-
1
-
-
0033200063
-
Protein misfolding, evolution and disease
-
Dobson, C. M. 1999. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24: 329-332.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 329-332
-
-
Dobson, C.M.1
-
2
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
Chiti, F., and C. M. Dobson. 2006. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75: 333-366.
-
(2006)
Annu. Rev. Biochem.
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
3
-
-
34248190279
-
A β oligomers - A decade of discovery
-
Walsh, D. M., and D. J. Selkoe. 2007. A β oligomers - a decade of discovery. J. Neurochem. 101: 1172-1184.
-
(2007)
J. Neurochem.
, vol.101
, pp. 1172-1184
-
-
Walsh, D.M.1
Selkoe, D.J.2
-
4
-
-
2542455537
-
Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease
-
Klein, W. L., W. B. Stine, Jr., and D. B. Teplow. 2004. Small assemblies of unmodified amyloid β-protein are the proximate neurotoxin in Alzheimer's disease. Neurobiol. Aging. 25: 569-580.
-
(2004)
Neurobiol. Aging.
, vol.25
, pp. 569-580
-
-
Klein, W.L.1
Stine Jr., W.B.2
Teplow, D.B.3
-
5
-
-
0037041420
-
Inherent toxicity of aggregates implies a common mechanism, for protein misfolding diseases
-
Bucciantini, M., E. Giannoni, ..., M. Stefani. 2002. Inherent toxicity of aggregates implies a common mechanism, for protein misfolding diseases. Nature. 416: 507-511.
-
(2002)
Nature
, vol.416
, pp. 507-511
-
-
Bucciantini, M.1
Giannoni, E.2
Stefani, M.3
-
6
-
-
24644448839
-
The most infectious prion protein particles
-
Silveira, J. R., G. J. Raymond, ..., B. Caughey. 2005. The most infectious prion protein particles. Nature. 437: 257-261.
-
(2005)
Nature
, vol.437
, pp. 257-261
-
-
Silveira, J.R.1
Raymond, G.J.2
Caughey, B.3
-
7
-
-
0242668337
-
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
-
Kayed, R., E. Head, ..., C. G. Glabe. 2003. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science. 300: 486-489.
-
(2003)
Science
, vol.300
, pp. 486-489
-
-
Kayed, R.1
Head, E.2
Glabe, C.G.3
-
8
-
-
0028308104
-
As an altered URE2 protein: Evidence for a prion analog in Saccharomyces cerevisiae
-
Wickner, R. B. 1994. [URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae. Science. 264: 566-569.
-
(1994)
Science
, vol.264
, pp. 566-569
-
-
Wickner, R.B.1
-
9
-
-
0029780647
-
Support for the prion hypothesis for inheritance of a phenotypic trait in yeast
-
Patino, M. M., J. J. Liu, ..., S. Lindquist. 1996. Support for the prion hypothesis for inheritance of a phenotypic trait in yeast. Science. 273: 622-626.
-
(1996)
Science
, vol.273
, pp. 622-626
-
-
Patino, M.M.1
Liu, J.J.2
Lindquist, S.3
-
10
-
-
20444440728
-
Structure of the cross-β spine of amyloid-like fibrils
-
Nelson, R., M. R. Sawaya, ..., D. Eisenberg. 2005. Structure of the cross-β spine of amyloid-like fibrils. Nature. 435: 773-778.
-
(2005)
Nature
, vol.435
, pp. 773-778
-
-
Nelson, R.1
Sawaya, M.R.2
Eisenberg, D.3
-
11
-
-
0035956924
-
An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid
-
Balbimie, M., R. Grothe, and D. S. Eisenberg. 2001. An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid. Proc, Natl. Acad. Sci. USA. 98: 2375-2380.
-
(2001)
Proc, Natl. Acad. Sci. USA
, vol.98
, pp. 2375-2380
-
-
Balbimie, M.1
Grothe, R.2
Eisenberg, D.S.3
-
12
-
-
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., U. Haberthür, and A. Caflisch. 2003. 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, 100: 5154-5159.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5154-5159
-
-
Gsponer, J.1
Haberthür, U.2
Caflisch, A.3
-
13
-
-
10844230140
-
Replica exchange molecular dynamics simulations of amyloid peptide aggregation
-
Cecchini, M., F. Rao, ..., A. Caflisch. 2004. Replica exchange molecular dynamics simulations of amyloid peptide aggregation, J. Chem. Phys. 121: 10748-10756.
