-
1
-
-
13944282886
-
Amyloid beta-protein: monomer structure and early aggregation states of Abeta42 and its Pro19 alloform
-
Bernstein S.L., Wyttenbach T., Baumketner A., Shea J.E., Bitan G., Teplow D.B., and Bowers M.T. Amyloid beta-protein: monomer structure and early aggregation states of Abeta42 and its Pro19 alloform. J. Am. Chem. Soc. 127 (2005) 2075-2084
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 2075-2084
-
-
Bernstein, S.L.1
Wyttenbach, T.2
Baumketner, A.3
Shea, J.E.4
Bitan, G.5
Teplow, D.B.6
Bowers, M.T.7
-
2
-
-
33751104733
-
Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure
-
Boucher G., Mousseau N., and Derreumaux P. Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure. Proteins 65 (2006) 877-888
-
(2006)
Proteins
, vol.65
, pp. 877-888
-
-
Boucher, G.1
Mousseau, N.2
Derreumaux, P.3
-
3
-
-
0028264860
-
Molecular-dynamics simulation of protein denaturation-solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch A., and Karplus M. Molecular-dynamics simulation of protein denaturation-solvation of the hydrophobic cores and secondary structure of barnase. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 1746-1750
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
4
-
-
57749174350
-
Mechanism of coupled folding and binding in the siRNA-PAZ complex
-
Chen H.F. Mechanism of coupled folding and binding in the siRNA-PAZ complex. J. Chem. Theory Comput. 4 (2008) 1360-1368
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1360-1368
-
-
Chen, H.F.1
-
5
-
-
33947252405
-
Binding induced folding in p53-MDM2 complex
-
Chen H.F., and Luo R. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 129 (2007) 2930-2937
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 2930-2937
-
-
Chen, H.F.1
Luo, R.2
-
6
-
-
10044265557
-
Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations
-
Chong L.T., Snow C.D., Rhee Y.M., and Pande V.S. Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. J. Mol. Biol. 345 (2005) 869-878
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 869-878
-
-
Chong, L.T.1
Snow, C.D.2
Rhee, Y.M.3
Pande, V.S.4
-
7
-
-
8844247180
-
Mechanism of prion propagation: amyloid growth occurs by monomer addition
-
Collins S.R., Douglass A., Vale R.D., and Weissman J.S. Mechanism of prion propagation: amyloid growth occurs by monomer addition. PLoS Biol. 2 (2004) e321
-
(2004)
PLoS Biol.
, vol.2
-
-
Collins, S.R.1
Douglass, A.2
Vale, R.D.3
Weissman, J.S.4
-
8
-
-
0029981188
-
Structure of the transition state for folding of a protein derived from experiment and simulation
-
Daggett V., Li A.J., Itzhaki L.S., Otzen D.E., and Fersht A.R. Structure of the transition state for folding of a protein derived from experiment and simulation. J. Mol. Biol. 257 (1996) 430-440
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 430-440
-
-
Daggett, V.1
Li, A.J.2
Itzhaki, L.S.3
Otzen, D.E.4
Fersht, A.R.5
-
9
-
-
1442330474
-
From conversion to aggregation: protofibril formation of the prion protein
-
DeMarco M.L., and Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 2293-2298
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 2293-2298
-
-
DeMarco, M.L.1
Daggett, V.2
-
10
-
-
0033200063
-
Protein misfolding, evolution and disease
-
Dobson C.M. Protein misfolding, evolution and disease. Trends Biochem. Sci. 24 (1999) 329-332
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 329-332
-
-
Dobson, C.M.1
-
11
-
-
33746800825
-
Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation
-
Esposito L., Pedone C., and Vitagliano L. Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 11533-11538
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 11533-11538
-
-
Esposito, L.1
Pedone, C.2
Vitagliano, L.3
-
12
-
-
33644536691
-
Atomic-level description of amyloid beta-dimer formation
-
Gnanakaran S., Nussinov R., and Garcia A.E. Atomic-level description of amyloid beta-dimer formation. J. Am. Chem. Soc. 128 (2006) 2158-2159
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 2158-2159
-
-
Gnanakaran, S.1
Nussinov, R.2
Garcia, A.E.3
-
13
-
-
0035946940
-
Role of native topology investigated by multiple unfolding simulations of four SH3 domains
-
Gsponer J., and Caflisch A. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J. Mol. Biol. 309 (2001) 285-298
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 285-298
-
-
Gsponer, J.1
Caflisch, A.2
-
14
-
-
0037076334
-
Molecular dynamics simulations of protein folding from the transition state
-
Gsponer J., and Caflisch A. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 6719-6724
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 6719-6724
-
-
Gsponer, J.1
Caflisch, A.2
-
15
-
-
0242668337
-
Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
-
Kayed R., Head E., Thompson J.L., McIntire T.M., Milton S.C., Cotman C.W., and Glabe C.G. Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300 (2003) 486-489
-
(2003)
Science
, vol.300
, 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
Glabe, C.G.7
-
16
-
-
44949166524
-
Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment
-
Kent A., Jha A.K., Fitzgerald J.E., and Freed K.F. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment. J. Phys. Chem. B 112 (2008) 6175-6186
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6175-6186
