-
1
-
-
33746377894
-
Protein Misfolding, Functional Amyloid, and Human Disease
-
Chiti, F.; Dobson, C. M. 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
-
2
-
-
0034725535
-
The Protofilament Substructure of Amyloid Fibrils
-
Serpell, L. C.; Sunde, M.; Benson, M. D.; Tennent, G. A.; Pepys, M. B.; Fraser, P. E. The Protofilament Substructure of Amyloid Fibrils J. Mol. Biol. 2000, 300, 1033-1039
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1033-1039
-
-
Serpell, L.C.1
Sunde, M.2
Benson, M.D.3
Tennent, G.A.4
Pepys, M.B.5
Fraser, P.E.6
-
3
-
-
0030801746
-
The Structure of Amyloid Fibrils by Electron Microscopy and X-ray Diffraction
-
Sunde, M.; Blake, C. The Structure of Amyloid Fibrils by Electron Microscopy and X-ray Diffraction Adv. Protein Chem. 1997, 50, 123-159
-
(1997)
Adv. Protein Chem.
, vol.50
, pp. 123-159
-
-
Sunde, M.1
Blake, C.2
-
4
-
-
0031444010
-
Atomic Force Microscopic Imaging of Seeded Fibril Formation and Fibril Branching by the Alzheimer's Disease amyloid-beta protein
-
Harper, D. J.; Lieber, C. M.; Lansbury, P. T. J. Atomic Force Microscopic Imaging of Seeded Fibril Formation and Fibril Branching by the Alzheimer's Disease amyloid-beta protein Chem. Biol. 1997, 4, 951-959
-
(1997)
Chem. Biol.
, vol.4
, pp. 951-959
-
-
Harper, D.J.1
Lieber, C.M.2
Lansbury, P.T.J.3
-
5
-
-
0037168655
-
A Structural Model for Alzheimer's beta -amyloid Fibrils Based on Experimental Constraints from Solid State NMR
-
Petkova, A. T.; Ishii, Y.; Balbach, J. J.; Antzutkin, O. N.; Leapman, R. D.; Delaglio, F.; Tycko, R. A Structural Model for Alzheimer's beta -amyloid Fibrils Based on Experimental Constraints from Solid State NMR Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 16742-16747
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, 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
-
6
-
-
0034700129
-
Multiple Quantum Solid-state NMR Indicates a Parallel, not Antiparallel, Organization of β -sheets in Alzheimer's beta -amyloid Fibrils
-
Antzutkin, O. N.; Balbach, J. J.; Leapman, R. D.; Rizzo, N. W.; Reed, J.; Tycko, R. Multiple Quantum Solid-state NMR Indicates a Parallel, not Antiparallel, Organization of β -sheets in Alzheimer's beta -amyloid Fibrils Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13045-13050
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 13045-13050
-
-
Antzutkin, O.N.1
Balbach, J.J.2
Leapman, R.D.3
Rizzo, N.W.4
Reed, J.5
Tycko, R.6
-
7
-
-
28444442999
-
3D Structure of Alzheimer's Amyloid-β(1-42) Fibrils
-
Luhrs, T.; Ritter, C.; Adrian, M.; Riek-Loher, D.; Bohrmann, B.; H, D.; Schubert, D.; Riek, R. 3D Structure of Alzheimer's Amyloid-β(1-42) Fibrils Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17342-17347
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 17342-17347
-
-
Luhrs, T.1
Ritter, C.2
Adrian, M.3
Riek-Loher, D.4
Bohrmann, B.H.D.5
Schubert, D.6
Riek, R.7
-
8
-
-
20444440728
-
Structure of the Cross-beta Spine of Amyloid-like Fibrils
-
Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A.; 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.4
Riekel, C.5
Grothe, R.6
Eisenberg, D.7
-
9
-
-
26444514550
-
Intersheet Rearrangement of Polypeptides during Nucleation of β-sheet Aggregates
-
Petty, S. A.; Decatur, S. M. Intersheet Rearrangement of Polypeptides During Nucleation of β-sheet Aggregates Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 14272-14277
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 14272-14277
-
-
Petty, S.A.1
Decatur, S.M.2
-
10
-
-
35448993331
-
Multidimensional Ultrafast Spectroscopy Special Feature: Automated 2D IR Spectroscopy Using a mid-IR Pulse Shaper and Application of this Technology to the Human Islet Amyloid Polypeptide
-
Shim, S. H.; Strasfeld, D. B.; Ling, Y. L.; Zanni, M. T. Multidimensional Ultrafast Spectroscopy Special Feature: Automated 2D IR Spectroscopy Using a mid-IR Pulse Shaper and Application of this Technology to the Human Islet Amyloid Polypeptide Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14197-14202
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 14197-14202
-
-
Shim, S.H.1
Strasfeld, D.B.2
Ling, Y.L.3
Zanni, M.T.4
-
11
-
-
77951271571
-
Principles Governing Oligomer Formation in Amyloidogenic Peptides
-
Straub, J. E.; Thirumalai, D. Principles Governing Oligomer Formation in Amyloidogenic Peptides Curr. Opin. Struct. Biol. 2010, 20, 1-9
-
(2010)
Curr. Opin. Struct. Biol.
