hall, C.K.1
Wagoner, V.A.2
-
37
-
-
33748689799
-
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation
-
Ma J, Nussinov R. Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol 2006; 10: 445-452.
-
(2006)
Curr Opin Chem Biol
, vol.10
, pp. 445-452
-
-
Ma, J.1
Nussinov, R.2
-
39
-
-
19544375553
-
Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations
-
López de la Paz M, de Mori M, Serrano L, Colombo G. Sequence dependence of amyloid fibril formation: insights from molecular dynamics simulations. J Mol Biol 2005; 349: 583-596.
-
(2005)
J Mol Biol
, vol.349
, pp. 583-596
-
-
López de la Paz, M.1
de Mori, M.2
Serrano, L.3
Colombo, G.4
-
40
-
-
33644536691
-
Atomic-level description of amyloid beta-dimer formation
-
Gnanakaran S, Nussinov R, García AE. Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc 2006; 128: 2158-2159.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 2158-2159
-
-
Gnanakaran, S.1
Nussinov, R.2
García, A.E.3
-
41
-
-
10644242867
-
Molecular dynamics simulation of amyloid β dimer formation
-
Urbanc B, Cruz L, Ding F, Sammond D, Khare S, Buldyrev SV, Stanley HE, Dokholyan Molecular dynamics simulation of amyloid β dimer formation. Biophys J 2004; 87: 2310-2321.
-
(2004)
Biophys J
, vol.87
, pp. 2310-2321
-
-
Urbanc, B.1
Cruz, L.2
Ding, F.3
Sammond, D.4
Khare, S.5
Buldyrev, S.V.6
Stanley, H.E.7
Dokholyan8
-
42
-
-
9244260521
-
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
-
Nguyen HD, Hall CK. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci USA 2004; 101: 16180-16185.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 16180-16185
-
-
Nguyen, H.D.1
Hall, C.K.2
-
43
-
-
33745727173
-
Interpreting the aggregation kinetics of amyloid peptides
-
Pellarin R, Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol 2006; 360: 882-892.
-
(2006)
J Mol Biol
, vol.360
, pp. 882-892
-
-
Pellarin, R.1
Caflisch, A.2
-
44
-
-
35748943830
-
Pathways and intermediates of amyloid fibril formation
-
Pellarin R, Guarnera E, Caflisch A. Pathways and intermediates of amyloid fibril formation. J Mol Biol 2007; 374: 917-924.
-
(2007)
J Mol Biol
, vol.374
, pp. 917-924
-
-
Pellarin, R.1
Guarnera, E.2
Caflisch, A.3
-
45
-
-
33845652619
-
Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations
-
Marchut AJ, Hall CK. Effects of chain length on the aggregation of model polyglutamine peptides: molecular dynamics simulations. Proteins 2007; 66: 96-109.
-
(2007)
Proteins
, vol.66
, pp. 96-109
-
-
Marchut, A.J.1
Hall, C.K.2
-
46
-
-
62549097355
-
Characterization of the nucleation barriers for protein aggregation and amyloid formation
-
Auer S, Dobson CM, Vendruscolo M. Characterization of the nucleation barriers for protein aggregation and amyloid formation. HFSP J 2007; 1: 137-146.
-
(2007)
HFSP J
, vol.1
, pp. 137-146
-
-
Auer, S.1
Dobson, C.M.2
Vendruscolo, M.3
-
47
-
-
65249190783
-
Effect of β-sheet propensity on peptide aggregation
-
Bellesia G, Shea JE. Effect of β-sheet propensity on peptide aggregation. J Chem Phys 2009; 130: 145103.
-
(2009)
J Chem Phys
, vol.130
, pp. 145103
-
-
Bellesia, G.1
Shea, J.E.2
-
48
-
-
72949120775
-
Diversity of kinetic pathways in amyloid fibril formation
-
Bellesia G, Shea JE. Diversity of kinetic pathways in amyloid fibril formation. J Chem Phys 2009; 131: 111102.
-
(2009)
J Chem Phys
, vol.131
, pp. 111102
-
-
Bellesia, G.1
Shea, J.E.2
-
49
-
-
22144448838
-
The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent
-
Wu C, Lei H, Duan Y. The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J 2005; 88: 2897-2906.