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 10748-10756
-
-
Cecchini, M.1
Rao, F.2
Caflisch, A.3
-
14
-
-
33746765060
-
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35
-
Zheng, J., B. Ma, ..., R. Nussinov. 2006. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys. J. 91: 824-833.
-
(2006)
Biophys. J.
, vol.91
, pp. 824-833
-
-
Zheng, J.1
Ma, B.2
Nussinov, R.3
-
15
-
-
34548627237
-
Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35
-
Zhang, Z., H. Chen.....L. Lai. 2007. Molecular dynamics simulations on the oligomer-formation process of the GNNQQNY peptide from yeast prion protein Sup35. Biophys. J. 93: 1484-1492.
-
(2007)
Biophys. J.
, vol.93
, pp. 1484-1492
-
-
Zhang, Z.1
Chen, H.2
Lai, L.3
-
16
-
-
19444380574
-
Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: Simulation by reaction path annealing
-
Lipfert, J., J. Franklin, ..., S. Doniach. 2005. Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. J. Mol. Biol. 349: 648-658.
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 648-658
-
-
Lipfert, J.1
Franklin, J.2
Doniach, S.3
-
17
-
-
33746800825
-
Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation
-
Esposito, L., C. Pedone, and L. Vitagliano. 2006. Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation. Proc. Natl. Acad. Sci. USA. 103: 11533-11538.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 11533-11538
-
-
Esposito, L.1
Pedone, C.2
Vitagliano, L.3
-
18
-
-
68849107584
-
Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation
-
Berryman, J. T., S. E. Radford, and S. A. Harris. 2009. Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation. Biophys. J. 97: 1-11.
-
(2009)
Biophys. J.
, vol.97
, pp. 1-11
-
-
Berryman, J.T.1
Radford, S.E.2
Harris, S.A.3
-
20
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis, P. G., D. Chandler, ..., P. L. Geissler. 2002. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53: 291-318.
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Geissler, P.L.3
-
21
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E., B. Hess, and D. van der Spoel. 2001, GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7: 306-317.
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
22
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel, D., E. Lindahl, ..., H. J. Berendsen. 2005. GROMACS: fast, flexible, and free. J. Comput. Chem. 26: 1701-1718.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Berendsen, H.J.3
-
23
-
-
33846823909
-
Particle mesh Ewald: An N log (TV) method for Ewald sums in large systems
-
Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N log (TV) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
24
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., L. Perera, ..., L. Pedersen. 1.995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Pedersen, L.3
-
25
-
-
33750587438
-
Molecular dynamics with, coupling to an external bath
-
Berendsen, H., J. Postma, ..., J. Haak. 1.984. Molecular dynamics with, coupling to an external bath. J. Chem, Phys. 81: 3684-3690.
-
(1984)
J. Chem, Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Haak, J.3
-
26
-
-
0034294024
-
Multidimensional replicaexchange method for free-energy calculations
-
Sugita, Y., A. Kitao, and Y. Okamoto. 2000. Multidimensional replicaexchange method for free-energy calculations. J. Chem. Phys. 113: 6042-6052.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6052
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
27
-
-
0034229302
-
Hyperparallel tempering Monte Carlo simulation of polymeric systems
-
Yan, Q., and J. de Pablo. 2000. Hyperparallel tempering Monte Carlo simulation of polymeric systems. J. Chem. Phys. 113: 1276-1282.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 1276-1282
-
-
Yan, Q.1
De Pablo, J.2
-
28
-
-
0036536011
-
Multicanonical parallel tempering
-
Faller, R., Q. Yan, and J. de Pablo. 2002. Multicanonical parallel tempering. J. Chem. Phys. 116: 5419-5423.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 5419-5423
-
-
Faller, R.1
Yan, Q.2
De Pablo, J.3
-
29
-
-
69549086151
-
Effect of trehalose on amyloid β (29-40)-membrane interaction
-
Reddy, A. S., A. Izmitli, and J. J. de Pablo. 2009. Effect of trehalose on amyloid β (29-40)-membrane interaction. J. Chem. Phys. 131: 085101.