, vol.20
, pp. 1-9
-
-
Straub, J.E.1
Thirumalai, D.2
-
12
-
-
33748689799
-
Simulations as Analytical Tools to Understand Protein Aggregation and Predict Amyloid Conformation
-
Ma, B.; 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, B.1
Nussinov, R.2
-
13
-
-
0003544049
-
-
Vdf Hochschulverlag AG an der ETH: Zurich
-
van Gunsteren, W.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W.; Tironi, I. Biomolecular Simulation: The GROMOS96 Manual and User Guide; Vdf Hochschulverlag AG an der ETH: Zurich, 1996.
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.7
Tironi, I.8
-
14
-
-
0035913529
-
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins Via Comparison with Accurate Quantum Chemical Calculations on Peptides
-
Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins Via Comparison with Accurate Quantum Chemical Calculations on Peptides J. Phys. Chem. B 2001, 105, 6474-6487
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
15
-
-
0001398008
-
How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?
-
Wang, J.; Cieplak, P.; Kollman, P. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? J. Comput. Chem. 2000, 21, 1049-1074
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.3
-
18
-
-
84869186159
-
Dynamical Stability and Assembly Cooperativity of β-Sheet Amyloid Oligomer-Effect of Polarization
-
Li, Y.; Ji, C.; Xu, W.; Zhang, J. Z. Dynamical Stability and Assembly Cooperativity of β-Sheet Amyloid Oligomer-Effect of Polarization J. Phys. Chem. B 2012, 116, 13368-13373
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 13368-13373
-
-
Li, Y.1
Ji, C.2
Xu, W.3
Zhang, J.Z.4
-
19
-
-
79955770935
-
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization
-
Matthes, D.; Gapsys, V.; Daebel, V.; de Groot, B. L. Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization PLoS ONE 2011, 6, e19129
-
(2011)
PLoS ONE
, vol.6
, pp. 19129
-
-
Matthes, D.1
Gapsys, V.2
Daebel, V.3
De Groot, B.L.4
-
20
-
-
84864187173
-
Structure and Dynamics of Amyloid-β Segmental Polymorphisms
-
Berhanu, W. M.; Hansmann, U. H. E. Structure and Dynamics of Amyloid-β Segmental Polymorphisms PLoS ONE 2012, 7, e41479
-
(2012)
PLoS ONE
, vol.7
, pp. 41479
-
-
Berhanu, W.M.1
Hansmann, U.H.E.2
-
21
-
-
84863528795
-
Amyloid Peptide Aβ40 Inhibits Aggregation of Aβ42: Evidence from Molecular Dynamics Simulations
-
Viet, M. H.; Li, M. S. Amyloid Peptide Aβ40 Inhibits Aggregation of Aβ42: Evidence from Molecular Dynamics Simulations J. Chem. Phys. 2012, 136, 245105
-
(2012)
J. Chem. Phys.
, vol.136
, pp. 245105
-
-
Viet, M.H.1
Li, M.S.2
-
22
-
-
36549058381
-
Structure and Aggregation Mechanisms of Human beta2-microglobulin(83-99) Peptides Studied by Molecular Dynamics Simulations
-
Liang, C.; Derreumaux, P.; Wei, G. Structure and Aggregation Mechanisms of Human beta2-microglobulin(83-99) Peptides Studied by Molecular Dynamics Simulations Biophys. J. 2007, 93, 3353-3362
-
(2007)
Biophys. J.