-
(2005)
Biophys J
, vol.88
, pp. 2897-2906
-
-
Wu, C.1
Lei, H.2
Duan, Y.3
-
50
-
-
0037627715
-
The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35
-
Gsponer J, Haberthur U, Caflisch A. The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35. Proc Natl Acad Sci USA 2003; 100: 5154.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5154
-
-
Gsponer, J.1
Haberthur, U.2
Caflisch, A.3
-
51
-
-
27644540293
-
A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide
-
Han W, Wu YD. A strand-loop-strand structure is a possible intermediate in fibril elongation: long time simulations of amyloid-beta peptide. J Am Chem Soc 2005; 127: 15408-15416.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 15408-15416
-
-
Han, W.1
Wu, Y.D.2
-
52
-
-
61549084018
-
Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study
-
Davis CH, Berkowitz ML. Interaction between amyloid-beta (1-42) peptide and phospholipid bilayers: a molecular dynamics study. Biophys J 2009; 96: 785-797.
-
(2009)
Biophys J
, vol.96
, pp. 785-797
-
-
Davis, C.H.1
Berkowitz, M.L.2
-
53
-
-
70350397192
-
Structure of the amyloid-b (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study
-
Davis CH, Berkowitz ML. Structure of the amyloid-b (1-42) monomer absorbed to model phospholipid bilayers: a molecular dynamics study. J Phys Chem B 2009; 113: 14480-14486.
-
(2009)
J Phys Chem B
, vol.113
, pp. 14480-14486
-
-
Davis, C.H.1
Berkowitz, M.L.2
-
54
-
-
34548753401
-
In silico tilted properties of the 67-78 fragment of α-synuclein are responsible for membrane destabilization and neurotoxicity
-
Crowet JM, Lins L, Dupiereux I, Elmoualija B, Lorin A, Charloteaux B, Stroobant V, Heinen E, Brasseur R. In silico tilted properties of the 67-78 fragment of α-synuclein are responsible for membrane destabilization and neurotoxicity. Proteins 2007; 68: 936-947.
-
(2007)
Proteins
, vol.68
, pp. 936-947
-
-
Crowet, J.M.1
Lins, L.2
Dupiereux, I.3
Elmoualija, B.4
Lorin, A.5
Charloteaux, B.6
Stroobant, V.7
Heinen, E.8
Brasseur, R.9
-
55
-
-
34548788549
-
Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process
-
Jang H, Zheng J, Nussinov R. Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J 2007; 93: 1938.
-
(2007)
Biophys J
, vol.93
, pp. 1938
-
-
Jang, H.1
Zheng, J.2
Nussinov, R.3
-
56
-
-
49649122274
-
β-hairpin folding by a model amyloid peptide in solution and at an interface
-
Knecht V. β-hairpin folding by a model amyloid peptide in solution and at an interface. J Phys Chem B 2008; 112: 9476-9483.
-
(2008)
J Phys Chem B
, vol.112
, pp. 9476-9483
-
-
Knecht, V.1
-
57
-
-
38349077350
-
A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer
-
Lemkul JA, Bevan DR. A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer. Arch Biochem Biophys 2008; 470: 54-63.
-
(2008)
Arch Biochem Biophys
, vol.470
, pp. 54-63
-
-
Lemkul, J.A.1
Bevan, D.R.2
-
58
-
-
65549152828
-
Perturbation of membranes by the amyloid b-peptide-A molecular dynamics study
-
Lemkul JA, Bevan DR. Perturbation of membranes by the amyloid b-peptide-A molecular dynamics study. FEBS J 2009; 276: 3060-3075.
-
(2009)
FEBS J
, vol.276
, pp. 3060-3075
-
-
Lemkul, J.A.1
Bevan, D.R.2
-
59
-
-
71749085062
-
Structures of beta-amyloid peptide 1-40, 1-42, and the 672-726 fragment of APP in a membrane environment with implications for interactions with gamma-secretase
-
Miyashita N, Straub JE, Thirumalai D. Structures of beta-amyloid peptide 1-40, 1-42, and the 672-726 fragment of APP in a membrane environment with implications for interactions with gamma-secretase. J Am Chem Soc 2009; 131: 17843-17852.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 17843-17852
-
-
Miyashita, N.1
Straub, J.E.2
Thirumalai, D.3
-
60
-
-
2942666417
-
Modeling amyloid beta-peptide insertion into lipid bilayers
-
Mobley DL, Cox DL, Singh RRP, Maddox MW, Longo ML. Modeling amyloid beta-peptide insertion into lipid bilayers. Biophys J 2004; 86: 3585-3597.
