-
1
-
-
0242668337
-
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
-
DOI 10.1126/science.1079469
-
Kayed, R.; Head, E.; Thompson, J.L.; McIntire, T.M.; Milton, S.C.; Cotman, C.W.; Glabe, C.G. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science, 2003, 300, 486-489. (Pubitemid 36444329)
-
(2003)
Science
, vol.300
, Issue.5618
, pp. 486-489
-
-
Kayed, R.1
Head, E.2
Thompson, J.L.3
McIntire, T.M.4
Milton, S.C.5
Cotman, C.W.6
Glabel, C.G.7
-
2
-
-
38549169530
-
The two faces of protein misfolding: Gain- and loss-of-function in neurodegenerative diseases
-
DOI 10.1038/sj.emboj.7601930, PII 7601930
-
Winklhofer, K.; Tatzelt, J.; Haass, C. The two faces of protein misfolding: Gain- and loss-of-function in neurodegenerative diseases. EMBO J., 2008, 27, 336-349. (Pubitemid 351161650)
-
(2008)
EMBO Journal
, vol.27
, Issue.2
, pp. 336-349
-
-
Winklhofer, K.F.1
Tatzelt, J.2
Haass, C.3
-
3
-
-
33746377894
-
Protein misfolding, functional amyloid, and human disease
-
DOI 10.1146/annurev.biochem.75.101304.123901
-
Chiti, F.; Dobson, C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem., 2006, 75, 333-366. (Pubitemid 44118036)
-
(2006)
Annual Review of Biochemistry
, vol.75
, pp. 333-366
-
-
Chiti, F.1
Dobson, C.M.2
-
4
-
-
34250796761
-
Insights into prion strains and neurotoxicity
-
DOI 10.1038/nrm2204, PII NRM2204
-
Aguzzi, A.; Heikenwalder, M.; Polymenidou, M. Insights into prion strains and neurotoxicity. Nat. Rev. Mol. Cell. Biol., 2007, 8, 552-561. (Pubitemid 46985384)
-
(2007)
Nature Reviews Molecular Cell Biology
, vol.8
, Issue.7
, pp. 552-561
-
-
Aguzzi, A.1
Heikenwalder, M.2
Polymenidou, M.3
-
5
-
-
3943084181
-
Emerging principles of conformation-based prion inheritance
-
DOI 10.1146/annurev.biochem.72.121801.161837
-
Chien, P.; Weissman, J.S.; DePace, A.H. Emerging principles of conformation-based prion inheritance. Annu. Rev. Biochem., 2004, 73, 617-656. (Pubitemid 39050382)
-
(2004)
Annual Review of Biochemistry
, vol.73
, pp. 617-656
-
-
Chien, P.1
Weissman, J.S.2
DePace, A.H.3
-
6
-
-
20444440728
-
Structure of the cross-β spine of amyloid-like fibrils
-
DOI 10.1038/nature03680
-
Nelson, R.; Sawaya, M.R.; Balbirnie, M.; Madsen, A.O.; Riekel, C.; Grothe, R.; Eisenberg, D. Structure of the cross-beta spine of amyloid-like fibrils. Nature, 2005, 435, 773-778. (Pubitemid 40839722)
-
(2005)
Nature
, vol.435
, Issue.7043
, 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
-
7
-
-
34249290108
-
Atomic structures of amyloid cross-β spines reveal varied steric zippers
-
DOI 10.1038/nature05695, PII NATURE05695
-
Sawaya, M.R.; Sambashivan, S.; Nelson, R.; Ivanova, M.I.; Sievers, S.A.; Apostol, M.I.; Thompson, M.J.; Balbirnie, M.; Wiltzius, J.J.; McFarlane, H.T.; Madsen, A.O.; Riekel, C.; Eisenberg, D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature, 2007, 447, 453-457. (Pubitemid 46816731)
-
(2007)
Nature
, vol.447
, Issue.7143
, 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.O.11
Riekel, C.12
Eisenberg, D.13
-
8
-
-
69949187643
-
Molecular mechanisms for protein-encoded inheritance
-
Wiltzius, J.J.; Landau, M.; Nelson, R.; Sawaya, M.R.; Apostol, M.I.; Goldschmidt, L.; Soriaga, A.B.; Cascio, D.; Rajashankar, K.; Eisenberg, D. Molecular mechanisms for protein-encoded inheritance. Nat. Struct. Mol. Biol., 2009, 16, 973-978.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 973-978
-
-
Wiltzius, J.J.1
Landau, M.2
Nelson, R.3
Sawaya, M.R.4
Apostol, M.I.5
Goldschmidt, L.6
Soriaga, A.B.7
Cascio, D.8
Rajashankar, K.9
Eisenberg, D.10
-
9
-
-
33746765060
-
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35
-
DOI 10.1529/biophysj.106.083246
-
Zheng, J.; Ma, B.; Tsai, C.J.; Nussinov, R. Structural stability and dynamics of an amyloid-forming peptide gnnqqny from the yeast prion sup-35. Biophys. J., 2006, 91, 824-833. (Pubitemid 44161914)
-
(2006)
Biophysical Journal
, vol.91
, Issue.3
, pp. 824-833
-
-
Zheng, J.1
Ma, B.2
Tsai, C.-J.3
Nussinov, R.4
-
10
-
-
33751170680
-
Consensus features in amyloid fibrils: Sheet-sheet recognition via a (polar or nonpolar) zipper structure
-
Zheng, J.; Ma, B.; Nussinov, R. Consensus features in amyloid fibrils: Sheet-sheet recognition via a (polar or nonpolar) zipper structure. Phys. Biol., 2006, 3, P1-4.