, vol.93
, pp. 3353-3362
-
-
Liang, C.1
Derreumaux, P.2
Wei, G.3
-
23
-
-
77952324067
-
Low Molecular Weight Oligomers of Amyloid Peptides Display β-barrel Conformations: A Replica Exchange Molecular Dynamics Study in Explicit Solvent
-
De Simone, A.; Derreumaux, P. Low Molecular Weight Oligomers of Amyloid Peptides Display β-barrel Conformations: A Replica Exchange Molecular Dynamics Study in Explicit Solvent J. Chem. Phys. 2010, 132, 165103
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 165103
-
-
De Simone, A.1
Derreumaux, P.2
-
25
-
-
84864686048
-
Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25-35) Peptide
-
Larini, L.; Shea, J. E. Role of β-Hairpin Formation in Aggregation: The Self-Assembly of the Amyloid-β(25-35) Peptide Biophys. J. 2012, 103, 576-586
-
(2012)
Biophys. J.
, vol.103
, pp. 576-586
-
-
Larini, L.1
Shea, J.E.2
-
26
-
-
84863989280
-
Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations
-
Matthes, D.; Gapsys, V.; de Groot, B. L. Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations J. Mol. Biol. 2012, 421, 390-416
-
(2012)
J. Mol. Biol.
, vol.421
, pp. 390-416
-
-
Matthes, D.1
Gapsys, V.2
De Groot, B.L.3
-
27
-
-
34249071886
-
A Bias-exchange Approach to Protein Folding
-
Piana, S.; Laio, A. A Bias-exchange Approach to Protein Folding J. Phys. Chem. B 2007, 111, 4553-4559
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 4553-4559
-
-
Piana, S.1
Laio, A.2
-
28
-
-
84857770472
-
A Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
-
Baftizadeh, F.; Biarnes, X.; Pietrucci, F.; Affinito, F.; Laio, A. A Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail J. Am. Chem. Soc. 2012, 134, 3886
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 3886
-
-
Baftizadeh, F.1
Biarnes, X.2
Pietrucci, F.3
Affinito, F.4
Laio, A.5
-
29
-
-
0031696773
-
Effect of Denaturant and Protein Concentrations upon Protein Refolding and Aggregation: A Simple lattice Model
-
Gupta, P.; Hall, C. K.; Voegler, A. C. Effect of Denaturant and Protein Concentrations upon Protein Refolding and Aggregation: A Simple lattice Model Protein Sci. 1998, 7, 2642-2652
-
(1998)
Protein Sci.
, vol.7
, pp. 2642-2652
-
-
Gupta, P.1
Hall, C.K.2
Voegler, A.C.3
-
30
-
-
0035079856
-
Conformational Propagation with Prion-like Characteristics in a Simple Model of Protein Folding
-
Harrison, P. M.; Chan, H. S.; Prusiner, S. B.; Cohen, F. E. Conformational Propagation with Prion-like Characteristics in a Simple Model of Protein Folding Protein Sci. 2001, 10, 819-835
-
(2001)
Protein Sci.
, vol.10
, pp. 819-835
-
-
Harrison, P.M.1
Chan, H.S.2
Prusiner, S.B.3
Cohen, F.E.4
-
31
-
-
0036228167
-
Exploring Protein Aggregation and Self-propagation Using Lattice Models:Phase Diagram and Kinetics
-
Dima, R. I.; Thirumalai, D. Exploring Protein Aggregation and Self-propagation Using Lattice Models:Phase Diagram and Kinetics Protein Sci. 2002, 11, 1036-1049
-
(2002)
Protein Sci.