-
(2004)
Biophys J
, vol.86
, pp. 3585-3597
-
-
Mobley, D.L.1
Cox, D.L.2
Singh, R.R.P.3
Maddox, M.W.4
Longo, M.L.5
-
61
-
-
17244372981
-
Conformational transition of amyloid β-peptide
-
Xu Y, Shen J, Luo X, Zhu W, Chen K, Ma J, Jang H. 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.1
Shen, J.2
Luo, X.3
Zhu, W.4
Chen, K.5
Ma, J.6
Jang, H.7
-
63
-
-
0035250292
-
Nanostructure formation through β-sheet self-assembly in silk-based materials
-
Rathore O, Sogah DY. Nanostructure formation through β-sheet self-assembly in silk-based materials. Macromolecules 2001; 34: 1477-1486.
-
(2001)
Macromolecules
, vol.34
, pp. 1477-1486
-
-
Rathore, O.1
Sogah, D.Y.2
-
64
-
-
33646365344
-
Metallopolymer-peptide conjugates: synthesis and self-assembly of polyferrocenylsilane graft and block copolymers containing a β-sheet forming Gly-Ala-Gly-Ala tetrapeptide segment
-
Vandermeulen GWM, Kim KT, Wang Z, Manners I. Metallopolymer-peptide conjugates: synthesis and self-assembly of polyferrocenylsilane graft and block copolymers containing a β-sheet forming Gly-Ala-Gly-Ala tetrapeptide segment. Biomacromol 2006; 7: 1005-1010.
-
(2006)
Biomacromol
, vol.7
, pp. 1005-1010
-
-
Vandermeulen, G.W.M.1
Kim, K.T.2
Wang, Z.3
Manners, I.4
-
65
-
-
33846250450
-
Proline and glycine control protein self-organization into elastomeric or amyloid fibrils
-
Rauscher S, Baud S, Miao M, Keeley FW, Pomès R. Proline and glycine control protein self-organization into elastomeric or amyloid fibrils. Structure 2006; 14: 1667-1676.
-
(2006)
Structure
, vol.14
, pp. 1667-1676
-
-
Rauscher, S.1
Baud, S.2
Miao, M.3
Keeley, F.W.4
Pomès, R.5
-
66
-
-
0035132984
-
Voltage-dependent insertion of alamethicin at phosholipid/water and octane/water interfaces
-
Tieleman DP, Berendsen HJC, Sansom MSP. Voltage-dependent insertion of alamethicin at phosholipid/water and octane/water interfaces. Biophys J 2001; 80: 331-346.
-
(2001)
Biophys J
, vol.80
, pp. 331-346
-
-
Tieleman, D.P.1
Berendsen, H.J.C.2
Sansom, M.S.P.3
-
67
-
-
3142747401
-
Direct simulation of transmembrane helix association: role of asparagines
-
Stockner T, Ash WL, MacCallum JL, Tieleman DP. Direct simulation of transmembrane helix association: role of asparagines. Biophys J 2004; 87: 1650-1656.
-
(2004)
Biophys J
, vol.87
, pp. 1650-1656
-
-
Stockner, T.1
Ash, W.L.2
MacCallum, J.L.3
Tieleman, D.P.4
-
68
-
-
0029912748
-
Development and testing of the OPLS all-atom force-field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force-field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225-11236.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
69
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926.
-
(1983)
J Chem Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
70
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001; 7: 306-317.
-
(2001)
J Mol Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
71
-
-
0029633168
-
GROMACS: a message-passing parallel molecular dynamics implementation
-
Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp Phys Comm 1995; 91: 43-56.
-
(1995)
Comp Phys Comm
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
van der Spoel, D.2
van Drunen, R.3
-
72
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Dardent T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995; 103: 8577-8593.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Dardent, T.4
Lee, H.5
Pedersen, L.G.6
-
73
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
75
-
-
84986440341
-
Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto S, Kollman PA. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comp Chem 1992; 13: 952-962.
-
(1992)
J Comp Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
77
-
-
54849417403
-
Calculation of absolute protein-ligand binding affinities using distributed replica sampling
-
Rodinger T, Howell PL, Pomès R. Calculation of absolute protein-ligand binding affinities using distributed replica sampling. J Chem Phys 2008; 129: 155102.
-
(2008)
J Chem Phys
, vol.129
, pp. 155102
-
-
Rodinger, T.1
Howell, P.L.2
Pomès, R.3
-
78
-
-
73949096788
-
Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling
-
Rauscher S, Neale C, Pomès R. Simulated tempering distributed replica sampling, virtual replica exchange, and other generalized-ensemble methods for conformational sampling. J Chem Theory Comput 2009; 5: 2640-2662.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2640-2662
-
-
Rauscher, S.1
Neale, C.2
Pomès, R.3
-
79
-
-
84943502952
-
A molecular-dynamics method for simulations in the canonical ensemble
-
Nosé S. A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys 1984; 52: 255-268.