-
(2006)
Phys. Biol.
, vol.3
, pp. 1-4
-
-
Zheng, J.1
Ma, B.2
Nussinov, R.3
-
11
-
-
33646794342
-
Polyglutamine repeats and β-helix structure: Molecular dynamics study
-
DOI 10.1002/prot.20941
-
Merlino, A.; Esposito, L.; Vitagliano, L. Polyglutamine repeats and -helix structure: A molecular dynamics study. Proteins, 2006, 63, 918-927. (Pubitemid 43765143)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.63
, Issue.4
, pp. 918-927
-
-
Merlino, A.1
Esposito, L.2
Vitagliano, L.3
-
12
-
-
56349091416
-
Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association
-
Vitagliano, L.; Esposito, L.; Pedone, C.; De Simone, A. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association. Biochem. Biophys. Res. Commun., 2008, 377, 1036-1041.
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.377
, pp. 1036-1041
-
-
Vitagliano, L.1
Esposito, L.2
Pedone, C.3
De Simone, A.4
-
13
-
-
50349099883
-
Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses
-
De Simone, A.; Esposito, L.; Pedone, C.; Vitagliano, L. Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses. Biophys. J., 2008, 95, 1965-1973.
-
(2008)
Biophys. J.
, vol.95
, pp. 1965-1973
-
-
De Simone, A.1
Esposito, L.2
Pedone, C.3
Vitagliano, L.4
-
14
-
-
43849090507
-
Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations
-
Esposito, L.; Paladino, A.; Pedone, C.; Vitagliano, L. Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations. Biophys. J., 2008, 94, 4031-4040.
-
(2008)
Biophys. J.
, vol.94
, pp. 4031-4040
-
-
Esposito, L.1
Paladino, A.2
Pedone, C.3
Vitagliano, L.4
-
15
-
-
33746800825
-
Molecular dynamics analyses of cross-β-spine steric zipper models: β-sheet twisting and aggregation
-
DOI 10.1073/pnas.0602345103
-
Esposito, L.; Pedone, C.; Vitagliano, L. Molecular dynamics analyses of cross-beta-spine steric zipper models: Beta-sheet twisting and aggregation. Proc. Natl. Acad. Sci. USA, 2006, 103, 11533-11538. (Pubitemid 44182486)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.31
, pp. 11533-11538
-
-
Esposito, L.1
Pedone, C.2
Vitagliano, L.3
-
16
-
-
71749100900
-
Dynamics and stability of amyloid-like steric zipper assemblies with hydrophobic dry interfaces
-
Vitagliano, L.; Stanzione, F.; De Simone, A.; Esposito, L. Dynamics and stability of amyloid-like steric zipper assemblies with hydrophobic dry interfaces. Biopolymers, 2009, 91, 1161-1171.
-
(2009)
Biopolymers
, vol.91
, pp. 1161-1171
-
-
Vitagliano, L.1
Stanzione, F.2
De Simone, A.3
Esposito, L.4
-
17
-
-
38549138415
-
Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A
-
DOI 10.1002/prot.21648
-
Colombo, G.; Meli, M.; De Simone, A. Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A. Proteins, 2008, 70, 863-872. (Pubitemid 351161945)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 863-872
-
-
Colombo, G.1
Meli, M.2
De Simone, A.3
-
18
-
-
44849096158
-
Investigating the mechanism of peptide aggregation: Insights from mixed monte carlo-molecular dynamics simulations
-
Meli, M.; Morra, G.; Colombo, G. Investigating the mechanism of peptide aggregation: Insights from mixed monte carlo-molecular dynamics simulations. Biophys. J., 2008, 94, 4414-4426.
-
(2008)
Biophys. J.