, vol.11
, pp. 1036-1049
-
-
Dima, R.I.1
Thirumalai, D.2
-
32
-
-
55849105547
-
Probing the Mechanisms of Fibril Formation Using Lattice Models
-
Li, M. S.; Klimov, D. K.; Straub, J. E.; Thirumalai, D. Probing the Mechanisms of Fibril Formation Using Lattice Models J. Chem. Phys. 2008, 129, 175101
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 175101
-
-
Li, M.S.1
Klimov, D.K.2
Straub, J.E.3
Thirumalai, D.4
-
33
-
-
9244260521
-
Molecular Dynamics Simulations of Spontaneous Fibril Formation by Random-coil Peptides
-
Nguyen, H. D.; Hall, C. K. Molecular Dynamics Simulations of Spontaneous Fibril Formation by Random-coil Peptides Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16180-16185
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 16180-16185
-
-
Nguyen, H.D.1
Hall, C.K.2
-
34
-
-
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
-
35
-
-
34548804689
-
Computational Simulations of the Early Steps of Protein Aggregation
-
Wei, G.; Mousseau, N.; Derreumaux, P. Computational Simulations of the Early Steps of Protein Aggregation Prion 2007, 1, 3-8
-
(2007)
Prion
, vol.1
, pp. 3-8
-
-
Wei, G.1
Mousseau, N.2
Derreumaux, P.3
-
36
-
-
44049099816
-
Protofibril Assemblies of the Arctic, Dutch, and Flemish Mutants of the Alzheimer's A-beta(1-40) Peptide
-
Fawzi, N. L.; Kohlstedt, K. L.; Okabe, Y.; Head-Gordon, T. Protofibril Assemblies of the Arctic, Dutch, and Flemish Mutants of the Alzheimer's A-beta(1-40) Peptide Biophys. J. 2008, 94, 2007-2016
-
(2008)
Biophys. J.
, vol.94
, pp. 2007-2016
-
-
Fawzi, N.L.1
Kohlstedt, K.L.2
Okabe, Y.3
Head-Gordon, T.4
-
37
-
-
72949120775
-
Diversity of Kinetic Pathways in Amyloid Fibril Formation
-
Bellesia, G.; Shea, J. E. Diversity of Kinetic Pathways in Amyloid Fibril Formation J. Chem. Phys. 2009, 131, 111102-1-111102-4
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 1111021-1111024
-
-
Bellesia, G.1
Shea, J.E.2
-
38
-
-
10644278760
-
In silico Study of Amyloid β-protein Folding and Oligomerization
-
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. U.S.A. 2004, 101, 17345-17350
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 17345-17350
-
-
Urbanc, B.1
Cruz, L.2
Yun, S.3
Buldyrev, S.V.4
Bitan, G.5
Teplow, D.B.6
Stanley, H.E.7
-
39
-
-
33846234246
-
Coarse-grained Protein Molecular Dynamics Simulations
-
Derreumaux, P.; Mousseau, N. Coarse-grained Protein Molecular Dynamics Simulations J. Chem. Phys. 2007, 126, 025101-025106
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 025101-025106
-
-
Derreumaux, P.1
Mousseau, N.2
-
40
-
-
84870676017
-
Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
-
Sorensen, J.; Periole, X.; Skeby, K. K.; Marrink, S. J.; Schiott, B. Protofibrillar Assembly Toward the Formation of Amyloid Fibrils Phys. Chem. Lett. 2012, 2, 2385-2390
-
(2012)
Phys. Chem. Lett.