-
(1984)
Mol Phys
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
80
-
-
0001538909
-
Canonical dynamics-equilibrium phase-space distributions
-
Hoover WG. Canonical dynamics-equilibrium phase-space distributions. Phys Rev A 1985; 31: 1695-1697.
-
(1985)
Phys Rev A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
81
-
-
0041706333
-
An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface
-
Pandit SA, Bostick D, Berkowitz ML. An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface. J Chem Phys 2003; 119: 2199.
-
(2003)
J Chem Phys
, vol.119
, pp. 2199
-
-
Pandit, S.A.1
Bostick, D.2
Berkowitz, M.L.3
-
82
-
-
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
-
83
-
-
0003451443
-
Computer Simulation of Liquids
-
Clarendon Press; Oxford
-
Allen MP, Tildesley DJ. Computer Simulation of Liquids. Clarendon Press; Oxford 1987.
-
(1987)
-
-
Allen, M.P.1
Tildesley, D.J.2
-
84
-
-
33845280446
-
Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution
-
Radzicka A, Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988; 27: 1664-1670.
-
(1988)
Biochemistry
, vol.27
, pp. 1664-1670
-
-
Radzicka, A.1
Wolfenden, R.2
-
85
-
-
34247626293
-
Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment
-
MacCallum JL, Bennett WF, Tieleman DP. Partitioning of amino acid side chains into lipid bilayers: results from computer simulations and comparison to experiment. J Gen Physiol 2007; 129: 371-377.
-
(2007)
J Gen Physiol
, vol.129
, pp. 371-377
-
-
MacCallum, J.L.1
Bennett, W.F.2
Tieleman, D.P.3
-
86
-
-
0030005250
-
Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
-
Wimley WC, Creamer TP, White SH. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochemistry 1996; 35: 5109-5124.
-
(1996)
Biochemistry
, vol.35
, pp. 5109-5124
-
-
Wimley, W.C.1
Creamer, T.P.2
White, S.H.3
-
87
-
-
61649121892
-
Amyloid aggregation on lipid bilayers and its impact on membrane permeability
-
Friedman R, Pellarin R, Caflisch A. Amyloid aggregation on lipid bilayers and its impact on membrane permeability. J Mol Biol 2009; 378: 407-415.
-
(2009)
J Mol Biol
, vol.378
, pp. 407-415
-
-
Friedman, R.1
Pellarin, R.2
Caflisch, A.3
-
88
-
-
70049090008
-
A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation
-
Auer S, Trovato A, Vendruscolo M. A condensation-ordering mechanism in nanoparticle-catalyzed peptide aggregation. PLoS Comput Biol 2009; 5: e1000458.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Auer, S.1
Trovato, A.2
Vendruscolo, M.3
-
89
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75: 333-336.
-
(2006)
Annu Rev Biochem
, vol.75
, pp. 333-336
-
-
Chiti, F.1
Dobson, C.M.2
-
90
-
-
34547156274
-
Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins
-
Murphy RM. Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins. Biochim Biophys Acta 2007; 1768: 1923-1934.
-
(2007)
Biochim Biophys Acta
, vol.1768
, pp. 1923-1934
-
-
Murphy, R.M.1
-
91
-
-
48249092311
-
Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly
-
Xue W-F, Homans SW, Radford SE. Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly. Proc Natl Acad Sci USA 2008; 105: 8926-8931.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 8926-8931
-
-
Xue, W.1
Homans, S.W.2
Radford, S.E.3
-
92
-
-
67651098677
-
Aggregation of amyloidogenic peptides near hydrophobic and hydrophillic surfaces
-
Brovchenko I, Singh G, Winter R. Aggregation of amyloidogenic peptides near hydrophobic and hydrophillic surfaces. Langmuir 2009; 25: 8111-8116.
-
(2009)
Langmuir
, vol.25
, pp. 8111-8116
-
-
Brovchenko, I.1
Singh, G.2
Winter, R.3
-
93
-
-
0037207098
-
Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces
-
Sharp JS, Forrest JA, Jones RAL. Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces. Biochemistry 2002; 41: 15810-15819.
-
(2002)
Biochemistry
, vol.41
, pp. 15810-15819
-
-
Sharp, J.S.1
Forrest, J.A.2
Jones, R.A.L.3
-
94
-
-
43649094583
-
Distribution of amino acids in a lipid bilayer from computer simulations
-
MacCallum JL, Bennett WF, Tieleman DP. Distribution of amino acids in a lipid bilayer from computer simulations. Biophys J 2008; 94: 3393-3404.