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 085101
-
-
Reddy, A.S.1
Izmitli, A.2
De Pablo, J.J.3
-
30
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method
-
Kumar, S., J. Rosenberg, ..., P. Kollman. 1992. THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13: 1011-1021.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Rosenberg, J.2
Kollman, P.3
-
31
-
-
0034321137
-
Transition path sampling of cavitation between molecular scale solvophobic surfaces
-
Bolhuis, P., and D. Chandler. 2000. Transition path sampling of cavitation between molecular scale solvophobic surfaces. J. Chem. Phys. 113: 8154-8160.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 8154-8160
-
-
Bolhuis, P.1
Chandler, D.2
-
33
-
-
37549055108
-
Thermodynamics and kinetics of aggregation for the GNNQQNY peptide
-
Strodel, B., C. S. Whittleston, and D. J. Wales. 2007. Thermodynamics and kinetics of aggregation for the GNNQQNY peptide. J. Am. Chem. Soc. 129: 16005-16014.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 16005-16014
-
-
Strodel, B.1
Whittleston, C.S.2
Wales, D.J.3
-
34
-
-
56349091416
-
Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association
-
Vitagliano, L., L. Esposito, ..., A. De Simone. 2008. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association. Biochem. Biophys. Res. Commun. 377: 1036-1041.
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.377
, pp. 1036-1041
-
-
Vitagliano, L.1
Esposito, L.2
De Simone, A.3
-
35
-
-
0035543109
-
The architecture of parallel β-helices and related folds
-
Jenkins, J., and R. Pickersgill. 2001. The architecture of parallel β-helices and related folds. Prog. Biophys. Mol. Biol. 77: 111-175.
-
(2001)
Prog. Biophys. Mol. Biol.
, vol.77
, pp. 111-175
-
-
Jenkins, J.1
Pickersgill, R.2
-
36
-
-
33744807442
-
Sequence and structure analysis of parallel β helices: Implication for constructing amyloid structural, models
-
Tsai, H. H., K. Gunasekaran, and R. Nussinov. 2006. Sequence and structure analysis of parallel β helices: implication for constructing amyloid structural, models. Structure. 14: 1059-1072.
-
(2006)
Structure
, vol.14
, pp. 1059-1072
-
-
Tsai, H.H.1
Gunasekaran, K.2
Nussinov, R.3
-
37
-
-
20444363123
-
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: Significant role of Asn ladder
-
Tsai, H. H., M. Reches, ..., R. Nussinov. 2005. Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc. Natl. Acad. Sci. USA. 102: 8174-8179.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 8174-8179
-
-
Tsai, H.H.1
Reches, M.2
Nussinov, R.3
-
39
-
-
33846036362
-
Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism
-
Nguyen, P. H., M. S. Li, ..., D. Thirumalai. 2007. Monomer adds to preformed structured oligomers of Aβ-peptides by a two-stage dock-lock mechanism. Proc. Natl. Acad. Sci. USA. 104: 111-116.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 111-116
-
-
Nguyen, P.H.1
Li, M.S.2
Thirumalai, D.3
-
40
-
-
67749110404
-
Dynamics of locking of peptides onto growing amyloid fibrils
-
Reddy, G., J. E. Straub, and D. Thirumalai. 2009. Dynamics of locking of peptides onto growing amyloid fibrils. Proc. Natl. Acad. Sci. USA. 106: 11948-11953.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 11948-11953
-
-
Reddy, G.1
Straub, J.E.2
Thirumalai, D.3
-
41
-
-
0029994633
-
Arrest of β-amyloid fibril formation by a pentapeptide ligand
-
Tjernberg, L. O., J. Näslund, ..., C. Nordstedt. 1996. Arrest of β-amyloid fibril formation by a pentapeptide ligand. J. Biol. Chem. 271: 8545-8548.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 8545-8548
-
-
Tjernberg, L.O.1
Näslund, J.2
Nordstedt, C.3
-
42
-
-
0035823520
-
Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide. An experimental support for the key role of the phenylalanine residue in amyloid formation
-
Azriel, R., and E. Gazit. 2001, Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide. An experimental support for the key role of the phenylalanine residue in amyloid formation. J. Biol. Chem. 276: 34156-34161.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 34156-34161
-
-
Azriel, R.1
Gazit, E.2
-
43
-
-
0036135139
-
A possible role for π-stacking in the self-assembly of amyloid fibrils
-
Gazit, E. 2002. A possible role for π-stacking in the self-assembly of amyloid fibrils. FASEB J. 16: 77-83.
-
(2002)
FASEB J.
, vol.16
, pp. 77-83
-
-
Gazit, E.1
-
44
-
-
12244285938
-
Molecular basis for amyloid fibril formation and stability
-
Makin, O. S., E. Atkins, ..., L. C. Serpell. 2005. Molecular basis for amyloid fibril formation and stability. Proc. Natl. Acad. Sci. USA. 102: 315-320.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 315-320
-
-
Makin, O.S.1
Atkins, E.2
Serpell, L.C.3
|