, vol.2
, pp. 2385-2390
-
-
Sorensen, J.1
Periole, X.2
Skeby, K.K.3
Marrink, S.J.4
Schiott, B.5
-
41
-
-
58149174069
-
Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment
-
Li, D. W.; Mohanty, S.; Irback, A.; Huo, S. Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment PLoS Comput. Biol. 2008, 4, e1000238
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000238
-
-
Li, D.W.1
Mohanty, S.2
Irback, A.3
Huo, S.4
-
42
-
-
79958122197
-
A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-forming Peptide GNNQQNY from the Yeast Prion sup-35
-
Nasica-Labouze, J.; Meli, M.; Derreumaux, P.; Colombo, G.; Mousseau, N. A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-forming Peptide GNNQQNY from the Yeast Prion sup-35 PLoS Comput. Biol. 2011, 7, 1002051
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. 1002051
-
-
Nasica-Labouze, J.1
Meli, M.2
Derreumaux, P.3
Colombo, G.4
Mousseau, N.5
-
43
-
-
66149094245
-
16-22 Protofibril Disassembly by N-methylated Inhibitors: A Numerical Study
-
16-22 Protofibril Disassembly by N-methylated Inhibitors: A Numerical Study Proteins 2009, 75, 442-452
-
(2009)
Proteins
, vol.75
, pp. 442-452
-
-
Chebaro, Y.1
Derreumaux, P.2
-
44
-
-
84868096591
-
Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations
-
Bieler, N. S.; Knowles, T. P. J.; Frenkel, D.; Vacha, R. Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations PLoS Comput. Biol. 2012, 8, e1002692
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. 1002692
-
-
Bieler, N.S.1
Knowles, T.P.J.2
Frenkel, D.3
Vacha, R.4
-
45
-
-
33748278029
-
Structures of Soluble Amyloid Oligomers from Computer Simulation
-
Melquiond, A.; Mousseau, N.; Derreumaux, P. Structures of Soluble Amyloid Oligomers From Computer Simulation Proteins 2006, 65, 180-191
-
(2006)
Proteins
, vol.65
, pp. 180-191
-
-
Melquiond, A.1
Mousseau, N.2
Derreumaux, P.3
-
46
-
-
66149189211
-
Thermodynamics and Dynamics of Amyloid Peptide Oligomerization are Sequence Dependent
-
Lu, Y.; Derreumaux, P.; Guo, Z.; Mousseau, N.; Wei, G. Thermodynamics and Dynamics of Amyloid Peptide Oligomerization are Sequence Dependent Proteins 2009, 75, 954-963
-
(2009)
Proteins
, vol.75
, pp. 954-963
-
-
Lu, Y.1
Derreumaux, P.2
Guo, Z.3
Mousseau, N.4
Wei, G.5
-
49
-
-
34548067360
-
Following the Aggregation of Amyloid-forming Peptides by Computer Simulations
-
Melquiond, A.; Boucher, G.; Mousseau, N.; Derreumaux, P. Following the Aggregation of Amyloid-forming Peptides by Computer Simulations J. Chem. Phys. 2005, 122, 174904
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 174904
-
-
Melquiond, A.1
Boucher, G.2
Mousseau, N.3
Derreumaux, P.4
-
50
-
-
46449133376
-
Self-assembly of the beta 2-microglobulin NHVTLSQ Peptide Using a Coarse-grained Protein Model Reveals β-barrel Species
-
Song, W.; Wei, G.; Mousseau, N.; Derreumaux, P. Self-assembly of the beta 2-microglobulin NHVTLSQ Peptide Using a Coarse-grained Protein Model Reveals β-barrel Species J. Phys. Chem. B 2008, 112, 4410-4418
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 4410-4418
-
-
Song, W.1
Wei, G.2
Mousseau, N.3
Derreumaux, P.4
-
51
-
-
34249290108
-
Atomic Structures of Amyloid Cross-β Spines Reveal Varied Steric Zippers
-
Sawaya, M. R.; Sambashivan, S.; Nelson, R.; Ivanova, M. I.; Sievers, S. A.; Apostol, M. I.; Thompson, M. J.; Balbirnie, M.; Wiltzius, J. J. W.; McFarlane, H. T. Atomic Structures of Amyloid Cross-β Spines Reveal Varied Steric Zippers Nature 2005, 447, 453-457
-
(2005)
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
-
52
-
-
78650750083
-
Dry Amyloid Fibril Assembly in a yeast Prion Peptide is Mediated by Long-lived Structures Containing Water Wires