-
(2008)
Biophys J
, vol.94
, pp. 3393-3404
-
-
MacCallum, J.L.1
Bennett, W.F.2
Tieleman, D.P.3
-
95
-
-
39749132236
-
Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
-
Johansson AC, Lindahl E. Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations. Proteins 2008; 70: 1332-1344.
-
(2008)
Proteins
, vol.70
, pp. 1332-1344
-
-
Johansson, A.C.1
Lindahl, E.2
-
97
-
-
36248932202
-
Computer simulation of antimicrobial peptides
-
Matyus E, Kandt C, Tieleman DP. Computer simulation of antimicrobial peptides. Curr Med Chem 2008; 14: 2789-2798.
-
(2008)
Curr Med Chem
, vol.14
, pp. 2789-2798
-
-
Matyus, E.1
Kandt, C.2
Tieleman, D.P.3
-
98
-
-
31544474881
-
Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces
-
Aliste MP, Tieleman DP. Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces. BMC Biochem 2005; 6: 30.
-
(2005)
BMC Biochem
, vol.6
, pp. 30
-
-
Aliste, M.P.1
Tieleman, D.P.2
-
99
-
-
0034598954
-
Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis
-
Broome BM, Hecht MH. Nature disfavors sequences of alternating polar and non-polar amino acids: implications for amyloidogenesis. J Mol Biol 2000; 296: 961-968.
-
(2000)
J Mol Biol
, vol.296
, pp. 961-968
-
-
Broome, B.M.1
Hecht, M.H.2
-
100
-
-
0032987478
-
Membrane protein folding and stability: physical principles
-
White SH, Wimley WC. Membrane protein folding and stability: physical principles. Annu Rev Biophys Biomol Struct 1999; 28: 319-365.
-
(1999)
Annu Rev Biophys Biomol Struct
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
101
-
-
13444262028
-
Recognition of transmembrane helices by the endoplasmic reticulum translocon
-
Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, Nilsson I, White SH, von Heijne G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature 2005; 433: 377-381.
-
(2005)
Nature
, vol.433
, pp. 377-381
-
-
Hessa, T.1
Kim, H.2
Bihlmaier, K.3
Lundin, C.4
Boekel, J.5
Andersson, H.6
Nilsson, I.7
White, S.H.8
von Heijne, G.9
-
102
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Prot Chem 1959; 14: 1-63.
-
(1959)
Adv Prot Chem
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
103
-
-
0019052221
-
Hydrophobic basis of packing in soluble proteins
-
Rose GD, Roy S. Hydrophobic basis of packing in soluble proteins. Proc Natl Acad Sci USA 1980; 77: 4643-4647.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 4643-4647
-
-
Rose, G.D.1
Roy, S.2
-
105
-
-
0036404919
-
On the significance of alternating patterns of polar and non-polar residues in β-strands
-
Mandel-Gutfreund Y, Gregoret LM. On the significance of alternating patterns of polar and non-polar residues in β-strands. J Mol Biol 2002; 323: 453-461.
-
(2002)
J Mol Biol
, vol.323
, pp. 453-461
-
-
Mandel-Gutfreund, Y.1
Gregoret, L.M.2
-
106
-
-
67149096041
-
Folding by numbers: primary sequence statistics and their use in studying protein folding
-
Wathen B, Jia Z. Folding by numbers: primary sequence statistics and their use in studying protein folding. Int J Mol Sci 2009; 10: 1567-1589.
-
(2009)
Int J Mol Sci
, vol.10
, pp. 1567-1589
-
-
Wathen, B.1
Jia, Z.2
-
107
-
-
34547631623
-
Prevention of amyloid-like aggregation as a driving force of protein evolution
-
Monsellier E, Chiti F. Prevention of amyloid-like aggregation as a driving force of protein evolution. EMBO Rep 2007; 8: 737-742.
-
(2007)
EMBO Rep
, vol.8
, pp. 737-742
-
-
Monsellier, E.1
Chiti, F.2
-
108
-
-
7044247850
-
Folding and assembly of β-barrel membrane proteins
-
Tamm LK, Hong H, Liang B. Folding and assembly of β-barrel membrane proteins. Biochim Biophys Acta 2004; 1666: 250-263.
-
(2004)
Biochim Biophys Acta
, vol.1666
, pp. 250-263
-
-
Tamm, L.K.1
Hong, H.2
Liang, B.3
|