-
-
Kent, A.1
Jha, A.K.2
Fitzgerald, J.E.3
Freed, K.F.4
-
17
-
-
0032555115
-
Synergy between simulation and experiment in describing the energy landscape of protein folding
-
Ladurner A.G., Itzhaki L.S., Daggett V., and Fersht A.R. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 8473-8478
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 8473-8478
-
-
Ladurner, A.G.1
Itzhaki, L.S.2
Daggett, V.3
Fersht, A.R.4
-
18
-
-
19444380574
-
Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing
-
Lipfert J., Franklin J., Wu F., and Doniach S. Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. J. Mol. Biol. 349 (2005) 648-658
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 648-658
-
-
Lipfert, J.1
Franklin, J.2
Wu, F.3
Doniach, S.4
-
19
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor U., Johnson C.M., Daggett V., and Fersht A.R. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 13518-13522
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 13518-13522
-
-
Mayor, U.1
Johnson, C.M.2
Daggett, V.3
Fersht, A.R.4
-
20
-
-
0037456298
-
The complete folding pathway of a protein from nanoseconds to microseconds
-
Mayor U., Guydosh N.R., Johnson C.M., Grossmann J.G., Sato S., Jas G.S., Freund S.M.V., Alonso D.O.V., Daggett V., and Fersht A.R. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421 (2003) 863-867
-
(2003)
Nature
, vol.421
, pp. 863-867
-
-
Mayor, U.1
Guydosh, N.R.2
Johnson, C.M.3
Grossmann, J.G.4
Sato, S.5
Jas, G.S.6
Freund, S.M.V.7
Alonso, D.O.V.8
Daggett, V.9
Fersht, A.R.10
-
21
-
-
28844499140
-
Exploring the early steps of amyloid peptide aggregation by computers
-
Mousseau N., and Derreumaux P. Exploring the early steps of amyloid peptide aggregation by computers. Acc. Chem. Res. 38 (2005) 885-891
-
(2005)
Acc. Chem. Res.
, vol.38
, pp. 885-891
-
-
Mousseau, N.1
Derreumaux, P.2
-
22
-
-
20444440728
-
Structure of the cross-beta spine of amyloid-like fibrils
-
Nelson R., Sawaya M.R., Balbirnie M., Madsen A.O., Riekel C., Grothe R., and Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature 435 (2005) 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
-
23
-
-
9244260521
-
Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides
-
Nguyen H.D., and Hall C.K. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 16180-16185
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 16180-16185
-
-
Nguyen, H.D.1
Hall, C.K.2
-
24
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
-
Pande V.S., and Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 9062-9067
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 9062-9067
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
25
-
-
34249290108
-
Atomic structures of amyloid cross-beta 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., McFarlane H.T., Madsen A.O., Riekel C., and Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447 (2007) 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.9
McFarlane, H.T.10
Madsen, A.O.11
Riekel, C.12
Eisenberg, D.13
-
26
-
-
0033849738
-
Review: history of the amyloid fibril
-
Sipe J.D., and Cohen A.S. Review: history of the amyloid fibril. J. Struct. Biol. 130 (2000) 88-98
-
(2000)
J. Struct. Biol.
, vol.130
, pp. 88-98
-
-
Sipe, J.D.1
Cohen, A.S.2
-
27
-
-
33645238380
-
The 3D profile method for identifying fibril-forming segments of proteins
-
Thompson M.J., Sievers S.A., Karanicolas J., Ivanova M.I., Baker D., and Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 4074-4078
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 4074-4078
-
-
Thompson, M.J.1
Sievers, S.A.2
Karanicolas, J.3
Ivanova, M.I.4
Baker, D.5
Eisenberg, D.6
-
28
-
-
10644242867
-
Molecular dynamics simulation of amyloid beta dimer formation
-
Urbanc B., Cruz L., Ding F., Sammond D., Khare S., Buldyrev S.V., Stanley H.E., and Dokholyan N.V. Molecular dynamics simulation of amyloid beta dimer formation. Biophys. J. 87 (2004) 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
Dokholyan, N.V.8
-
29
-
-
16344367783
-
Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations
-
Wu C., Lei H., and Duan Y. Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys. J. 87 (2004) 3000-3009
-
(2004)
Biophys. J.
, vol.87
, pp. 3000-3009
-
-
Wu, C.1
Lei, H.2
Duan, Y.3
-
30
-
-
25844456992
-
Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent
-
Wu C., Lei H., and Duan Y. Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with explicit solvent. J. Am. Chem. Soc. 127 (2005) 13530-13537
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 13530-13537
-
-
Wu, C.1
Lei, H.2
Duan, Y.3
-
31
-
-
33746765060
-
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35
-
Zheng J., Ma B., Tsai C.J., and Nussinov R. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys. J. 91 (2006) 824-833
-
(2006)
Biophys. J.
, vol.91
, pp. 824-833
-
-
Zheng, J.1
Ma, B.2
Tsai, C.J.3
Nussinov, R.4
-
32
-
-
39749090561
-
Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific
-
Zheng J., Jang H., and Nussinov R. Beta2-microglobulin amyloid fragment organization and morphology and its comparison to Abeta suggests that amyloid aggregation pathways are sequence specific. Biochemistry 47 (2008) 2497-2509
-
(2008)
Biochemistry
, vol.47
, pp. 2497-2509
-
-
Zheng, J.1
Jang, H.2
Nussinov, R.3
|