-
Reddy, G.; Straub, J. E.; Thirumalai, D. Dry Amyloid Fibril Assembly in a yeast Prion Peptide is Mediated by Long-lived Structures Containing Water Wires Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 21459-21464
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 21459-21464
-
-
Reddy, G.1
Straub, J.E.2
Thirumalai, D.3
-
53
-
-
0025858688
-
Molecular-dynamics Simulations of the Unfolding of an Alpha-helical Analog of Ribonuclease-A S-peptide in Water
-
Tirado-Rives, J.; Jorgensen, W. L. Molecular-dynamics Simulations of the Unfolding of an Alpha-helical Analog of Ribonuclease-A S-peptide in Water Biochemistry 1991, 30, 3864-3871
-
(1991)
Biochemistry
, vol.30
, pp. 3864-3871
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
54
-
-
0041784950
-
All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, J. A.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, J.A.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
-
55
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics With Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
56
-
-
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. Mod. 2001, 7, 306-317
-
(2001)
J. Mol. Mod.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
57
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
-
Ryckaert, J. P.; Cicotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Cicotti, G.2
Berendsen, H.J.C.3
-
58
-
-
33846823909
-
Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
59
-
-
41549127613
-
A Temperature Predictor for Parallel Tempering Simulations
-
Patriksson, A.; van der Spoel, D. A Temperature Predictor for Parallel Tempering Simulations Phys. Chem. Chem. Phys. 2008, 10, 2073-2077
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2073-2077
-
-
Patriksson, A.1
Van Der Spoel, D.2
-
60
-
-
84891725778
-
-
http://folding.bmc.uu.se/remd/index.php.
-
-
-
-
61
-
-
0037337271
-
16-22 Amyloid Peptides into Antiparallel β sheets
-
16-22 Amyloid Peptides into Antiparallel β sheets Structure 2003, 11, 295-307
-
(2003)
Structure
, vol.11
, pp. 295-307
-
-
Klimov, D.K.1
Thirumalai, D.2
-
62
-
-
0029619259
-
Knowledge-Based Protein Secondary Structure Assignment Proteins
-
Frishman, D.; Argos, P. Knowledge-Based Protein Secondary Structure Assignment Proteins Proteins 1995, 23, 566-579
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
64
-
-
33846036362
-
Monomer Adds to Preformed Structured Oligomers of Aβ-peptides by a Two-stage Dock-lock Mechanism
-
Nguyen, P.; Li, M. S.; Stock, G.; Staub, J. E.; Thirumalai, D. Monomer Adds to Preformed Structured Oligomers of Aβ-peptides by a Two-stage Dock-lock Mechanism Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 111-116
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 111-116
-
-
Nguyen, P.1
Li, M.S.2
Stock, G.3
Staub, J.E.4
Thirumalai, D.5
-
65
-
-
0034714351
-
Nucleated Conformational Conversion and the Replication of Conformational Information by a Prion Determinant
-
Serio, T. R.; Cashikar, A. G.; Kowal, A. S.; Sawicki, G. J.; Moslehi, J. J.; Serpell, L.; Arnsdorf, M. F.; Lindquist, S. L. Nucleated Conformational Conversion and the Replication of Conformational Information by a Prion Determinant Science 2000, 25, 1317-1321
-
(2000)
Science
, vol.25
, pp. 1317-1321
-
-
Serio, T.R.1
Cashikar, A.G.2
Kowal, A.S.3
Sawicki, G.J.4
Moslehi, J.J.5
Serpell, L.6
Arnsdorf, M.F.7
Lindquist, S.L.8
-
66
-
-
34848929022
-
Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
-
Cheon, M.; Chang, I.; Mohanty, S.; Luheshi, L. M.; Dobson, C. M.; Vendruscolo, M.; Favrin, G. Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils PLoS Comput. Biol. 2007, 3, e173
-
(2007)
PLoS Comput. Biol.