, vol.94
, pp. 4414-4426
-
-
Meli, M.1
Morra, G.2
Colombo, G.3
-
19
-
-
61949163833
-
Factors that affect the degree of twist in beta-sheet structures: A molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide
-
Periole, X.; Rampioni, A.; Vendruscolo, M.; Mark, A.E. Factors that affect the degree of twist in beta-sheet structures: A molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. J. Phys. Chem. B, 2009, 113, 1728-1737.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1728-1737
-
-
Periole, X.1
Rampioni, A.2
Vendruscolo, M.3
Mark, A.E.4
-
20
-
-
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
-
DOI 10.1073/pnas.0835307100
-
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, 5154-5159. (Pubitemid 36542674)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.9
, pp. 5154-5159
-
-
Gsponer, J.1
Haberthur, U.2
Caflisch, A.3
-
21
-
-
37549007231
-
Structure dynamics, and stability of assemblies of the human prion fragment snqnnf
-
De Simone, A.; Pedone, C.; Vitagliano, L. Structure, dynamics, and stability of assemblies of the human prion fragment snqnnf. Biochem. Biophys. Res. Commun., 2008, 366, 800-806.
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.366
, pp. 800-806
-
-
De Simone, A.1
Pedone, C.2
Vitagliano, L.3
-
22
-
-
19644385843
-
Prion and water: Tight and dynamical hydration sites have a key role in structural stability
-
DOI 10.1073/pnas.0501748102
-
De Simone, A.; Dodson, G.G.; Verma, C.S.; Zagari, A.; Fraternali, F. Prion and water: Tight and dynamical hydration sites have a key role in structural stability. Proc. Natl. Acad. Sci. USA, 2005, 102, 7535-7540. (Pubitemid 40741006)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.21
, pp. 7535-7540
-
-
De Simone, A.1
Dodson, G.G.2
Verma, C.S.3
Zagari, A.4
Fraternali, F.5
-
23
-
-
70349658765
-
Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine
-
Park, J.; Kahng, B.; Hwang, W. Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine. PLoS Comput. Biol., 2009, 5, e1000492.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Park, J.1
Kahng, B.2
Hwang, W.3
-
24
-
-
0034632806
-
Islet amyloid and type 2 diabetes mellitus
-
DOI 10.1056/NEJM200008103430607
-
Hoppener, J.W.; Ahren, B.; Lips, C.J. Islet amyloid and type 2 diabetes mellitus. N. Engl. J. Med., 2000, 343, 411-419. (Pubitemid 30626125)
-
(2000)
New England Journal of Medicine
, vol.343
, Issue.6
, pp. 411-419
-
-
Hoppener, J.W.M.1
Ahren, B.2
Lips, C.J.M.3
-
25
-
-
50049095633
-
Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin)
-
Wiltzius, J.J.; Sievers, S.A.; Sawaya, M.R.; Cascio, D.; Popov, D.; Riekel, C.; Eisenberg, D. Atomic structure of the cross-beta 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
-
26
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
DOI 10.1002/jcc.20291
-
van der Spoel, D.; Lindhal, E.; Berk, H.; Groenhof, G.; Mark, A.E.; Berendsen, H.J.C. Gromacs: Fast, flexible, and free. J. Comput. Chem., 2005, 26, 1701-1718. (Pubitemid 43076182)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
27
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W.; Hunenberger, P.; ITironi, I.; Mark, A.; Billeter, S.; Fennen, J.; Torda, A.; Huber, T.; Kruger, P.; van Gunsteren, W. The gromos biomolecular simulation program package. J. Phys. Chem. A, 1999, 103, 3596-3607. (Pubitemid 129570863)
-
(1999)
Journal of Physical Chemistry A
, vol.103
, Issue.19
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
28
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
DOI 10.1021/ja9621760, PII S0002786396021762
-
Jorgensen, W.; Maxwell, D.; 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. (Pubitemid 26399746)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
29
-
-
0029878720
-
VMD: Visual molecular dynamics
-
DOI 10.1016/0263-7855(96)00018-5
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph., 1996, 14, 33-38, 27-38. (Pubitemid 26152973)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.1
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
30
-
-
33749818217
-
The structural biology of protein aggregation diseases: Fundamental questions and some answers
-
Eisenberg, D.; Nelson, R.; Sawaya, M.R.; Balbirnie, M.; Sambashivan, S.; Ivanova, M.I.; Madsen, A.O.; Riekel, C. The structural biology of protein aggregation diseases: Fundamental questions and some answers. Acc. Chem. Res., 2006, 39, 568-575.
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 568-575
-
-
Eisenberg, D.1
Nelson, R.2
Sawaya, M.R.3
Balbirnie, M.4
Sambashivan, S.5
Ivanova, M.I.6
Madsen, A.O.7
Riekel, C.8
-
31
-
-
79959791904
-
Towards a pharmacophore for amyloid
-
Landau, M.; Sawaya, M.R.; Faull, K.F.; Laganowsky, A.; Jiang, L.; Sievers, S.A.; Liu, J.; Barrio, J.R.; Eisenberg, D. Towards a pharmacophore for amyloid. PLoS Biol., 2011, 9, e1001080.
-
(2011)
PLoS Biol.
, vol.9
-
-
Landau, M.1
Sawaya, M.R.2
Faull, K.F.3
Laganowsky, A.4
Jiang, L.5
Sievers, S.A.6
Liu, J.7
Barrio, J.R.8
Eisenberg, D.9
|