, vol.3
, pp. 173
-
-
Cheon, M.1
Chang, I.2
Mohanty, S.3
Luheshi, L.M.4
Dobson, C.M.5
Vendruscolo, M.6
Favrin, G.7
-
67
-
-
84870679774
-
Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence
-
Nasica-Labouze, J.; Mousseau, N. Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence PLoS Comput. Biol. 2012, 8, 1002782
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. 1002782
-
-
Nasica-Labouze, J.1
Mousseau, N.2
-
68
-
-
10044289451
-
Sampling the Self-assembly Pathways of KFFE Hexamers
-
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, G.1
Mousseau, N.2
Derreumaux, P.3
-
69
-
-
81255184472
-
16-22 Fibrils in Large-scale Molecular-dynamics Simulations
-
16-22 Fibrils in Large-scale Molecular-dynamics Simulations Biophys. J. 2011, 101, 2493-2501
-
(2011)
Biophys. J.
, vol.101
, pp. 2493-2501
-
-
Cheon, M.1
Chang, I.2
Hall, C.K.3
-
70
-
-
61549102795
-
What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?
-
Bellesia, G.; Shea, J. E. What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils? Biophys. J. 2009, 96, 875-886
-
(2009)
Biophys. J.
, vol.96
, pp. 875-886
-
-
Bellesia, G.1
Shea, J.E.2
-
71
-
-
84863971692
-
Structural, Thermodynamical, and Dynamical Properties of Oligomers Formed by the Amyloid NNQQ Peptide: Insights from Coarse-grained Simulations
-
Lu, Y.; Wei, G.; Derreumaux, P. Structural, Thermodynamical, and Dynamical Properties of Oligomers Formed by the Amyloid NNQQ Peptide: Insights from Coarse-grained Simulations J. Chem. Phys. 2012, 137, 025101
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 025101
-
-
Lu, Y.1
Wei, G.2
Derreumaux, P.3
-
72
-
-
84857360124
-
Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation
-
Wagoner, V. A.; Cheon, M.; Chang, I.; Hall, C. K. Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation J. Mol. Biol. 2012, 416, 598-609
-
(2012)
J. Mol. Biol.
, vol.416
, pp. 598-609
-
-
Wagoner, V.A.1
Cheon, M.2
Chang, I.3
Hall, C.K.4
-
73
-
-
84866606825
-
Influence of Temperature on Formation of Perfect tau Fragment Fibrils Using PRIME20/DMD Simulations
-
Cheon, M.; Chang, I.; Hall, C. K. Influence of Temperature on Formation of Perfect tau Fragment Fibrils Using PRIME20/DMD Simulations Protein Sci. 2012, 21, 1514-1527
-
(2012)
Protein Sci.
, vol.21
, pp. 1514-1527
-
-
Cheon, M.1
Chang, I.2
Hall, C.K.3
-
74
-
-
25844456992
-
Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL) Observed in Molecular Dynamics Simulations with Explicit Solvent
-
Wu, C.; Hei, H. X.; Duan, Y. Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL) Observed in Molecular Dynamics Simulations with Explicit Solvent J. Am. Chem. Soc. 2005, 127, 13530-13537
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 13530-13537
-
-
Wu, C.1
Hei, H.X.2
Duan, Y.3
-
75
-
-
84865694928
-
Two-step Nucleation of Amyloid Fibrils: Omnipresent or Not?
-
Auer, S.; Ricchiuto, P.; Kashchiev, D. Two-step Nucleation of Amyloid Fibrils: Omnipresent or Not? J. Mol. Biol. 2012, 422, 723-730
-
(2012)
J. Mol. Biol.
, vol.422
, pp. 723-730
-
-
Auer, S.1
Ricchiuto, P.2
Kashchiev, D.3
-
76
-
-
72149118250
-
An Analytical Solution to the Kinetics of Breakable Filament Assembly
-
Knowles, T. P. J.; Waudby, C. A.; Devlin, G. L.; Cohen, S. I. A.; Aguzzi, A.; Vendruscolo, M.; Terentjev, E. M.; Welland, M. E.; Dobson, C. M. An Analytical Solution to the Kinetics of Breakable Filament Assembly Science 2009, 326, 1533-1537
-
(2009)
Science
, vol.326
, pp. 1533-1537
-
-
Knowles, T.P.J.1
Waudby, C.A.2
Devlin, G.L.3
Cohen, S.I.A.4
Aguzzi, A.5
Vendruscolo, M.6
Terentjev, E.M.7
Welland, M.E.8
Dobson, C.M.9
-
77
-
-
77958491288
-
Amyloid Fibril Polymorphism is under Kinetic Control
-
Pellarin, R.; Schuetz, P.; Guarnera, E.; Caflisch, A. Amyloid Fibril Polymorphism is Under Kinetic Control J. Am. Chem. Soc. 2009, 132, 14960-14970
-
(2009)
J. Am. Chem. Soc.
, vol.132
, pp. 14960-14970
-
-
Pellarin, R.1
Schuetz, P.2
Guarnera, E.3
Caflisch, A.4
-
78
-
-
34047157022
-
Hydrophobic Cooperativity as a Mechanism for Amyloid Nucleation
-
Hills, R. D.; Brooks-III, C. L. Hydrophobic Cooperativity as a Mechanism for Amyloid Nucleation J. Mol. Biol. 2007, 368, 894-901
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 894-901
-
-
Hills, R.D.1
Brooks-Iii, C.L.2
-
80
-
-
84866141812
-
New Method for Determining Size of Critical Nucleus of Fibril Formation of Polypeptide Chains
-
Co, N. T.; Li, M. S. New Method for Determining Size of Critical Nucleus of Fibril Formation of Polypeptide Chains J. Chem. Phys. 2007, 137, 095101
-
(2007)
J. Chem. Phys.
, vol.137
, pp. 095101
-
-
Co, N.T.1
Li, M.S.2
-
81
-
-
79952754330
-
Structural Evolution of Iowa Mutant beta-amyloid Fibrils from Polymorphic to Homogeneous States under Repeated Seeded Growth
-
Qiang, W. Q. Q.; Yau, W. M.; Tycko, R. Structural Evolution of Iowa Mutant beta-amyloid Fibrils from Polymorphic to Homogeneous States under Repeated Seeded Growth J. Am. Chem. Soc. 2011, 133, 4018-4029
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 4018-4029
-
-
Qiang, W.Q.Q.1
Yau, W.M.2
Tycko, R.3
-
82
-
-
80054752317
-
Molecular Basis for Amyloid-β Polymorphism
-
Colletier, J. P.; Laganowsky, A.; Landau, M.; Zhao, M.; Soriaga, A. B.; Goldschmidt, L.; Flot, D.; Cascio, D.; Sawaya, M. R.; Eisenberg, D. Molecular Basis for Amyloid-β Polymorphism Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16938-16943
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 16938-16943
-
-
Colletier, J.P.1
Laganowsky, A.2
Landau, M.3
Zhao, M.4
Soriaga, A.B.5
Goldschmidt, L.6
Flot, D.7
Cascio, D.8
Sawaya, M.R.9
Eisenberg, D.10
-
83
-
-
0028804827
-
Structural Model for the beta-amyloid Fibril Based on Interstrand Alignment of an Antiparallel-sheet Comprising a C-terminal Peptide
-
Lansbury, P. T.; Costa, P. R.; Griffiths, J. M.; Simon, E. J.; Auger, M.; Halverson, K. J.; Kocisko, D. A.; Hendsch, Z. S.; Ashburn, T. T.; Spencer, R. G. Structural Model for the beta-amyloid Fibril Based on Interstrand Alignment of an Antiparallel-sheet Comprising a C-terminal Peptide Nat. Struct. Mol. Biol. 1995, 2, 990-998
-
(1995)
Nat. Struct. Mol. Biol.
, vol.2
, pp. 990-998
-
-
Lansbury, P.T.1
Costa, P.R.2
Griffiths, J.M.3
Simon, E.J.4
Auger, M.5
Halverson, K.J.6
Kocisko, D.A.7
Hendsch, Z.S.8
Ashburn, T.T.9
Spencer, R.G.10
|